Sangwan Naseer

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Sangwan
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Naseer
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  • Article
    Recovering complete and draft population genomes from metagenome datasets
    (BioMed Central, 2016-03-08) Sangwan, Naseer ; Xia, Fangfang ; Gilbert, Jack A.
    Assembly of metagenomic sequence data into microbial genomes is of fundamental value to improving our understanding of microbial ecology and metabolism by elucidating the functional potential of hard-to-culture microorganisms. Here, we provide a synthesis of available methods to bin metagenomic contigs into species-level groups and highlight how genetic diversity, sequencing depth, and coverage influence binning success. Despite the computational cost on application to deeply sequenced complex metagenomes (e.g., soil), covarying patterns of contig coverage across multiple datasets significantly improves the binning process. We also discuss and compare current genome validation methods and reveal how these methods tackle the problem of chimeric genome bins i.e., sequences from multiple species. Finally, we explore how population genome assembly can be used to uncover biogeographic trends and to characterize the effect of in situ functional constraints on the genome-wide evolution.
  • Preprint
    Ecological succession and viability of human-associated microbiota on restroom surfaces
    ( 2014-11-08) Gibbons, Sean M. ; Schwartz, Tara ; Fouquier, Jennifer ; Mitchell, Michelle ; Sangwan, Naseer ; Gilbert, Jack A. ; Kelley, Scott T.
    Human-associated bacteria dominate the built environment (BE). Following decontamination of floors, toilet seats, and soap dispensers in 4 public restrooms, in situ bacterial communities were characterized hourly, daily, and weekly to determine their successional ecology. The viability of cultivable bacteria, following the removal of dispersal agents (humans), was also assessed hourly. A late successional community developed within 5-8 hours on restroom floors, and showed remarkable stability over weeks to months. Despite late successional dominance by skin- and outdoor-associated bacteria, the most ubiquitous organisms were predominantly gut-associated taxa, which persisted following exclusion of humans. Staphylococcus represented the majority of the cultivable community, even after several hours of human-exclusion. MRSA-associated virulence genes were found on floors, but were not present in assembled Staphylococcus pan-genomes. Viral abundances, which were predominantly enterophage, human papilloma and herpes viruses, were significantly correlated with bacteria abundances, and showed an unexpectedly low virus-to-bacteria ratio in surface-associated samples, suggesting that bacterial hosts are mostly dormant on BE surfaces.
  • Article
    Invasive plants rapidly reshape soil properties in a grassland ecosystem
    (American Society for Microbiology, 2017-03-07) Gibbons, Sean M. ; Lekberg, Ylva ; Mummey, Daniel ; Sangwan, Naseer ; Ramsey, Philip W. ; Gilbert, Jack A.
    Plant invasions often reduce native plant diversity and increase net primary productivity. Invaded soils appear to differ from surrounding soils in ways that impede restoration of diverse native plant communities. We hypothesize that invader-mediated shifts in edaphic properties reproducibly alter soil microbial community structure and function. Here, we take a holistic approach, characterizing plant, prokaryotic, and fungal communities and soil physicochemical properties in field sites, invasion gradients, and experimental plots for three invasive plant species that cooccur in the Rocky Mountain West. Each invader had a unique impact on soil physicochemical properties. We found that invasions drove shifts in the abundances of specific microbial taxa, while overall belowground community structure and functional potential were fairly constant. Forb invaders were generally enriched in copiotrophic bacteria with higher 16S rRNA gene copy numbers and showed greater microbial carbohydrate and nitrogen metabolic potential. Older invasions had stronger effects on abiotic soil properties, indicative of multiyear successions. Overall, we show that plant invasions are idiosyncratic in their impact on soils and are directly responsible for driving reproducible shifts in the soil environment over multiyear time scales.
  • Article
    Metagenomic analysis of basal ice from an Alaskan glacier
    (BMC, 2018-07-05) Kayani, Masood ur Rehman ; Doyle, Shawn M. ; Sangwan, Naseer ; Wang, Guanqun ; Gilbert, Jack A. ; Christner, Brent C. ; Zhu, Ting F.
    Glaciers cover ~ 10% of land but are among the least explored environments on Earth. The basal portion of glaciers often harbors unique aquatic microbial ecosystems in the absence of sunlight, and knowledge on the microbial community structures and their metabolic potential is very limited. Here, we provide insights into the microbial lifestyle present at the base of the Matanuska Glacier, Alaska. DNA and RNA were extracted from samples of the Matanuska Glacier basal ice. Using Illumina MiSeq and HiSeq sequencing, we investigated the microbial diversity with the metagenomic shotgun reads and 16S ribosomal RNA data. We further assembled 9 partial and draft bacterial genomes from the metagenomic assembly, and identified key metabolic pathways such as sulfur oxidation and nitrification. Collectively, our analyses suggest a prevalence of lithotrophic and heterotrophic metabolisms in the subglacial microbiome. Our results present the first metagenomic assembly and bacterial draft genomes for a subglacial environment. These results extend our understanding of the chemical and biological processes in subglacial environments critically influenced by global climate change.