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metagenomics

  • Open Access
    High-Fiber, Whole-Food Dietary Intervention Alters the Human Gut Microbiome but Not Fecal Short-Chain Fatty Acids
    Research Article
    High-Fiber, Whole-Food Dietary Intervention Alters the Human Gut Microbiome but Not Fecal Short-Chain Fatty Acids

    A profound decrease in the consumption of dietary fiber in many parts of the world in the last century may be associated with the increasing prevalence of type II diabetes, colon cancer, and other health problems. A typical U.S. diet includes about ∼15 g of fiber per day, far less fiber than the daily recommended allowance.

    Andrew Oliver, Alexander B. Chase, Claudia Weihe, Stephanie B. Orchanian, Stefan F. Riedel, Clark L. Hendrickson, Mi Lay, Julia Massimelli Sewall, Jennifer B. H. Martiny, Katrine Whiteson
  • Open Access
    Uncultivated Viral Populations Dominate Estuarine Viromes on the Spatiotemporal Scale
    Research Article
    Uncultivated Viral Populations Dominate Estuarine Viromes on the Spatiotemporal Scale

    This is the first systematic study about spatial and temporal variation of virioplankton communities in estuaries by using deep metagenomics sequencing. It is among the highest-quality viromic data sets to date, showing remarkably consistent sequencing depth and quality across samples.

    Mengqi Sun, Yuanchao Zhan, David Marsan, David Páez-Espino, Lanlan Cai, Feng Chen
  • Open Access
    Complex Response of the Chlorarachniophyte <span class="named-content genus-species" id="named-content-1">Bigelowiella natans</span> to Iron Availability
    Research Article | Molecular Biology and Physiology
    Complex Response of the Chlorarachniophyte Bigelowiella natans to Iron Availability

    Despite low iron availability in the ocean, marine phytoplankton require considerable amounts of iron for their growth and proliferation. While there is a constantly growing knowledge of iron uptake and its role in the cellular processes of the most abundant marine photosynthetic groups, there are still largely overlooked branches of the eukaryotic tree of life, such as the chlorarachniophytes.

    Eva Kotabova, Ronald Malych, Juan José Pierella Karlusich, Elena Kazamia, Meri Eichner, Jan Mach, Emmanuel Lesuisse, Chris Bowler, Ondřej Prášil, Robert Sutak
  • Open Access
    Deciphering a Marine Bone-Degrading Microbiome Reveals a Complex Community Effort
    Research Article | Applied and Environmental Science
    Deciphering a Marine Bone-Degrading Microbiome Reveals a Complex Community Effort

    Bones are an underexploited, yet potentially profitable feedstock for biotechnological advances and value chains, due to the sheer amounts of residues produced by the modern meat and poultry processing industry. In this metagenomic study, we decipher the microbial pathways and enzymes that we postulate to be involved in bone degradation in the marine environment.

    Erik Borchert, Antonio García-Moyano, Sergio Sanchez-Carrillo, Thomas G. Dahlgren, Beate M. Slaby, Gro Elin Kjæreng Bjerga, Manuel Ferrer, Sören Franzenburg, Ute Hentschel
  • Open Access
    Evaluation of CRISPR Diversity in the Human Skin Microbiome for Personal Identification
    Research Article | Host-Microbe Biology
    Evaluation of CRISPR Diversity in the Human Skin Microbiome for Personal Identification

    Microbial community diversity analysis can be utilized to characterize the personal microbiome that varies between individuals. CRISPR sequences, which reflect virome structure, in the human skin environment may be highly personalized similar to the structures of individual viromes.

    Kochi Toyomane, Ryo Yokota, Ken Watanabe, Tomoko Akutsu, Ai Asahi, Satoshi Kubota
  • Open Access
    Distribution of Mixotrophy and Desiccation Survival Mechanisms across Microbial Genomes in an Arid Biological Soil Crust Community
    Research Article | Applied and Environmental Science
    Distribution of Mixotrophy and Desiccation Survival Mechanisms across Microbial Genomes in an Arid Biological Soil Crust Community

    This study represents a comprehensive community-wide genome-centered metagenome analysis of biological soil crust (BSC) communities in arid environments, providing insights into the distribution of genes encoding different energy generation mechanisms, as well as survival strategies, among populations in an arid soil ecosystem. It reveals the metabolic potential of several uncultured and previously unsequenced microbial genera, families...

