ORCID Profile
0000-0001-5359-3100
Current Organisation
Flinders University
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Publisher: Microbiology Society
Date: 04-09-2023
Publisher: Cold Spring Harbor Laboratory
Date: 04-04-2023
DOI: 10.1101/2023.04.04.535632
Abstract: Microbial communities found within the human gut have a strong influence on human health. Intestinal bacteria and viruses influence gastrointestinal diseases such as inflammatory bowel disease. Viruses infecting bacteria, known as bacteriophages, play a key role in modulating bacterial communities within the human gut. However, the identification and characterisation of novel bacteriophages remain a challenge. Available tools use similarities between sequences, nucleotide composition, and the presence of viral genes roteins. Most available tools consider in idual contigs to determine whether they are of viral origin. As a result of the challenges in viral assembly, fragmentation of viral genomes can occur, leading to the need for new approaches in viral identification. We introduce Phables, a new computational method to resolve bacteriophage genomes from fragmented viral metagenomic assemblies. Phables identifies bacteriophage-like components in the assembly graph, models each component as a flow network, and uses graph algorithms and flow decomposition techniques to identify genomic paths. Experimental results of viral metagenomic s les obtained from different environments show that over 80% of the bacteriophage genomes resolved by Phables have high quality and are longer than the in idual contigs identified by existing viral identification tools. Phables is available on GitHub at github.com/Vini2 hables (DOI: 10.5281/zenodo.7645166). vijini.mallawaarachchi@flinders.edu.au
Publisher: Springer Science and Business Media LLC
Date: 13-06-2020
DOI: 10.1186/S40168-020-00840-X
Abstract: The vertebrate clade erged into Chondrichthyes (sharks, rays, and chimeras) and Osteichthyes fishes (bony fishes) approximately 420 mya, with each group accumulating vast anatomical and physiological differences, including skin properties. The skin of Chondrichthyes fishes is covered in dermal denticles, whereas Osteichthyes fishes are covered in scales and are mucous rich. The ergence time among these two fish groups is hypothesized to result in predictable variation among symbionts. Here, using shotgun metagenomics, we test if patterns of ersity in the skin surface microbiome across the two fish clades match predictions made by phylosymbiosis theory. We hypothesize (1) the skin microbiome will be host and clade-specific, (2) evolutionary difference in elasmobranch and teleost will correspond with a concomitant increase in host-microbiome dissimilarity, and (3) the skin structure of the two groups will affect the taxonomic and functional composition of the microbiomes. We show that the taxonomic and functional composition of the microbiomes is host-specific. Teleost fish had lower average microbiome within clade similarity compared to among clade comparison, but their composition is not different among clade in a null based model. Elasmobranch’s average similarity within clade was not different than across clade and not different in a null based model of comparison. In the comparison of host distance with microbiome distance, we found that the taxonomic composition of the microbiome was related to host distance for the elasmobranchs, but not the teleost fishes. In comparison, the gene function composition was not related to the host-organism distance for elasmobranchs but was negatively correlated with host distance for teleost fishes. Our results show the patterns of phylosymbiosis are not consistent across both fish clades, with the elasmobranchs showing phylosymbiosis, while the teleost fish are not. The discrepancy may be linked to alternative processes underpinning microbiome assemblage, including possible historical host-microbiome evolution of the elasmobranchs and convergent evolution in the teleost which filter specific microbial groups. Our comparison of the microbiomes among fishes represents an investigation into the microbial relationships of the oldest ergence of extant vertebrate hosts and reveals that microbial relationships are not consistent across evolutionary timescales.
