Mina Rho

The advances of next-generation sequencing technology have facilitated metagenomics research that attempts to determine directly the whole collection of genetic material within an environmental sample (i.e. the metagenome). Identification of genes directly from short reads has become an important yet challenging problem in annotating metagenomes, since the assembly of metagenomes is often not available. Gene predictors developed for whole genomes (e.g. Glimmer) and recently developed for metagen

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) loci, together with cas (CRISPR-associated) genes, form the CRISPR/Cas adaptive immune system, a primary defense strategy that eubacteria and archaea mobilize against foreign nucleic acids, including phages and conjugative plasmids. Short spacer sequences separated by the repeats are derived from foreign DNA and direct interference to future infections. The availability of hundreds of shotgun metagenomic datasets from the Human M

We demonstrated a fundamental methodology for linking genomic and transcriptomic datasets to examine functional activities of specific bacterial species in a complicated microbial environment. We investigated the normal flora of the mouse gut using three different approaches and identified Muribaculaceae, Lachnospiraceae, and Deferribacteraceae as the predominant families. The functional distribution of these families was reflected in the entire microbiome. By comparing the metagenomic and metat

We report a novel method for de novo identification of LTR retrotransposons in eukaryotic genomes with favorable performance over the existing methods.

Antibiotic resistome was more pervasive in swine than in cattle. Specifically, prevalent antibiotic resistance genes (prevalence >50%) were found more in swine than in cattle. Genomic investigation of specific resistance genes from the gut microbiomes of swine and cattle in this study should provide opportunities to better understand the exchange of antibiotic resistance genes in farm animals.

Viruses are ubiquitous in humans and various environments and continually mutate themselves. Identifying viruses in an environment without cultivation is challenging; however, promoting the screening of novel viruses and expanding the knowledge of viral space is essential. Homology-based methods that identify viruses using known viral genomes rely on sequence alignments, making it difficult to capture remote homologs of the known viruses. To accurately capture viral signals from metagenomic samp

With the emergence of next-generation sequencing (NGS) technology, there have been a large number of metagenomic studies that estimated the bacterial composition via 16S ribosomal RNA (16S rRNA) amplicon sequencing. In particular, subsets of the hypervariable regions in 16S rRNA, such as V1-V2 and V3-V4, are targeted using high-throughput sequencing. The sequences from different taxa are assigned to a specific taxon based on the sequence homology. Since such sequences are highly homologous or id

Given the importance of LTR retroelements activity in the evolution of other genomes, this comprehensive survey provides insight into the potential impact of LTR retroelements on the genome of D. pulex, a cyclically parthenogenetic microcrustacean that has served as an ecological model for over a century.

Microorganisms play a vital role in living systems in numerous ways. In the soil or ocean environment, microbes are involved in diverse processes, such as carbon and nitrogen cycle, nutrient recycling, and energy acquisition. The relation between microbial dysbiosis and disease developments has been extensively studied. In particular, microbial communities in the human gut are associated with the pathophysiology of several chronic diseases such as inflammatory bowel disease and diabetes. Therefo

With recent advances in biotechnology and sequencing technology, the microbial community has been intensively studied and discovered to be associated with many chronic as well as acute diseases. Even though a tremendous number of studies describing the association between microbes and diseases have been published, text mining methods that focus on such associations have been rarely studied. We propose a framework that combines machine learning and natural language processing methods to analyze t

The routine therapeutic use of antibiotics has caused resistance genes to be disseminated across microbial populations. In particular, bacterial strains having antibiotic resistance genes are frequently observed in the human microbiome. Moreover, multidrug-resistant pathogens are now widely spread, threatening public health. Such genes are transferred and spread among bacteria even in different environments. Advances in high throughput sequencing technology and computational algorithms have acce

Although it is generally accepted that major changes in the earth's history are significant drivers of phylogenetic diversification and extinction, such episodes may also have long-lasting effects on genomic architecture. Here we show that widespread reductions in genome size have occurred in multiple lineages of mammals subsequent to the Cretaceous-Tertiary (KT) boundary, whereas there is no evidence for such changes in other vertebrate, invertebrate, or land plant lineages. Although the mechan

Polymyxins are the last-line antibiotics used to treat Gram-negative pathogens. Thus, the discovery and biochemical characterization of the resistance genes against polymyxins are urgently needed for diagnosis, treatment, and novel antibiotic design. Herein, we report novel polymyxin-resistance genes identified from sediment and seawater microbiome. Despite their low sequence identity against the known <i>pmrE</i> and <i>pmrF</i>, they show <i>in vitro</i> activities in UDP-glucose oxidation and