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metagenomics

  • Open Access
    Metagenomic Quantification of Genes with Internal Standards
    Research Article | Applied and Environmental Science
    Metagenomic Quantification of Genes with Internal Standards

    qPCR and metagenomics are central molecular techniques that have offered insights into biological processes for decades, from monitoring spatial and temporal gene dynamics to tracking ARGs or pathogens. Still needed is a tool that can quantify thousands of relevant genes in a sample as gene copies per sample mass or volume.

    Emily Crossette, Jordan Gumm, Kathryn Langenfeld, Lutgarde Raskin, Melissa Duhaime, Krista Wigginton
  • Open Access
    Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants
    Research Article | Clinical Science and Epidemiology
    Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants

    Viral genome sequencing has guided our understanding of the spread and extent of genetic diversity of SARS-CoV-2 during the COVID-19 pandemic. SARS-CoV-2 viral genomes are usually sequenced from nasopharyngeal swabs of individual patients to track viral spread.

    Alexander Crits-Christoph, Rose S. Kantor, Matthew R. Olm, Oscar N. Whitney, Basem Al-Shayeb, Yue Clare Lou, Avi Flamholz, Lauren C. Kennedy, Hannah Greenwald, Adrian Hinkle, Jonathan Hetzel, Sara Spitzer, Jeffery Koble, Asako Tan, Fred Hyde, Gary Schroth, Scott Kuersten, Jillian F. Banfield, Kara L. Nelson
  • Open Access
    Competitive Exclusion and Metabolic Dependency among Microorganisms Structure the Cellulose Economy of an Agricultural Soil
    Research Article | Ecological and Evolutionary Science
    Competitive Exclusion and Metabolic Dependency among Microorganisms Structure the Cellulose Economy of an Agricultural Soil

    Our study reveals the ecogenomic traits of microorganisms participating in the cellulose economy of soil. We identified three major categories of participants in this economy: (i) independent primary degraders, (ii) interdependent primary degraders, and (iii) secondary consumers (mutualists, opportunists, and parasites).

    Roland C. Wilhelm, Charles Pepe-Ranney, Pamela Weisenhorn, Mary Lipton, Daniel H. Buckley
  • Open Access
    Metagenomic Next-Generation Sequencing of Nasopharyngeal Specimens Collected from Confirmed and Suspect COVID-19 Patients
    Research Article | Clinical Science and Epidemiology
    Metagenomic Next-Generation Sequencing of Nasopharyngeal Specimens Collected from Confirmed and Suspect COVID-19 Patients

    SARS-CoV-2 has presented a rapidly accelerating global public health crisis. The ability to detect and analyze viral RNA from minimally invasive patient specimens is critical to the public health response. Metagenomic next-generation sequencing (mNGS) offers an opportunity to detect SARS-CoV-2 from nasopharyngeal (NP) swabs. This approach also provides information on the composition of the respiratory microbiome and its relationship to...

    Heba H. Mostafa, John A. Fissel, Brian Fanelli, Yehudit Bergman, Victoria Gniazdowski, Manoj Dadlani, Karen C. Carroll, Rita R. Colwell, Patricia J. Simner
  • Open Access
    The Role of the Gut Microbiome in Resisting Norovirus Infection as Revealed by a Human Challenge Study
    Research Article | Host-Microbe Biology
    The Role of the Gut Microbiome in Resisting Norovirus Infection as Revealed by a Human Challenge Study

    The role of the human gut microbiome in determining whether an individual infected with norovirus will be symptomatic is poorly understood. This study provides important data on microbes that distinguish asymptomatic from symptomatic microbiomes and links these features to infection responses in a human challenge study. The results have implications for understanding resistance to and treatment of norovirus infections.