Publisher: MDPI AG
Date: 08-05-2022
DOI: 10.3390/MICROORGANISMS10050985
Abstract: Acinetobacter baumannii is an opportunistic human pathogen responsible for numerous severe nosocomial infections. Genome analysis on the A. baumannii clinical isolate 04117201 revealed the presence of 13 two-component signal transduction systems (TCS). Of these, we examined the putative TCS named here as StkSR. The stkR response regulator was deleted via homologous recombination and its progeny, ΔstkR, was phenotypically characterized. Antibiogram analyses of ΔstkR cells revealed a two-fold increase in resistance to the clinically relevant polymyxins, colistin and polymyxin B, compared to wildtype. PAGE-separation of silver stained purified lipooligosaccharide isolated from ΔstkR and wildtype cells ruled out the complete loss of lipooligosaccharide as the mechanism of colistin resistance identified for ΔstkR. Hydrophobicity analysis identified a phenotypical change of the bacterial cells when exposed to colistin. Transcriptional profiling revealed a significant up-regulation of the pmrCAB operon in ΔstkR compared to the parent, associating these two TCS and colistin resistance. These results reveal that there are multiple levels of regulation affecting colistin resistance the suggested ‘cross-talk’ between the StkSR and PmrAB two-component systems highlights the complexity of these systems.
Publisher: Springer Science and Business Media LLC
Date: 15-08-2023
DOI: 10.1007/S00248-022-02094-6
Abstract: The coral holobiont is comprised of a highly erse microbial community that provides key services to corals such as protection against pathogens and nutrient cycling. The coral surface mucus layer (SML) microbiome is very sensitive to external changes, as it constitutes the direct interface between the coral host and the environment. Here, we investigate whether the bacterial taxonomic and functional profiles in the coral SML are shaped by the local reef zone and explore their role in coral health and ecosystem functioning. The analysis was conducted using metagenomes and metagenome-assembled genomes (MAGs) associated with the coral Pseudodiploria strigosa and the water column from two naturally distinct reef environments in Bermuda: inner patch reefs exposed to a fluctuating thermal regime and the more stable outer reefs. The microbial community structure in the coral SML varied according to the local environment, both at taxonomic and functional levels. The coral SML microbiome from inner reefs provides more gene functions that are involved in nutrient cycling (e.g., photosynthesis, phosphorus metabolism, sulfur assimilation) and those that are related to higher levels of microbial activity, competition, and stress response. In contrast, the coral SML microbiome from outer reefs contained genes indicative of a carbohydrate-rich mucus composition found in corals exposed to less stressful temperatures and showed high proportions of microbial gene functions that play a potential role in coral disease, such as degradation of lignin-derived compounds and sulfur oxidation. The fluctuating environment in the inner patch reefs of Bermuda could be driving a more beneficial coral SML microbiome, potentially increasing holobiont resilience to environmental changes and disease.
Publisher: Cold Spring Harbor Laboratory
Date: 06-03-2023
DOI: 10.1101/2023.03.05.531146
Abstract: Bacteroides, the prominent bacteria in the human gut, play a crucial role in degrading complex polysaccharides. Their abundance is influenced by phages belonging to the Crassvirales order. Despite identifying over 600 Crassvirales genomes computationally, only few have been successfully isolated. Continued efforts in isolation of more Crassvirales genomes can provide insights into phage-host-evolution and infection mechanisms. We focused on wastewater s les, as potential sources of phages infecting various Bacteroides hosts. Sequencing, assembly, and characterization of isolated phages revealed 14 complete genomes belonging to three novel Crassvirales species infecting Bacteroides cellulosilyticus WH2. These species, Kehishuvirus sp. ‘tikkala’ strain Bc01, Kolpuevirus sp. ‘frurule’ strain Bc03, and ‘Rudgehvirus jaberico’ strain Bc11, spanned two families, and three genera, displaying a broad range of virion productions. Upon testing all successfully cultured Crassvirales species and their respective bacterial hosts, we discovered that they do not exhibit co-evolutionary patterns with their bacterial hosts. Furthermore, we observed variations in gene similarity, with greater shared similarity observed within genera. However, despite belonging to different genera, the three novel species shared a unique structural gene that encodes the tail spike protein. When investigating the relationship between this gene and host interaction, we discovered evidence of purifying selection, indicating its functional importance. Moreover, our analysis demonstrated that this tail spike protein binds to the TonB-dependent receptors present on the bacterial host