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  • Production and Excretion of Polyamines To Tolerate High Ammonia, a Case Study on Soil Ammonia-Oxidizing Archaeon "Candidatus Nitrosocosmicus agrestis"
    Production and Excretion of Polyamines To Tolerate High Ammonia, a Case Study on Soil Ammonia-Oxidizing Archaeon "Candidatus Nitrosocosmicus agrestis"
  • A Novel Group of Promiscuous Podophages Infecting Diverse Gammaproteobacteria from River Communities Exhibits Dynamic Intergenus Host Adaptation
    A Novel Group of Promiscuous Podophages Infecting Diverse Gammaproteobacteria from River Communities Exhibits Dynamic Intergenus Host Adaptation
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Latest Articles

  • Modeling Growth Kinetics, Interspecies Cell Fusion, and Metabolism of a <span class="named-content genus-species" id="named-content-1">Clostridium acetobutylicum</span>/<span class="named-content genus-species" id="named-content-2">Clostridium ljungdahlii</span> Syntrophic Coculture
    Research Article
    Modeling Growth Kinetics, Interspecies Cell Fusion, and Metabolism of a Clostridium acetobutylicum/Clostridium ljungdahlii Syntrophic Coculture

    Widespread cell fusion and protein exchange between microbial organisms as observed in synthetic C. acetobutylicum/C. ljungdahlii culture is a novel observation that has not been explored in silico. The mechanisms responsible for the observed cell fusion events in this culture are still unknown.

    Charles Foster, Kamil Charubin, Eleftherios T. Papoutsakis, Costas D. Maranas
    23 Feb 2021
  • Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities
    Perspective | Applied and Environmental Science
    Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities

    Microbiome samples are inherently defined by the environment in which they are found. Therefore, data that provide context and enable interpretation of measurements produced from biological samples, often referred to as metadata, are critical.

    Pajau Vangay, Josephine Burgin, Anjanette Johnston, Kristen L. Beck, Daniel C. Berrios, Kai Blumberg, Shane Canon, Patrick Chain, John-Marc Chandonia, Danielle Christianson, Sylvain V. Costes, Joan Damerow, William D. Duncan, Jose Pablo Dundore-Arias, Kjiersten Fagnan, Jonathan M. Galazka, Sean M. Gibbons, David Hays, Judson Hervey, Bin Hu, Bonnie L. Hurwitz, Pankaj Jaiswal, Marcin P. Joachimiak, Linda Kinkel, Joshua Ladau, Stanton L. Martin, Lee Ann McCue, Kayd Miller, Nigel Mouncey, Chris Mungall, Evangelos Pafilis, T. B. K. Reddy, Lorna Richardson, Simon Roux, Justin P. Shaffer, Jagadish Chandrabose Sundaramurthi, Luke R. Thompson, Ruth E. Timme, Jie Zheng, Elisha M. Wood-Charlson, Emiley A. Eloe-Fadrosh
    23 Feb 2021
  • Data Analysis Strategies for Microbiome Studies in Human Populations—a Systematic Review of Current Practice
    Research Article | Clinical Science and Epidemiology
    Data Analysis Strategies for Microbiome Studies in Human Populations—a Systematic Review of Current Practice

    The human microbiome has emerged as an important factor in the development of health and disease. Growing interest in this topic has led to an increasing number of studies investigating the human microbiome using high-throughput sequencing methods.

    Sven Kleine Bardenhorst, Tom Berger, Frank Klawonn, Marius Vital, André Karch, Nicole Rübsamen
    23 Feb 2021
  • Identifying Potentially Beneficial Genetic Mutations Associated with Monophyletic Selective Sweep and a Proof-of-Concept Study with Viral Genetic Data
    Methods and Protocols | Ecological and Evolutionary Science
    Identifying Potentially Beneficial Genetic Mutations Associated with Monophyletic Selective Sweep and a Proof-of-Concept Study with Viral Genetic Data

    In biology, research on evolution is important to understand the significance of genetic mutation. When there is a significantly beneficial mutation, a population of species with the mutation prospers and predominates, in a process called “selective sweep.” However, there are few methods that can find such a mutation causing selective sweep from genetic data.

    Yuki Furuse
    23 Feb 2021
  • Characterization of Bicistronic Transcription in Budding Yeast
    Research Article | Ecological and Evolutionary Science
    Characterization of Bicistronic Transcription in Budding Yeast

    Operons, where a single mRNA transcript encodes multiple adjacent proteins, are a widespread feature of bacteria and archaea. In contrast, the genes of eukaryotes are generally considered monocistronic.

