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metabolomics

  • Open Access
    Presence of Bromotyrosine Alkaloids in Marine Sponges Is Independent of Metabolomic and Microbiome Architectures
    Research Article
    Presence of Bromotyrosine Alkaloids in Marine Sponges Is Independent of Metabolomic and Microbiome Architectures

    Our work demonstrates that phylogenetically and geographically distant sponges with very different microbiomes can harbor natural product chemical classes that are united in their core chemical structures and biosynthetic logic. Furthermore, we show that independent of geographical dispersion, natural product chemistry, and microbial abundance, overall sponge metabolomes tightly correlate with their microbiomes.

    Ipsita Mohanty, Subhasish Tapadar, Samuel G. Moore, Jason S. Biggs, Christopher J. Freeman, David A. Gaul, Neha Garg, Vinayak Agarwal
  • Open Access
    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
  • Open Access
    Endogenous Metabolites Released by Sanitized Sprouting Alfalfa Seed Inhibit the Growth of <span class="named-content genus-species" id="named-content-1">Salmonella enterica</span>
    Research Article | Applied and Environmental Science
    Endogenous Metabolites Released by Sanitized Sprouting Alfalfa Seed Inhibit the Growth of Salmonella enterica

    Warm, humid, and nutrient-rich conditions that are used to produce sprouts encourage Salmonella enterica to proliferate. However, many disparate sanitation methods exist, and there is currently no single treatment that can guarantee pathogen-free seeds.

    Ga-Hee Ban, Yue Dai, Tao Huan, Alfred Ke, Pascal Delaquis, Siyun Wang
  • Open Access
    Sulfur Metabolites Play Key System-Level Roles in Modulating Denitrification
    Research Article | Molecular Biology and Physiology
    Sulfur Metabolites Play Key System-Level Roles in Modulating Denitrification

    Nitrate-reducing bacteria (NRB) and sulfate-reducing bacteria (SRB) colonize diverse anoxic environments, including soil subsurface, groundwater, and wastewater. NRB and SRB compete for resources, and their interplay has major implications on the global cycling of nitrogen and sulfur species, with undesirable outcomes in some contexts.

    Anne E. Otwell, Alex V. Carr, Erica L. W. Majumder, Maryann K. Ruiz, Regina L. Wilpiszeski, Linh T. Hoang, Bill Webb, Serdar Turkarslan, Sean M. Gibbons, Dwayne A. Elias, David A. Stahl, Gary Siuzdak, Nitin S. Baliga
  • Open Access
    Exometabolite Dynamics over Stationary Phase Reveal Strain-Specific Responses
    Editor's Pick Research Article | Applied and Environmental Science
    Exometabolite Dynamics over Stationary Phase Reveal Strain-Specific Responses

    Nongrowth states are common for bacteria that live in environments that are densely populated and predominantly nutrient exhausted, and yet these states remain largely uncharacterized in cellular metabolism and metabolite output. Here, we investigated and compared stationary-phase exometabolites and RNA transcripts for each of three environmental bacterial strains.

    John L. Chodkowski, Ashley Shade
  • Open Access
    A Subset of Roux-en-Y Gastric Bypass Bacterial Consortium Colonizes the Gut of Nonsurgical Rats without Inducing Host-Microbe Metabolic Changes
    Research Article | Host-Microbe Biology
    A Subset of Roux-en-Y Gastric Bypass Bacterial Consortium Colonizes the Gut of Nonsurgical Rats without Inducing Host-Microbe Metabolic Changes

    Roux-en-Y gastric bypass (RYGB) surgery results in a long-term gut bacterial shift toward Gammaproteobacteria in both patients and rodents. The contribution of this compositional shift, or the RYGB bacterial consortium, to the metabolic benefit of the surgery remains debatable.