surface. Combining these observations, our findings provide insights into phage-host interactions and present three Crassvirales species as an ideal system for controlled infectivity experiments on one of the most dominant members of the human enteric virome. Bacteriophages play a crucial role in shaping microbial communities within the human gut. Among the most dominant bacteriophages in the human gut microbiome are Crassvirales phages, which infect Bacteroides. Despite being widely distributed, only a few Crassvirales genomes have been isolated, leading to a limited understanding of their biology, ecology, and evolution. This study isolated and characterized three novel Crassvirales genomes belonging to two different families, and three genera, but infecting one bacterial host, Bacteroides cellulosilyticus WH2. Notably, the observation confirmed the phages are not co-evolving with their bacterial hosts, rather have a shared ability to exploit similar features in their bacterial host. Additionally, the identification of a critical viral protein undergoing purifying selection and interacting with the bacterial receptors opens doors to targeted therapies against bacterial infections. Given Bacteroides role in polysaccharide degradation in the human gut, our findings advance our understanding of the phage-host interactions and could have important implications for the development of phage-based therapies. These discoveries may hold implications for improving gut health and metabolism to support overall well-being. The genomes used in this research are available on Sequence Read Archive (SRA) within the project, PRJNA737576. Bacteroides cellulosilyticus WH2, Kehishuvirus sp. ‘tikkala’ strain Bc01, Kolpuevirus sp. ‘ frurule’ strain Bc03, and ‘Rudgehvirus jaberico’ strain Bc11 are all available on GenBank with accessions NZ_CP072251.1 ( B. cellulosilyticus WH2), QQ198717 (Bc01), QQ198718 (Bc03), and QQ198719 (Bc11), and we are working on making the strains available through ATCC. The 3D protein structures for the three Crassvirales genomes are available to download at 0.25451/flinders.21946034.
Publisher: Center for Open Science
Date: 19-09-2022
Abstract: There is a growing trend for releasing bioinformatics workflows as command line applications. This is a good thing as workflow management systems add both functionality and reliability, while command line interfaces are convenient for end users. Developing command line software in this way is considerably faster. However, there are many potential pitfalls that developers of bioinformatics tools should avoid. We outline ten simple rules for converting workflow manager pipelines into command line applications, and present working ex les that also function as templates using the two most popular workflow managers, Snakemake (eardymcjohnface/Snaketool) and Nextflow (eardymcjohnface/Nektool).
Publisher: Frontiers Media SA
Date: 02-03-2023
DOI: 10.3389/FMICB.2023.1031711
Abstract: Marine host-associated microbiomes are affected by a combination of species-specific (e.g., host ancestry, genotype) and habitat-specific features (e.g., environmental physiochemistry and microbial biogeography). The stingray epidermis provides a gradient of characteristics from high dermal denticles coverage with low mucus to reduce dermal denticles and high levels of mucus. Here we investigate the effects of host phylogeny and habitat by comparing the epidermal microbiomes of Myliobatis californica (bat rays) with a mucus rich epidermis, and Urobatis halleri (round rays) with a mucus reduced epidermis from two locations, Los Angeles and San Diego, California (a 150 km distance). We found that host microbiomes are species-specific and distinct from the water column, however composition of M. californica microbiomes showed more variability between in iduals compared to U. halleri. The variability in the microbiome of M. californica caused the microbial taxa to be similar across locations, while U. halleri microbiomes were distinct across locations. Despite taxonomic differences, Shannon ersity is the same across the two locations in U. halleri microbiomes suggesting the taxonomic composition are locally adapted, but ersity is maintained by the host. Myliobatis californica and U. halleri microbiomes maintain functional similarity across Los Angeles and San Diego and each ray showed several unique functional genes. Myliobatis californica has a greater relative abundance of RNA Polymerase III-like genes in the microbiome than U. halleri , suggesting specific adaptations to a heavy mucus environment. Construction of Metagenome Assembled Genomes (MAGs) identified novel microbial species within Rhodobacteraceae , Moraxellaceae , Caulobacteraceae , Alcanivoracaceae and Gammaproteobacteria. All MAGs had a high abundance of active RNA processing genes, heavy metal, and antibiotic resistant genes, suggesting the stingray mucus supports high microbial growth rates, which may drive high levels of competition within the microbiomes increasing the antimicrobial properties of the microbes.
