Biology subjects

Kosmopoulos, J. C.

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

4 recordsLinked to original sources

bioRxiv2024

V- and VL-Scores Uncover Viral Signatures and Origins of Protein Families

Viruses are key drivers of microbial diversity, nutrient cycling, and co-evolution in ecosystems, yet their study is hindered due to challenges in culturing. Traditional gene-centric methods, which focus on a few hallmark genes like for capsids, miss much of the viral genome, leaving key viral proteins and functions undiscovered. Here, we introduce two powerful annotation-free metrics, V-score and VL-score, designed to quantify the "virus-likeness" of protein families and genomes and create an open-access searchable database, V-Score-Search. By applying V- and VL-scores to public databases (KEGG, Pfam, and eggNOG), we link 38-77% of protein families with viruses, a 9-16x increase over current estimates. These metrics outperform existing approaches, enabling precise detection of viral genomes, prophages, and host-derived auxiliary viral genes (AVGs) from fragmented sequences, and significantly improving genome binning. Remarkably, we identify up to 17x more AVGs, dominated by non-metabolic proteins of unknown function. This innovation unlocks new insights into virus signatures and host interactions, with wide-ranging implications from genomics to biotechnology.

bioinformatics↗

bioRxiv2024

vClassifier: a toolkit for species-level classification of prokaryotic viruses

As the most abundant and diverse biological entities, prokaryotic viruses play pivotal roles in ecological systems. Their taxonomic classification has been instrumental in elucidating their diversity and ecological functions. However, determination of viral taxonomy remains a considerable challenge. Recently developed approaches succeed in assignment of viral taxonomy at higher ranks, such as at the family level and above, but struggle at the subfamily level and below to the genus and species resolutions. Here, we describe the vClassifier toolkit, a phylogeny-informed methodology to provide species-level taxonomic assignments of viruses. We used single-copy marker genes relevant to specific taxa and reference phylogenetic trees for these groups which facilitates direct comparisons with the taxonomic framework of the International Committee on Taxonomy of Viruses (ICTV). Our method demonstrated significant congruence with the ICTV taxonomy, showing 84-91% alignment at the subfamily and genus levels. For species-level classification, our strategy was integrated with average nucleotide identity, yielding a high congruence rate of over 92% with the taxonomic data from the NCBI Virus database. Benchmarking comparisons revealed that vClassifier matches or surpasses other available tools regarding precision and classification success rates. By achieving objectivity and high levels of consistency, vClassifier streamlines the taxonomic categorization of prokaryotic viral genomes. Accurate assignments at the subfamily, genus, and species levels will significantly refine the taxonomic resolution of viruses, fostering a deeper understanding of viral diversity in microbiomes and ecosystems.

evolutionary biology↗

bioRxiv2023

Co-inoculation with novel nodule-inhabiting bacteria reduces the benefits of legume-rhizobium symbiosis

The ecologically and economically vital symbiosis between nitrogen-fixing rhizobia and leguminous plants is often thought of as a bi-partite interaction, yet studies increasingly show the prevalence of non-rhizobial endophytes (NREs) that occupy nodules alongside rhizobia. Yet, what impact these NREs have on plant or rhizobium fitness remains unclear. Here, we investigated four NRE strains found to naturally co-occupy nodules of the legume Medicago truncatula alongside Sinorhizobium meliloti in native soils. Our objectives were to (1) examine the direct and indirect effects of NREs on M. truncatula and S. meliloti fitness, and (2), determine whether NREs can re-colonize root and nodule tissues upon reinoculation. We identified one NRE strain (522) as a novel Paenibacillus species, another strain (717A) as a novel Bacillus species, and the other two (702A and 733B) as novel Pseudomonas species. Additionally, we found that two NREs (Bacillus 717A and Pseudomonas 733B) reduced the fitness benefits obtained from symbiosis for both partners, while the other two (522, 702A) had little effect. Lastly, we found that NREs were able to co-infect host tissues alongside S. meliloti. This study demonstrates that variation of NREs present in natural populations must be considered to better understand legume-rhizobium dynamics in soil communities.

microbiology↗

bioRxiv2023

Viromes vs. mixed community metagenomes: choice of method dictates interpretation of viral community ecology

BackgroundViruses, the majority of which are uncultivated, are among the most abundant biological entities on Earth. From altering microbial physiology to driving community dynamics, viruses are fundamental members of microbiomes. While the number of studies leveraging viral metagenomics (viromics) for studying uncultivated viruses is growing, standards for viromics research are lacking. Viromics can utilize computational discovery of viruses from total metagenomes of all community members (hereafter metagenomes) or use physical separation of virus-specific fractions (hereafter viromes). However, differences in the recovery and interpretation of viruses from metagenomes and viromes obtained from the same samples remain understudied. ResultsHere, we compare viral communities from paired viromes and metagenomes obtained from 60 diverse samples across human gut, soil, freshwater, and marine ecosystems. Overall, viral communities obtained from viromes were more abundant and species rich than those obtained from metagenomes, although there were some exceptions. Despite this, metagenomes still contained many viral genomes not detected in viromes. We also found notable differences in the predicted lytic state of viruses detected in viromes vs metagenomes at the time of sequencing. Other forms of variation observed include genome presence/absence, genome quality, and encoded protein content between viromes and metagenomes, but the magnitude of these differences varied by environment. ConclusionsOverall, our results show that the choice of method can lead to differing interpretations of viral community ecology. We suggest that the choice of whether to target a metagenome or virome to study viral communities should be dependent on the environmental context and ecological questions being asked. However, our overall recommendation to researchers investigating viral ecology and evolution is to pair both approaches to maximize their respective benefits.

ecology↗