    Baojun Wu, Murray P. Cox
    23 Feb 2021
  • Impaired Intestinal <span class="named-content genus-species" id="named-content-1">Akkermansia muciniphila</span> and Aryl Hydrocarbon Receptor Ligands Contribute to Nonalcoholic Fatty Liver Disease in Mice
    Editor's Pick Research Article | Host-Microbe Biology
    Impaired Intestinal Akkermansia muciniphila and Aryl Hydrocarbon Receptor Ligands Contribute to Nonalcoholic Fatty Liver Disease in Mice

    Our findings indicate that the gut-liver signaling axis contributes to saccharin/sucralose consumption-induced NAFLD. Supplementation with metformin or fructo-oligosaccharide is a potential therapeutic strategy for NAFLD treatment. In addition, we also developed a new nutritional strategy by using a natural sweetener (neohesperidin dihydrochalcone [NHDC]) as a substitute for NAS and free sugars.

    Zunji Shi, Hehua Lei, Gui Chen, Peihong Yuan, Zheng Cao, Hooi-Leng Ser, Xuehang Zhu, Fang Wu, Caixiang Liu, Manyuan Dong, Yuchen Song, Yangyang Guo, Chuan Chen, Kexin Hu, Yifan Zhu, Xin-an Zeng, Jinlin Zhou, Yujing Lu, Andrew D. Patterson, Limin Zhang
    23 Feb 2021
  • Genomic and Chemical Diversity of <span class="named-content genus-species" id="named-content-1">Bacillus subtilis</span> Secondary Metabolites against Plant Pathogenic Fungi
    Research Article | Ecological and Evolutionary Science
    Genomic and Chemical Diversity of Bacillus subtilis Secondary Metabolites against Plant Pathogenic Fungi

    Secondary or specialized metabolites with antimicrobial activities define the biocontrol properties of microorganisms. Members of the Bacillus genus produce a plethora of secondary metabolites, of which nonribosomally produced lipopeptides in particular display strong antifungal activity.

    Heiko T. Kiesewalter, Carlos N. Lozano-Andrade, Mario Wibowo, Mikael L. Strube, Gergely Maróti, Dan Snyder, Tue Sparholt Jørgensen, Thomas O. Larsen, Vaughn S. Cooper, Tilmann Weber, Ákos T. Kovács
    23 Feb 2021
  • Comparative Genomics and Integrated Network Approach Unveiled Undirected Phylogeny Patterns, Co-mutational Hot Spots, Functional Cross Talk, and Regulatory Interactions in SARS-CoV-2
    Research Article
    Comparative Genomics and Integrated Network Approach Unveiled Undirected Phylogeny Patterns, Co-mutational Hot Spots, Functional Cross Talk, and Regulatory Interactions in SARS-CoV-2

    In the current study, we presented a global view of mutational pattern observed in SARS-CoV-2 virus transmission. This provided a who-infect-whom geographical model since the early pandemic.

    Vipin Gupta, Shazia Haider, Mansi Verma, Nirjara Singhvi, Kalaisaran Ponnusamy, Md. Zubbair Malik, Helianthous Verma, Roshan Kumar, Utkarsh Sood, Princy Hira, Shiva Satija, Yogendra Singh, Rup Lal
    23 Feb 2021
  • The <em>Azospirillum brasilense</em> Core Chemotaxis Proteins CheA1 and CheA4 Link Chemotaxis Signaling with Nitrogen Metabolism
    Research Article | Molecular Biology and Physiology
    The Azospirillum brasilense Core Chemotaxis Proteins CheA1 and CheA4 Link Chemotaxis Signaling with Nitrogen Metabolism

    Bacterial chemotaxis is widespread in bacteria, increasing competitiveness in diverse environments and mediating associations with eukaryotic hosts ranging from commensal to beneficial and pathogenic. In most bacteria, chemotaxis signaling is tightly linked to energy metabolism, with this coupling occurring through the sensory input of several energy-sensing chemoreceptors.

    Elena E. Ganusova, Lam T. Vo, Paul E. Abraham, Lindsey O’Neal Yoder, Robert L. Hettich, Gladys Alexandre
    16 Feb 2021
  • Machine Learning Reveals Time-Varying Microbial Predictors with Complex Effects on Glucose Regulation
    Research Article | Host-Microbe Biology
    Machine Learning Reveals Time-Varying Microbial Predictors with Complex Effects on Glucose Regulation

    Recent studies have shown a clear link between gut microbiota and type 2 diabetes. However, current results are based on cross-sectional studies that aim to determine the microbial dysbiosis when the disease is already prevalent.

    Oliver Aasmets, Kreete Lüll, Jennifer M. Lang, Calvin Pan, Johanna Kuusisto, Krista Fischer, Markku Laakso, Aldons J. Lusis, Elin Org
    16 Feb 2021
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