Publisher: Frontiers Media SA
Date: 14-11-2016
Publisher: American Society for Microbiology
Date: 28-04-2020
Abstract: Coral microbiome dysbiosis (i.e., shifts in the microbial community structure or complete loss of microbial symbionts) caused by environmental changes is a key player in the decline of coral health worldwide. Multiple factors in the water column and the surrounding biological community influence the dynamics of the coral microbiome. However, by including only temperature as an external factor, our model proved to be successful in describing the microbial community associated with the surface mucus layer (SML) of the coral P. strigosa . The dynamic model developed and validated in this study is a potential tool to predict the coral microbiome under different temperature conditions.
Publisher: American Association for Cancer Research (AACR)
Date: 07-2019
DOI: 10.1158/1538-7445.AM2019-5109
Abstract: National Center for Genomic Analysis Support (NCGAS) is an NSF-funded center whose goal is to help biologists optimize their bioinformatic pipelines to best address their research questions. To help reach these goals, NCGAS provides a range of services based on the researchers needs. We currently host gateways, Trinity Galaxy and Genepattern, with built-in workflows to support cancer researchers who have little background in command line work. Both these gateways are projects funded by the Information Technologies in Cancer Research (ITCR) program of NIH, NCI, to aid in the genomic and transcriptomic characterization of cancers. NSF-funded researchers comfortable in command line can gain access to IU cyberinfrastructure (HIPAA compliant), to run or develop bioinformatic workflows. Bioinformatic packages are already installed system wide, with reference databases, and new programs are always added upon user’s request. NCGAS is also an ambassador of Extreme Science and Engineering Discovery Environment (XSEDE) resources, providing access to other HIPAA compliant national cyberinfrastructure (Texas Advanced Computing Center, Pittsburgh Supercomputing Center, etc.), available to the entire research community. XSEDE resources include the Jetstream cloud, based at IU and TACC, allowing researchers to use preconfigured virtual machines (VMs) already setup, create custom VM environments for their own work, and to share with classes and collaborators. Data can be transferred and managed between all of these resources securely with already available Globus endpoints which allows transfer for terabytes of data quickly. Additionally, NCGAS hosts workshops to help researchers get started. These training events can be scheduled online or at your local university upon request. NCGAS currently supports projects working on transcriptome, genome-level assembly, phylogenetics, metagenomics, and meta-transcriptomics analysis through providing a range of compute resources that best serve the research project. Citation Format: Bhavya Papudeshi, Carrie Ganote, Sheri Sanders, Thomas G. Doak. National cyberinfrastructure and bioinformatic analysis support available to the cancer research community [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019 2019 Mar 29-Apr 3 Atlanta, GA. Philadelphia (PA): AACR Cancer Res 2019 (13 Suppl):Abstract nr 5109.
