Applied and Environmental Science
Research Article | Applied and Environmental ScienceNutraceuticals Induced Changes in the Broiler Gastrointestinal Tract MicrobiotaIn this trial, nutraceuticals were manufactured from waste products of food industry processing of Hungarian red sweet pepper and sour cherry and incorporated into the diet of poultry to investigate their effects on broilers’ growth and the broiler gastrointestinal tract microbiota. To avoid the generation of food waste products, we believe that this approach can be developed into a sustainable, green approach that can be implemented in...
Perspective | Applied and Environmental ScienceMicrobiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On ActivitiesMicrobiome 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.
Research Article | Applied and Environmental ScienceExperimentally Validated Reconstruction and Analysis of a Genome-Scale Metabolic Model of an Anaerobic Neocallimastigomycota FungusRecent genomic analyses have revealed that anaerobic gut fungi possess both the largest number and highest diversity of lignocellulolytic enzymes of all sequenced fungi, explaining their ability to decompose lignocellulosic substrates, e.g., agricultural waste, into fermentable sugars. Despite their potential, the development of engineering methods for these organisms has been slow due to their complex life cycle, understudied...
Research Article | Applied and Environmental ScienceEndogenous Metabolites Released by Sanitized Sprouting Alfalfa Seed Inhibit the Growth of Salmonella entericaWarm, 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.
Research Article | Applied and Environmental ScienceMicrobiota Assessments for the Identification and Confirmation of Slit Defect-Causing Bacteria in Milk and Cheddar CheeseFood production involves numerous control points for microorganisms to ensure quality and safety. These control points (e.g., pasteurization) are difficult to develop for fermented foods wherein some microbial contaminants are also expected to provide positive contributions to the final product and spoilage microbes may constitute only a small proportion of all microorganisms present.
Research Article | Applied and Environmental ScienceAssessing Biodegradability of Chemical Compounds from Microbial Community Growth Using Flow CytometryThe manifold effects of potentially toxic compounds on microbial communities are often difficult to discern. Some compounds may be transformed or completely degraded by few or multiple strains in the community, whereas others may present inhibitory effects.
Research Article | Applied and Environmental ScienceDeciphering a Marine Bone-Degrading Microbiome Reveals a Complex Community EffortBones 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.
Minireview | Applied and Environmental ScienceComputational Analysis of Microbial Flow Cytometry DataFlow cytometry is an important technology for the study of microbial communities. It grants the ability to rapidly generate phenotypic single-cell data that are both quantitative, multivariate and of high temporal resolution.
Research Article | Applied and Environmental SciencePhylogenetic Distribution of Plastic-Degrading MicroorganismsWe have collated the most complete database of microorganisms identified as being capable of degrading plastics to date. These data allow us to explore the phylogenetic distribution of these organisms and their enzymes, showing that traits for plastic degradation are predominantly not phylogenetically conserved.
Research Article | Applied and Environmental ScienceDistribution of Mixotrophy and Desiccation Survival Mechanisms across Microbial Genomes in an Arid Biological Soil Crust CommunityThis 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...