    ...
    N. V. Patin, A. Peña-Gonzalez, J. K. Hatt, C. Moe, A. Kirby, K. T. Konstantinidis
  • Open Access
    Atribacteria Reproducing over Millions of Years in the Atlantic Abyssal Subseafloor
    Research Article | Ecological and Evolutionary Science
    Atribacteria Reproducing over Millions of Years in the Atlantic Abyssal Subseafloor

    The deep subseafloor sedimentary biosphere is one of the largest ecosystems on Earth, where microbes subsist under energy-limited conditions over long timescales. It remains poorly understood how mechanisms of microbial metabolism promote increased fitness in these settings. We discovered that the candidate bacterial phylum “Candidatus Atribacteria” dominated a deep-sea subseafloor ecosystem, where it exhibited increased...

    Aurèle Vuillemin, Sergio Vargas, Ömer K. Coskun, Robert Pockalny, Richard W. Murray, David C. Smith, Steven D’Hondt, William D. Orsi
  • Open Access
    Bacterial Secondary Metabolite Biosynthetic Potential in Soil Varies with Phylum, Depth, and Vegetation Type
    Research Article | Applied and Environmental Science
    Bacterial Secondary Metabolite Biosynthetic Potential in Soil Varies with Phylum, Depth, and Vegetation Type

    Microbes produce specialized compounds to compete or communicate with one another and their environment. Some of these compounds, such as antibiotics, are also useful in medicine and biotechnology. Historically, most antibiotics have come from soil bacteria which can be isolated and grown in the lab. Though the vast majority of soil bacteria cannot be isolated, we can extract their genetic information and search it for genes which...

    Allison M. Sharrar, Alexander Crits-Christoph, Raphaël Méheust, Spencer Diamond, Evan P. Starr, Jillian F. Banfield
  • Open Access
    Advances in Understanding the Human Urinary Microbiome and Its Potential Role in Urinary Tract Infection
    Minireview | Host-Microbe Biology
    Advances in Understanding the Human Urinary Microbiome and Its Potential Role in Urinary Tract Infection

    Recent advances in the analysis of microbial communities colonizing the human body have identified a resident microbial community in the human urinary tract (UT). Compared to many other microbial niches, the human UT harbors a relatively low biomass. Studies have identified many genera and species that may constitute a core urinary microbiome. However, the contribution of the UT microbiome to urinary tract infection (UTI) and recurrent...

    Michael L. Neugent, Neha V. Hulyalkar, Vivian H. Nguyen, Philippe E. Zimmern, Nicole J. De Nisco
  • Open Access
    Metagenomic Exploration of the Marine Sponge <em>Mycale hentscheli</em> Uncovers Multiple Polyketide-Producing Bacterial Symbionts
    Research Article | Host-Microbe Biology
    Metagenomic Exploration of the Marine Sponge Mycale hentscheli Uncovers Multiple Polyketide-Producing Bacterial Symbionts

    Mycale hentscheli is a marine sponge that is rich in bioactive small molecules. Here, we use direct metagenomic sequencing to elucidate highly complete and contiguous genomes for the major symbiotic bacteria of this sponge. We identify complete biosynthetic pathways for the three potent cytotoxic polyketides which have previously been isolated from M. hentscheli. Remarkably, and in contrast to previous studies of...

    Mathew A. Storey, Sarah K. Andreassend, Joe Bracegirdle, Alistair Brown, Robert A. Keyzers, David F. Ackerley, Peter T. Northcote, Jeremy G. Owen
  • Open Access
    Humans Are Selectively Exposed to <span class="named-content genus-species" id="named-content-1">Pneumocystis jirovecii</span>
    Opinion/Hypothesis | Host-Microbe Biology
    Humans Are Selectively Exposed to Pneumocystis jirovecii

    Environmental exposure has a significant impact on human health. While some airborne fungi can cause life-threatening infections, the impact of environment on fungal spore dispersal and transmission is poorly understood. The democratization of shotgun metagenomics allows us to explore important questions about fungal propagation. We focus on Pneumocystis, a genus of host-specific fungi that infect mammals via airborne particles...

    Ousmane H. Cissé, Liang Ma, Chao Jiang, Michael Snyder, Joseph A. Kovacs

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