Publisher: MDPI AG
Date: 21-10-2022
DOI: 10.3390/MICROORGANISMS10102081
Abstract: Characterizations of shark-microbe systems in wild environments have outlined patterns of species-specific microbiomes however, whether captivity affects these trends has yet to be determined. We used high-throughput shotgun sequencing to assess the epidermal microbiome belonging to leopard sharks (Triakis semifasciata) in captive (Birch Aquarium, La Jolla California born and held permanently in captivity), semi-captive (held in captivity for year in duration and scheduled for release Scripps Institute of Oceanography, San Diego, CA, USA) and wild environments (Moss Landing and La Jolla, CA, USA). Here, we report captive environments do not drive epidermal microbiome compositions of T. semifasciata to significantly erge from wild counterparts as life-long captive sharks maintain a species-specific epidermal microbiome resembling those associated with semi-captive and wild populations. Major taxonomic composition shifts observed were inverse changes of top taxonomic contributors across captive duration, specifically an increase of Pseudoalteromonadaceae and consequent decrease of Pseudomonadaceae relative abundance as T. semifasciata increased duration in captive conditions. Moreover, we show captivity did not lead to significant losses in microbial α- ersity of shark epidermal communities. Finally, we present a novel association between T. semifasciata and the Muricauda genus as Metagenomes associated genomes revealed a consistent relationship across captive, semi-captive, and wild populations. Since changes in microbial communities is often associated with poor health outcomes, our report illustrates that epidermally associated microbes belonging to T. semifasciata are not suffering detrimental impacts from long or short-term captivity. Therefore, conservation programs which house sharks in aquariums are providing a healthy environment for the organisms on display. Our findings also expand on current understanding of shark epidermal microbiomes, explore the effects of ecologically different scenarios on benthic shark microbe associations, and highlight novel associations that are consistent across captive gradients.
Publisher: Oxford University Press (OUP)
Date: 21-09-2023
Publisher: Springer Science and Business Media LLC
Date: 07-08-2023
DOI: 10.1038/S41598-023-39184-5
Abstract: Microbiomes confer beneficial physiological traits to their host, but microbial ersity is inherently variable, challenging the relationship between microbes and their contribution to host health. Here, we compare the ersity and architectural complexity of the epidermal microbiome from 74 in idual whale sharks ( Rhincodon typus ) across five aggregations globally to determine if network properties may be more indicative of the microbiome-host relationship. On the premise that microbes are expected to exhibit biogeographic patterns globally and that distantly related microbial groups can perform similar functions, we hypothesized that microbiome co-occurrence patterns would occur independently of ersity trends and that keystone microbes would vary across locations. We found that whale shark aggregation was the most important factor in discriminating taxonomic ersity patterns. Further, microbiome network architecture was similar across all aggregations, with degree distributions matching Erdos–Renyi-type networks. The microbiome-derived networks, however, display modularity indicating a definitive microbiome structure on the epidermis of whale sharks. In addition, whale sharks hosted 35 high-quality metagenome assembled genomes (MAGs) of which 25 were present from all s le locations, termed the abundant ‘core’. Two main MAG groups formed, defined here as Ecogroup 1 and 2, based on the number of genes present in metabolic pathways, suggesting there are at least two important metabolic niches within the whale shark microbiome. Therefore, while variability in microbiome ersity is high, network structure and core taxa are inherent characteristics of the epidermal microbiome in whale sharks. We suggest the host-microbiome and microbe-microbe interactions that drive the self-assembly of the microbiome help support a functionally redundant abundant core and that network characteristics should be considered when linking microbiomes with host health.
Publisher: Frontiers Media SA
Date: 24-05-2023
DOI: 10.3389/FMICB.2023.963173
Abstract: The gut virome is an incredibly complex part of the gut ecosystem. Gut viruses play a role in many disease states, but it is unknown to what extent the gut virome impacts everyday human health. New experimental and bioinformatic approaches are required to address this knowledge gap. Gut virome colonization begins at birth and is considered unique and stable in adulthood. The stable virome is highly specific to each in idual and is modulated by varying factors such as age, diet, disease state, and use of antibiotics. The gut virome primarily comprises bacteriophages, predominantly order Crassvirales, also referred to as crAss-like phages, in industrialized populations and other Caudoviricetes (formerly Caudovirales ). The stability of the virome’s regular constituents is disrupted by disease. Transferring the fecal microbiome, including its viruses, from a healthy in idual can restore the functionality of the gut. It can alleviate symptoms of chronic illnesses such as colitis caused by Clostridiodes difficile . Investigation of the virome is a relatively novel field, with new genetic sequences being published at an increasing rate. A large percentage of unknown sequences, termed ‘viral dark matter’, is one of the significant challenges facing virologists and bioinformaticians. To address this challenge, strategies include mining publicly available viral datasets, untargeted metagenomic approaches, and utilizing cutting-edge bioinformatic tools to quantify and classify viral species. Here, we review the literature surrounding the gut virome, its establishment, its impact on human health, the methods used to investigate it, and the viral dark matter veiling our understanding of the gut virome.
