Lin-Xing Chen
YOU?
Author Swipe
View article: Bioleaching Microbial Community Metabolism and Composition Driven by Copper Sulphide Mineral Type
Bioleaching Microbial Community Metabolism and Composition Driven by Copper Sulphide Mineral Type Open
Copper bioleaching is a green technology for the recovery of copper from chalcopyrite (CuFeS 2 ) and chalcocite (Cu 2 S) ores. Much remains to be learned about how mineral type and surface chemistry influence microbial community compositio…
View article: Megaplasmids associate with <i>Escherichia coli</i> and other <i>Enterobacteriaceae</i>
Megaplasmids associate with <i>Escherichia coli</i> and other <i>Enterobacteriaceae</i> Open
Summary Humans and animals are ubiquitously colonized by Enterobacteriaceae , a bacterial family that contains both commensals and clinically significant pathogens. Here, we report Enterobacteriaceae megaplasmids of up to 1.58 Mbp in lengt…
View article: A prevalent huge phage clade in human and animal gut microbiomes
A prevalent huge phage clade in human and animal gut microbiomes Open
Huge phages are widespread in the biosphere, yet their prevalence and ecology in the human gut remain poorly characterized. Here, we report Jug (Jumbo gut) phages with genomes of 360-402 kilobase pairs that comprise ~1.1% of the reads in h…
View article: A prevalent huge phage clade in human and animal gut microbiomes
A prevalent huge phage clade in human and animal gut microbiomes Open
Huge phages are widespread in the biosphere, yet their prevalence and ecology in the human gut remain poorly characterized. Here, we report Jug (Jumbo gut) phages with genomes of 360-402 kilobase pairs that comprise ~1.1% of the reads in h…
View article: The hidden prevalence and unique protein folds of huge phages
The hidden prevalence and unique protein folds of huge phages Open
Huge phages are remarkable for their expansive genomes (≥200 kbp, and up to 841 kbp to date), global distribution, and intricate functional repertoires. However, their study has been hindered by challenges in genome identification and the …
View article: Discovery and analysis of an 841 kbp phage genome: the largest known to date
Discovery and analysis of an 841 kbp phage genome: the largest known to date Open
Viruses represent the most abundant biological entities on Earth, with bacteriophages (or phages) specifically infecting bacteria. Typically, double-strand DNA phages possess genomes around 50 kilobase pairs (kbp) in size, although the lar…
View article: Gastrointestinal jumbo phages possess independent synthesis and utilization systems of NAD+
Gastrointestinal jumbo phages possess independent synthesis and utilization systems of NAD+ Open
In summary, this study expands our understanding of the diversity and survival strategies of phages, and an in-depth study of the NAD-jumbo phages is crucial for understanding their role in ecological regulation. Video Abstract.
View article: Seasonal succession, host associations, and biochemical roles of aquatic viruses in a eutrophic lake plagued by cyanobacterial blooms
Seasonal succession, host associations, and biochemical roles of aquatic viruses in a eutrophic lake plagued by cyanobacterial blooms Open
Viruses are implicated to play key roles as biogeochemical mediators and ecological drivers in freshwater ecosystems. However, the dynamics of viruses and host associations throughout the seasons and during blooming periods in eutrophic fr…
View article: pH and thiosulfate dependent microbial sulfur oxidation strategies across diverse environments
pH and thiosulfate dependent microbial sulfur oxidation strategies across diverse environments Open
Sulfur oxidizing bacteria (SOB) play a key role in sulfur cycling in mine tailings impoundment (TI) waters, where sulfur concentrations are typically high. However, our understanding of SOB sulfur cycling via potential S oxidation pathways…
View article: Microbial Sulfur Pathways and Outcomes in Tailings Impoundments: A Mesocosm Study
Microbial Sulfur Pathways and Outcomes in Tailings Impoundments: A Mesocosm Study Open
In mine wastewaters, three microbial sulfur oxidation pathways have the potential to cause different water quality outcomes that can differ from abiotic model sulfate and acidity predictions, currently used to monitor potential sulfur risk…
View article: Targeted replacement of full-length CFTR in human airway stem cells by CRISPR-Cas9 for pan-mutation correction in the endogenous locus
Targeted replacement of full-length CFTR in human airway stem cells by CRISPR-Cas9 for pan-mutation correction in the endogenous locus Open
Cystic fibrosis (CF) is a monogenic disease caused by impaired production and/or function of the CF transmembrane conductance regulator (CFTR) protein. Although we have previously shown correction of the most common pathogenic mutation, th…
View article: Jumbo phages possess independent synthesis and utilization systems of NAD<sup>+</sup>
Jumbo phages possess independent synthesis and utilization systems of NAD<sup>+</sup> Open
Jumbo phages, phages with genomes >200 kbp, contain some unique genes for successful reproduction in their bacterial hosts. Due to complex and massive genomes analogous to those of small-celled bacteria, how do jumbo phages complete their …
View article: COBRA improves the completeness and contiguity of viral genomes assembled from metagenomes
COBRA improves the completeness and contiguity of viral genomes assembled from metagenomes Open
Viruses are often studied using metagenome-assembled sequences, but genome incompleteness hampers comprehensive and accurate analyses. Contig Overlap Based Re-Assembly (COBRA) resolves assembly breakpoints based on the de Bruijn graph and …
View article: Long-Term Axial Length Shortening in Myopic Orthokeratology: Incident Probability, Time Course, and Influencing Factors
Long-Term Axial Length Shortening in Myopic Orthokeratology: Incident Probability, Time Course, and Influencing Factors Open
Long-term AL shortening is possible in subjects receiving myopic orthokeratology. Although age notably affect the incident probability, the time course seems to not vary significantly.