    Zhigang Liu, Isabelle Coales, Nicholas Penney, Julie A. K. McDonald, Jutarop Phetcharaburanin, Florian Seyfried, Jia V. Li
  • Open Access
    Chemical Profiling Provides Insights into the Metabolic Machinery of Hydrocarbon-Degrading Deep-Sea Microbes
    Research Article | Ecological and Evolutionary Science
    Chemical Profiling Provides Insights into the Metabolic Machinery of Hydrocarbon-Degrading Deep-Sea Microbes

    High-throughput technologies and emerging informatics tools have significantly advanced knowledge of hydrocarbon metabolism by marine microbes. However, research into microbes inhabiting deep-sea sediments (>1,000 m) is limited compared to those found in shallow waters. In this study, a nontargeted and nonclassical approach was used to examine the diversity of bacterial taxa and the metabolic profiles of hydrocarbon-degrading deep-...

    Aldo Moreno-Ulloa, Victoria Sicairos Diaz, Javier A. Tejeda-Mora, Marla I. Macias Contreras, Fernando Díaz Castillo, Abraham Guerrero, Ricardo Gonzalez Sanchez, Omar Mendoza-Porras, Rafael Vazquez Duhalt, Alexei Licea-Navarro
  • Open Access
    Dietary Intervention Reverses Fatty Liver and Altered Gut Microbiota during Early-Life Undernutrition
    Research Article | Host-Microbe Biology
    Dietary Intervention Reverses Fatty Liver and Altered Gut Microbiota during Early-Life Undernutrition

    Nonalcoholic fatty liver disease (NAFLD) remains a global epidemic, but it is often studied in the context of obesity and aging. Nutritional deficits, however, also trigger hepatic steatosis, influencing health trajectories in undernourished pediatric populations. Here, we report that exposure to specific gut microbes impacts fatty liver pathology in mice fed a protein/fat-deficient diet. We utilize a multiomics approach to (i)...

    K. C. Bauer, K. E. Huus, E. M. Brown, T. Bozorgmehr, C. Petersen, M. S. Cirstea, S. E. Woodward, J. McCoy, J. Hun, R. Pamplona, V. Ayala, B. B. Finlay
  • Open Access
    Microbe-Metabolite Associations Linked to the Rebounding Murine Gut Microbiome Postcolonization with Vancomycin-Resistant <span class="named-content genus-species" id="named-content-1">Enterococcus faecium</span>
    Research Article | Host-Microbe Biology
    Microbe-Metabolite Associations Linked to the Rebounding Murine Gut Microbiome Postcolonization with Vancomycin-Resistant Enterococcus faecium

    This study demonstrates the importance and power of linking bacterial composition profiling with metabolomics to find the interactions between commensal gut bacteria and a specific pathogen. Knowledge from this research will inform gut microbiome engineering strategies, with the aim of translating observations from animal models to human-relevant therapeutic applications.

    Andre Mu, Glen P. Carter, Lucy Li, Nicole S. Isles, Alison F. Vrbanac, James T. Morton, Alan K. Jarmusch, David P. De Souza, Vinod K. Narayana, Komal Kanojia, Brunda Nijagal, Malcolm J. McConville, Rob Knight, Benjamin P. Howden, Timothy P. Stinear
  • Open Access
    Metabolomics and Machine Learning Approaches Combined in Pursuit for More Accurate Paracoccidioidomycosis Diagnoses
    Research Article | Novel Systems Biology Techniques
    Metabolomics and Machine Learning Approaches Combined in Pursuit for More Accurate Paracoccidioidomycosis Diagnoses

    Paracoccidioidomycosis (PCM) is a fungal infection typically found in Latin American countries, especially in Brazil. The identification of this disease is based on techniques that may fail sometimes. Intending to improve PCM detection in patient samples, this study used the combination of two of the newest technologies, artificial intelligence and metabolomics. This combination allowed PCM detection, independently of disease form,...

    Estela de Oliveira Lima, Luiz Claudio Navarro, Karen Noda Morishita, Camila Mika Kamikawa, Rafael Gustavo Martins Rodrigues, Mohamed Ziad Dabaja, Diogo Noin de Oliveira, Jeany Delafiori, Flávia Luísa Dias-Audibert, Marta da Silva Ribeiro, Adriana Pardini Vicentini, Anderson Rocha, Rodrigo Ramos Catharino

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