Publisher: Public Library of Science (PLoS)
Date: 15-12-2022
Publisher: Springer Science and Business Media LLC
Date: 28-11-2017
Publisher: MDPI AG
Date: 05-09-2022
DOI: 10.3390/V14091969
Abstract: The epidermal microbiome is a critical element of marine organismal immunity, but the epidermal virome of marine organisms remains largely unexplored. The epidermis of sharks represents a unique viromic ecosystem. Sharks secrete a thin layer of mucus which harbors a erse microbiome, while their hydrodynamic dermal denticles simultaneously repel environmental microbes. Here, we s led the virome from the epidermis of three shark species in the family Carcharhinidae: the genetically and morphologically similar Carcharhinus obscurus (n = 6) and Carcharhinus galapagensis (n = 10) and the outgroup Galeocerdo cuvier (n = 15). Virome taxonomy was characterized using shotgun metagenomics and compared with a suite of multivariate analyses. All three sharks retain species-specific but highly similar epidermal viromes dominated by uncharacterized bacteriophages which vary slightly in proportional abundance within and among shark species. Intraspecific variation was lower among C. galapagensis than among C. obscurus and G. cuvier. Using both the annotated and unannotated reads, we were able to determine that the Carcharhinus galapagensis viromes were more similar to that of G. cuvier than they were to that of C. obscurus, suggesting that behavioral niche may be a more prominent driver of virome than host phylogeny.
Publisher: American Society for Microbiology
Date: 27-06-2023
Abstract: Microbial populations and species are notoriously hard to delineate. We used a population genomics approach to examine the population structure and the spatial scale of gene flow in Xenorhabdus bovienii , an intriguing species that is both a specialized mutualistic symbiont of nematodes and a broadly virulent insect pathogen.
Publisher: Cold Spring Harbor Laboratory
Date: 21-04-2023
DOI: 10.1101/2023.04.20.537752
Abstract: Phages dominate every ecosystem on the planet. While virulent phages sculpt the microbiome by killing their bacterial hosts, temperate phages provide unique growth advantages to their hosts through lysogenic conversion. Many prophages benefit their host, and prophages are responsible for genotypic and phenotypic differences that separate in idual microbial strains. However, the microbes also endure a cost to maintain those phages: additional DNA to replicate and proteins to transcribe and translate. We have never quantified those benefits and costs. Here, we analysed over two and a half million prophages from over half a million bacterial genome assemblies. Analysis of the whole dataset and a representative subset of taxonomically erse bacterial genomes demonstrated that the normalised prophage density was uniform across all bacterial genomes above 2 Mbp. We identified a constant carrying capacity of phage DNA per bacterial DNA. We estimated that each prophage provides cellular services equivalent to approximately 2.4 % of the cell’s energy or 0.9 ATP per bp per hour. We demonstrate analytical, taxonomic, geographic, and temporal disparities in identifying prophages in bacterial genomes that provide novel targets for identifying new phages. We anticipate that the benefits bacteria accrue from the presence of prophages balance the energetics involved in supporting prophages. Furthermore, our data will provide a new framework for identifying phages in environmental datasets, erse bacterial phyla, and from different locations.
No related grants have been discovered for Bhavya Papudeshi.