Applied and Environmental Science
Research Article | Applied and Environmental ScienceSituations Leading to Reduced Effectiveness of Current Hand Hygiene against Infectious Mucus from Influenza Virus-Infected PatientsAntiseptic hand rubbing (AHR) and antiseptic hand washing (AHW) are important to prevent the spread of influenza A virus (IAV). This study elucidated the situations/mechanisms underlying the reduced efficacy of AHR against infectious mucus derived from IAV-infected individuals and indicated the weaknesses of the current hand hygiene regimens. Due to the low rate of diffusion/convection because of the physical properties of mucus as a...
Research Article | Applied and Environmental ScienceQuantitatively Partitioning Microbial Genomic Traits among Taxonomic Ranks across the Microbial Tree of LifeRecently, there has been great progress in defining a complete taxonomy of bacteria and archaea, which has been enabled by improvements in DNA sequencing technology and new bioinformatic techniques. A new, algorithmically defined microbial tree of life describes those linkages, relying solely on genetic data, which raises the issue of how microbial traits relate to taxonomy. Here, we adopted cluster of orthologous group functional...
Research Article | Applied and Environmental ScienceWhole-Genome Sequencing-Based Characterization of 100 Listeria monocytogenes Isolates Collected from Food Processing Environments over a Four-Year PeriodThis study extends current understanding of the genetic diversity among L. monocytogenes from various food products and food processing environments. Application of WGS-based strategies facilitated tracking of this pathogen of importance to human health along the production chain while providing insights into the pathogenic potential for some of the...
Research Article | Applied and Environmental ScienceDynamics of Bacterial Community and Fermentation Quality during Ensiling of Wilted and Unwilted Moringa oleifera Leaf Silage with or without Lactic Acid Bacterial InoculantsMoringa oleifera leaf is a high-quality feed source for livestock and is increasingly used all over the world. Ensiling might be an effective method for preservation of the leaves. In the practice of silage making, lactic acid bacterial inoculants and wilting are commonly used to improve nutrition preservation. Monitoring the changes in a bacterial community during fermentation gives an insight into understanding and improving...
Research Article | Applied and Environmental ScienceComponent Microenvironments and System Biogeography Structure Microorganism Distributions in Recirculating Aquaculture and Aquaponic SystemsRecirculating aquaculture systems (RAS) are agroecosystems for intensive on-land cultivation of products of fisheries. Practitioners that incorporate edible plant production into RAS refer to these facilities as aquaponic systems (AP). RAS have the potential to offset declining production levels of wild global fisheries while reducing waste and product distance to market, but system optimization is needed to reduce costs. Both RAS and...
Commentary | Applied and Environmental SciencemSphere of Influence: Engineering MicrobesPatrick J. McNamara works in the field of environmental engineering. In this mSphere of Influence article, he reflects on how the papers “Bacterial community structure in the drinking water microbiome is governed by filtration processes” (A. J. Pinto, C. Xi, and L.
Research Article | Applied and Environmental ScienceGenomic Analysis of Emerging Florfenicol-Resistant Campylobacter coli Isolated from the Cecal Contents of Cattle in the United StatesCampylobacter is a leading cause of foodborne diarrheal illness worldwide, with more than one million cases each year in the United States alone. The global emergence of antimicrobial resistance in this pathogen has become a growing public health concern. Florfenicol-resistant (FFNr) Campylobacter has been very rare in the United States. In this study, we employed whole-genome sequencing to characterize 16...
Research Article | Applied and Environmental ScienceFunctional Metagenomics Reveals a New Catalytic Domain, the Metallo-β-Lactamase Superfamily Domain, Associated with Phytase ActivityPhytic acid is a phosphorus storage molecule in many plant tissues, a source of phosphorus alternative to phosphate rocks, but it can also be a problematic antinutrient. In comparison to other phosphorus sources, phytic acid exhibits reduced bioavailability. Additionally, it influences functions of secondary messengers and acts as antioxidant in tumor growth prevention. The enzymatic capability to process phytate has been reported for a...
Research Article | Applied and Environmental ScienceMethylotetracoccus oryzae Strain C50C1 Is a Novel Type Ib Gammaproteobacterial Methanotroph Adapted to Freshwater EnvironmentsMost of the methane produced on our planet gets naturally oxidized by a group of methanotrophic microorganisms before it reaches the atmosphere. These microorganisms are able to oxidize methane, both aerobically and anaerobically, and use it as their sole energy source. Although methanotrophs have been studied for more than a century, there are still many unknown and uncultivated groups prevalent in various ecosystems. This study...
Research Article | Applied and Environmental ScienceAdventitious Virus Detection in Cells by High-Throughput Sequencing of Newly Synthesized RNAs: Unambiguous Differentiation of Cell Infection from Carryover of Viral Nucleic AcidsThe use of high-throughput sequencing (HTS) to identify viral contamination of biological products is extremely sensitive and provides a broad range of detection. Nevertheless, viral sequences identified can also be inert. Examples include contamination resulting from reagents or the presence of inactivated viruses in animal-derived components of the cell culture medium. We therefore developed a method that relies on the sequencing of...