Biology subjects

Zhong, K. X.

Publications and source records attributed to Zhong, K. X..

7 recordsLinked to original sources

bioRxiv2026

Oysters from five continents harbour a vast array of previously unknown RNA viruses, including many putative viruses of vertebrates

Oysters are vital to global aquaculture and marine ecosystems, yet, their associated RNA viruses remain largely unexplored. Here, we analysed ~1,000 publicly available metatranscriptomic datasets from 13 oyster species across 14 countries and 5 continents to characterize the oyster RNA virome (ORV). We identified 1,515 distinct RNA viruses putatively representing 17 viral orders and 766 species-level viral operational taxonomic units (vOTUs), with ~62% being previously undocumented putative species. These viruses not only populate extant branches of RNA virus evolution, but also represent previously unrecognized families and genera, and include viruses that putatively infect bacteria, fungi, protists, plants, invertebrates, and vertebrates. Based on sequence similarity, we found many calicivirus-like, orthoreovirus-like, astrovirus-like, and picornavirus-like viruses that do not infect invertebrates or microbes; thus, oysters accumulate diverse viruses from the surrounding water, and can potentially be interrogated as reporters of viruses circulating in the environment.

microbiology↗

bioRxiv2026

Mapping the Functional Landscape and Viral Diversity of 2A Peptides

2A peptides are short (~18 to 22 amino acid) sequences utilized by a subset of RNA viruses to process their polyproteins in an unusual co-translational event known as StopGo or ribosome skipping. This process involves ribosome pausing at a conserved C-terminal D(V/I)ExNPGP motif, followed by peptidyl-tRNA hydrolysis of the nascent peptide-tRNAGly, and continued translation from the downstream proline codon. However, how nascent 2A peptide interacts with the ribosomal exit tunnel to promote these event(s) remains poorly understood and the molecular determinants governing 2A mediated StopGo translation remain undefined. Here, we developed a mammalian fluorescence resonance energy transfer (FRET) based high-throughput reporter system to quantitatively measure 2A activity across large libraries of natural and engineered 2A peptides. Systematic mutational analysis of canonical viral 2A peptides from porcine tescovirus and foot-and-mouth disease virus (P2A, F2A) identified key residues required for activity and revealed critical contributions from previously uncharacterized N-terminal residues. Extending this approach to metagenomic viral datasets uncovered conserved sequences governing StopGo efficiency leading to functional ranking of diverse viral 2A peptides in mammalian cells, including identification of a novel subclass that supports high stop-go activity (>99%). Phylogenetic analysis of viral genomes revealed clustering of functional 2A peptides and specific motifs within specific viral lineages branches, suggesting an evolutionary trajectory underlying 2A diversification and optimization. These findings define the sequence and functional landscape of viral 2A peptides and provide mechanistic and evolutionary insights into how nascent peptide ribosome exit tunnel interactions mediate StopGo translation.

biochemistry↗

bioRxiv2024

The genome of Gallaecimonas pentaromativorans strain 10A, isolated from a Pacific oyster, reveals the potential for hydrocarbon degradation and CRISPR-Cas defense

Bacteria in the genus Gallaecimonas are known for their ability to breakdown complex hydrocarbons, making them of particular ecological and biotechnological significance. However, few species have been isolated to date, and their ecological distribution has yet to be examined. Here, we report a novel bacterium in the genus Gallaecimonas, designated as G. pentaromativorans strain 10A, which was isolated from a Pacific oyster (Magallana gigas, a.k.a. Crassostrea gigas) collected from a farm experiencing a mass mortality event in British Columbia, Canada. G. pentaromativorans strain 10A is a rod-shaped, motile bacterium and has a circular genome of 4,322,156 bp encoding 3,928 protein-coding sequences (CDS). Phylogenetic analysis showed that strain 10A is closely related to members of G. pentaromativorans. Like other Gallaecimonas members, strain 10A harbours specific pathways involved in degrading polycyclic aromatic hydrocarbons (PAHs) and xenobiotic compounds, producing biosurfactants, and assimilating nitrate and sulfate; however, it is uniquely equipped with an additional 166 genes belonging to 147 protein families, including a putative higB-higA that likely contributes to enhanced stress response. Strain 10A also possesses clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems (CRISPR-Cas), prevalent in Gallaecimonas (detected in three out of four species), implying a potential defense mechanism against exogenous mobile genetic elements such as plasmids and viruses. We also mined publicly available databases to establish the widespread distribution of bacteria in the genus Gallaecimonas in seawater, sediments, and freshwater across latitude, suggesting its versatility and importance to environmental processes. Ultimately, this study demonstrates that the genome of Gallaecimonas pentaromativorans strain 10A, isolated from a diseased Pacific oyster, encodes for a suite of putative functions, including oil degradation, xenobiotic breakdown, biosurfactants production, assimilatory nitrate and sulfate reduction, and viral defense. This plasticity and breadth in metabolic function help to explain the cosmopolitan distribution of members of this genus.

microbiology↗

bioRxiv2023

The core microbiome of cultured Pacific oyster spat develops with age but not mortality