    Dimitri V. Meier, Stefanie Imminger, Osnat Gillor, Dagmar Woebken
  • Open Access
    Traditional Human Populations and Nonhuman Primates Show Parallel Gut Microbiome Adaptations to Analogous Ecological Conditions
    Editor's Pick Research Article | Host-Microbe Biology
    Traditional Human Populations and Nonhuman Primates Show Parallel Gut Microbiome Adaptations to Analogous Ecological Conditions

    The results of this study highlight parallel gut microbiome traits in human and nonhuman primates, depending on subsistence strategy. Although these similarities have been reported before, the functional and ecological bases of this convergence are not fully understood.

    Ashok K. Sharma, Klara Petrzelkova, Barbora Pafco, Carolyn A. Jost Robinson, Terence Fuh, Brenda A. Wilson, Rebecca M. Stumpf, Manolito G. Torralba, Ran Blekhman, Bryan White, Karen E. Nelson, Steven R. Leigh, Andres Gomez
  • Open Access
    Geothermal Gases Shape the Microbial Community of the Volcanic Soil of Pantelleria, Italy
    Editor's Pick Research Article | Applied and Environmental Science
    Geothermal Gases Shape the Microbial Community of the Volcanic Soil of Pantelleria, Italy

    The Favara Grande nature reserve on the volcanic island of Pantelleria (Italy) is known for its geothermal gas emissions and high soil temperatures. These volcanic soil ecosystems represent “hot spots” of greenhouse gas emissions. The unique community might be shaped by the hostile conditions in the ecosystem, and it is involved in the cycling of elements such as carbon, hydrogen, sulfur, and nitrogen. Our metagenome study revealed that...

    Nunzia Picone, Carmen Hogendoorn, Geert Cremers, Lianna Poghosyan, Arjan Pol, Theo A. van Alen, Antonina L. Gagliano, Walter D’Alessandro, Paola Quatrini, Mike S. M. Jetten, Huub J. M. Op den Camp, Tom Berben
  • Open Access
    phyloFlash: Rapid Small-Subunit rRNA Profiling and Targeted Assembly from Metagenomes
    Methods and Protocols | Novel Systems Biology Techniques
    phyloFlash: Rapid Small-Subunit rRNA Profiling and Targeted Assembly from Metagenomes

    To track organisms across all domains of life, the SSU rRNA gene is the gold standard. Many environmental microbes are known only from high-throughput sequence data, but the SSU rRNA gene, the key to visualization by molecular probes and link to existing literature, is often missing from metagenome-assembled genomes (MAGs). The easy-to-use phyloFlash software suite tackles this gap with rapid, SSU rRNA-centered taxonomic classification...

    Harald R. Gruber-Vodicka, Brandon K. B. Seah, Elmar Pruesse
  • Open Access
    Deciphering the Microbial Taxonomy and Functionality of Two Diverse Mangrove Ecosystems and Their Potential Abilities To Produce Bioactive Compounds
    Research Article | Applied and Environmental Science
    Deciphering the Microbial Taxonomy and Functionality of Two Diverse Mangrove Ecosystems and Their Potential Abilities To Produce Bioactive Compounds

    This study comprehensively described the taxonomy and functionality of mangrove microbiomes, including their capacity for secondary metabolite biosynthesis and their ability to resist antibiotics. The microbial taxonomic and functional characteristics differed between geographical locations, corresponding to the environmental condition of two diverse mangrove regions. A large number of microbial biosynthetic gene clusters encoding novel...

    Shuilin Liao, Yayu Wang, Huan Liu, Guangyi Fan, Sunil Kumar Sahu, Tao Jin, Jianwei Chen, Pengfan Zhang, Lone Gram, Mikael Lenz Strube, Qiong Shi, Simon Ming Yuen Lee, Xin Liu

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