Browsing by Author "Tithi, Saima Sultana"

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    Computational Analysis of Viruses in Metagenomic Data
    Tithi, Saima Sultana (Virginia Tech, 2019-10-24)
    Viruses have huge impact on controlling diseases and regulating many key ecosystem processes. As metagenomic data can contain many microbiomes including many viruses, by analyzing metagenomic data we can analyze many viruses at the same time. The first step towards analyzing metagenomic data is to identify and quantify viruses present in the data. In order to answer this question, we developed a computational pipeline, FastViromeExplorer. FastViromeExplorer leverages a pseudoalignment based approach, which is faster than the traditional alignment based approach to quickly align millions/billions of reads. Application of FastViromeExplorer on both human gut samples and environmental samples shows that our tool can successfully identify viruses and quantify the abundances of viruses quickly and accurately even for a large data set. As viruses are getting increased attention in recent times, most of the viruses are still unknown or uncategorized. To discover novel viruses from metagenomic data, we developed a computational pipeline named FVE-novel. FVE-novel leverages a hybrid of both reference based and de novo assembly approach to recover novel viruses from metagenomic data. By applying FVE-novel to an ocean metagenome sample, we successfully recovered two novel viruses and two different strains of known phages. Analysis of viral assemblies from metagenomic data reveals that viral assemblies often contain assembly errors like chimeric sequences which means more than one viral genomes are incorrectly assembled together. In order to identify and fix these types of assembly errors, we developed a computational tool called VirChecker. Our tool can identify and fix assembly errors due to chimeric assembly. VirChecker also extends the assembly as much as possible to complete it and then annotates the extended and improved assembly. Application of VirChecker to viral scaffolds collected from an ocean meatgenome sample shows that our tool successfully fixes the assembly errors and extends two novel virus genomes and two strains of known phage genomes.
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    FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data
    Tithi, Saima Sultana; Aylward, Frank O.; Jensen, Roderick V.; Zhang, Liqing (PeerJ, 2018-01-12)
    With the increase in the availability of metagenomic data generated by next generation sequencing, there is an urgent need for fast and accurate tools for identifying viruses in host-associated and environmental samples. In this paper, we developed a stand-alone pipeline called FastViromeExplorer for the detection and abundance quantification of viruses and phages in large metagenomic datasets by performing rapid searches of virus and phage sequence databases. Both simulated and real data from human microbiome and ocean environmental samples are used to validate FastViromeExplorer as a reliable tool to quickly and accurately identify viruses and their abundances in large datasets.
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    Parallel Evolution of Genome Streamlining and Cellular Bioenergetics across the Marine Radiation of a Bacterial Phylum
    Getz, Eric W.; Tithi, Saima Sultana; Zhang, Liqing; Aylward, Frank O. (American Society for Microbiology, 2018-09)
    Diverse bacterial and archaeal lineages drive biogeochemical cycles in the global ocean, but the evolutionary processes that have shaped their genomic properties and physiological capabilities remain obscure. Here we track the genome evolution of the globally abundant marine bacterial phylum Marinimicrobia across its diversification into modern marine environments and demonstrate that extant lineages are partitioned between epipelagic and mesopelagic habitats. Moreover, we show that these habitat preferences are associated with fundamental differences in genomic organization, cellular bioenergetics, and metabolic modalities. Multiple lineages present in epipelagic niches independently acquired genes necessary for phototrophy and environmental stress mitigation, and their genomes convergently evolved key features associated with genome streamlining. In contrast, lineages residing in mesopelagic waters independently acquired nitrate respiratory machinery and a variety of cytochromes, consistent with the use of alternative terminal electron acceptors in oxygen minimum zones (OMZs). Further, while epipelagic clades have retained an ancestral Na+ -pumping respiratory complex, mesopelagic lineages have largely replaced this complex with canonical H+-pumping respiratory complex I, potentially due to the increased efficiency of the latter together with the presence of the more energy-limiting environments deep in the ocean's interior. These parallel evolutionary trends indicate that key features of genomic streamlining and cellular bioenergetics have occurred repeatedly and congruently in disparate clades and underscore the importance of environmental conditions and nutrient dynamics in driving the evolution of diverse bacterioplankton lineages in similar ways throughout the global ocean. IMPORTANCE Understanding long-term patterns of microbial evolution is critical to advancing our knowledge of past and present role microbial life in driving global biogeochemical cycles. Historically, it has been challenging to study the evolution of environmental microbes due to difficulties in obtaining genome sequences from lineages that could not be cultivated, but recent advances in metagenomics and single-cell genomics have begun to obviate many of these hurdles. Here we present an evolutionary genomic analysis of the Marinimicrobia, a diverse bacterial group that is abundant in the global ocean. We demonstrate that distantly related Marinimicrobia species that reside in similar habitats have converged to assume similar genome architectures and cellular bioenergetics, suggesting that common factors shape the evolution of a broad array of marine lineages. These findings broaden our understanding of the evolutionary forces that have given rise to microbial life in the contemporary ocean.