The Pacific oyster (Magallana gigas, also known as Crassostrea gigas) is the most widely cultured shellfish worldwide, but production has been affected by mortality events. This includes mortality events in hatcheries that can threaten the seed supply for growers. There are several pathogens that cause disease in oysters, but in many cases mortality events cannot be attributed to a single agent, and appear to be multifactorial and involve a combination of environmental variables, microbial interactions and disbiosis. In many organisms, a mature microbiome provides resilience against pathogens and environmental stressors. In this study we investigated the microbiomes of cohorts of freshly settled oyster spat, some of which experienced notable mortality. Deep sequencing of 16S rRNA gene fragments did not show a significant difference among the microbiomes of cohorts experiencing different levels of mortality, but revealed a characteristic core microbiome with 74 taxa. Irrespective of mortality, the spat core microbiomes changed significantly in the relative abundance of taxa as the spat aged; yet, remained distinct from the microbial community in the surrounding water. The core microbiome was dominated by bacteria in the families Rhodobacteraceae, Nitrosomonadaceae, Flavobacteriaceae, Pirellulaeceae and Saprospiraceae. Of these, 14 taxa were indicative for the change in the core microbiome, which we designated as the "Hard-Core Microbiome". The variability in diversity and richess of members of the core taxa decreased with oyster-spat aging, implying niche occupation. The study further accounts for the exchange of microbes with surrounding water during the core microbiome development. The observed shifts in the core microbiome with ageing oyster spat implies a crucial developmental period for the core microbiome of rearing spat. ImportanceThe Pacific oyster (Magallana gigas, also known as Crassostrea gigas) is the most widely cultivated shellfish and is important to the economy of many coastal communities. However, high mortality of spat during the first few days following metamorphosis can affect the seed supply to oyster growers. Here, we show that the microbiome composition of recently settled oyster spat experiencing low or high mortality were not significantly different. Instead, development of the core microbiome were associated with spat aging and was partially driven by dispersal through the water. These findings imply the importance of early stage rearing conditons for spat microbiome development in aquaculture facilities. Furthermore, shellfish growers could gain information about the developmental state of the oyster spat microbiome by assessing key taxa. Additionally, the study provides a baseline micriobiome for future hypothesis testing on developing spat.

microbiology↗

bioRxiv2023

The Prokaryotic and Eukaryotic Microbiome of Pacific Oyster Spat is Shaped by Ocean Warming but not Acidification

Pacific oysters (Magallana gigas, also known as Crassostrea gigas), the most widely farmed oysters, are under threat from climate change and emerging pathogens. In part, their resilience may be affected by their microbiome, which, in turn, may be influenced by ocean warming and acidification. Consequently, for three weeks, we exposed early-development Pacific oyster spat to different temperatures (18 and 24 {degrees}C) and pCO2 levels (800, 1600 and 2800 {micro}atm) in a fully crossed design. Under all conditions, the microbiome developed over time, with potentially pathogenic ciliates (Uronema marinum) greatly reduced in all treatments, suggesting that the spats microbiome undergoes adaptive shifts as the oysters age. The microbiome composition also differed significantly with temperature, but not acidification, indicating that M. gigas spat microbiomes can be altered by ocean warming but resilient to ocean acidification in our experiments. These findings highlight the spat microbiomes flexibility to environmental changes as well as its "protective" capability against potentially pathogenic microbes.

microbiology↗

bioRxiv2021

Extracellular ribosomal RNA provides a window into taxon-specific microbial lysis

Microbes are by far the dominant biomass in the worlds oceans and drive biogeochemical cycles that are critical to life on Earth. The composition of marine microbial communities is highly dynamic spatially and temporally, with consequent effects on their functional roles. In part, these changes in composition result from viral lysis, which is taxon-specific and estimated to account for about half of marine microbial mortality. Here we determined taxon-specific cell lysis of prokaryotes in coastal seawater by sequencing extracellular and cellular ribosomal RNA (rRNA). We detected lysis in about 15% of the 16946 prokaryotic amplicon sequence variants (ASVs) identified, and lysis of up to 34% of the ASVs within a water sample. High lysis was most commonly associated with rare but typically highly productive bacteria, while relatively low lysis was more common in taxa that are often abundant, consistent with the proposed model of "kill the winner", and the idea that less abundant taxa generally experience higher relative lysis than dominant taxa. These results provide an explanation to the long-standing conundrum of why highly productive bacteria that are readily isolated from seawater are often in very low abundance. One Sentence SummaryExtracellular rRNA shows wide variation in cell lysis among prokaryotic taxa.

microbiology↗

bioRxiv2020

The use of CRISPR-Cas Selective Amplicon Sequencing (CCSAS) to reveal the eukaryotic microbiome of metazoans

Characterization of the eukaryotic microbiome is required to understand the role of microbial communities in health and disease. Such investigation relies on sequencing 18S ribosomal RNA genes (rDNA), which serve as taxonomic markers; however, this is compromised by contaminating host rDNA sequences. To overcome this problem, we developed CRISPR-Cas Selective Amplicon Sequencing (CCSAS), a high-resolution and efficient approach for characterizing eukaryotic microbiomes. CCSAS uses taxon-specific single-guide RNA (sgRNA) to direct Cas9 to cut 18S rDNA sequences of the host. Validation shows that >96.5% of rDNA amplicons from ten model organisms were cleaved, while rDNA from protists and fungi were unaffected. In oyster spat, CCSAS resolved [~]8.5-fold more taxa, and several additional major phylogenetic groups when compared to the best available alternative approach. We designed taxon-specific sgRNA for [~]16,000 metazoan and plant taxa, making CCSAS widely available for characterizing eukaryotic microbiomes that have largely been neglected because of methodological challenges.

microbiology↗