View article: Host translation machinery is not a barrier to phages that interact with both CPR and non-CPR bacteria
Host translation machinery is not a barrier to phages that interact with both CPR and non-CPR bacteria Open
Within human microbiomes, Gracilibacteria, Absconditabacteria, and Saccharibacteria, members of Candidate Phyla Radiation (CPR), are increasingly correlated with human oral health and disease. We profiled the diversity of CRISPR-Cas system…
View article: Eukaryotic RNA-guided endonucleases evolved from a unique clade of bacterial enzymes
Eukaryotic RNA-guided endonucleases evolved from a unique clade of bacterial enzymes Open
RNA-guided endonucleases form the crux of diverse biological processes and technologies, including adaptive immunity, transposition, and genome editing. Some of these enzymes are components of insertion sequences (IS) in the IS200/IS605 an…
View article: Seasonal Succession, Host Associations and Biochemical Roles of Aquatic Viruses in a Eutrophic Lake Plagued by Cyanobacterial Blooms
Seasonal Succession, Host Associations and Biochemical Roles of Aquatic Viruses in a Eutrophic Lake Plagued by Cyanobacterial Blooms Open
Background. Viruses are important biogeochemical mediators and ecological drivers in freshwater ecosystems. Although the environmental implications of viruses in ecosystems have been preliminarily explored, the dynamics of viruses and host…
View article: CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes
CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes Open
CRISPR-Cas enzymes enable RNA-guided bacterial immunity and are widely used for biotechnological applications including genome editing. In particular, the Class 2 CRISPR-associated enzymes (Cas9, Cas12 and Cas13 families), have been deploy…
View article: CasPEDIA Database: A Functional Classification System for Class 2 CRISPR-Cas Enzymes
CasPEDIA Database: A Functional Classification System for Class 2 CRISPR-Cas Enzymes Open
CRISPR-Cas enzymes enable RNA-guided bacterial immunity and are widely used for biotechnological applications including genome editing. In particular, the Class 2 CRISPR-associated enzymes (Cas9, Cas12 and Cas13 families), have been deploy…
View article: Myopic progression in school-aged children with moderate intermittent exotropia
Myopic progression in school-aged children with moderate intermittent exotropia Open
Objective It is still controversial whether intermittent exotropia (IXT) affects myopic progression during the critical period of visual development. This study retrospectively analyzed the long-term myopic changes and the impact of IXT su…
View article: Eukaryotic RNA-guided endonucleases evolved from a unique clade of bacterial enzymes
Eukaryotic RNA-guided endonucleases evolved from a unique clade of bacterial enzymes Open
RNA-guided endonucleases form the crux of diverse biological processes and technologies, including adaptive immunity, transposition, and genome editing. Some of these enzymes are components of insertion sequences (IS) in the IS200/IS605 an…
View article: Methanotrophic<i>Methanoperedens</i>archaea host diverse and interacting extrachromosomal elements
Methanotrophic<i>Methanoperedens</i>archaea host diverse and interacting extrachromosomal elements Open
Methane emissions that contribute to climate change can be mitigated by anaerobic methane-oxidizing archaea such as Methanoperedens . Some Methanoperedens have huge extrachromosomal genetic elements (ECEs) called Borgs that may modulate th…
View article: COBRA improves the quality of viral genomes assembled from metagenomes
COBRA improves the quality of viral genomes assembled from metagenomes Open
Microbial and viral diversity, distribution, and ecological impacts are often studied using metagenome-assembled sequences, but genome incompleteness hampers comprehensive and accurate analyses. Here we introduce COBRA (Contig Overlap Base…
View article: COBRA improves the quality of viral genomes assembled from metagenomes
COBRA improves the quality of viral genomes assembled from metagenomes Open
Microbial and viral diversity, distribution, and ecological impacts are often studied using metagenome-assembled sequences, but genome incompleteness hampers comprehensive and accurate analyses. Here we introduce COBRA ( C ontig O verlap B…
View article: O2 partitioning of sulfur oxidizing bacteria drives acidity and thiosulfate distributions in mining waters
O2 partitioning of sulfur oxidizing bacteria drives acidity and thiosulfate distributions in mining waters Open
The acidification of water in mining areas is a global environmental issue primarily catalyzed by sulfur-oxidizing bacteria (SOB). Little is known about microbial sulfur cycling in circumneutral pH mine tailing impoundment waters. Here we …
View article: RNA reads
RNA reads Open
The fastq files of the three metatranscriptomic samples analyzed in Whaley-Martin and Chen et al., 2023, “O2 partitioning of sulfur oxidizing bacteria drives acidity and thiosulfate distributions in mining waters” (https://doi.org/10.1038/…
View article: viral.genomes.fasta
viral.genomes.fasta Open
The 12118 high-quality or complete genomes obtained by COBRA analyses from 231 freshwater metagenomes.