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Data From: Habitat type and host grazing regimen influence the soil microbial diversity and communities within potential biting midge larval habitats

    Culicoides biting midges are important vectors of diverse microbes such as viruses, protozoa, and nematodes that cause diseases in wild and domestic animals. To investigate the role of microbial communities in midge larval habitat utilization in the wild, we characterized microbial communities (bacterial, protistan, fungal and metazoan) in soils from disturbed (bison and cattle grazed) and undisturbed (non-grazed) pond and spring potential midge larval habitats. We evaluated the influence of habitat and grazing disturbance and their interaction on microbial communities, diversity, presence of midges, and soil properties.

    Data from: Attraction, mobility, and preference by Lasioderma serricorne (F.) (Coleoptera: Ptinidae) to microbially-mediated volatile emissions by two species of fungi in stored grain

      Our goals were to 1) isolate, and culture two fungal morphotypes, 2) characterize the volatile emissions from grain inoculated by each fungal morphotype (Aspergillus flavus or Fusarium spp.) compared to uninoculated and sanitized grain, and 3) understand how MVOCs from each morphotype affects mobility, attraction, and preference by L. serricorne.

      Irrigation Residue Removal Study for Greenhouse gas Reduction through Agricultural Carbon Enhancement network and Resilient Economic Agricultural Practices in Lincoln, Nebraska

        USDA-ARS REAP Study (Ithaca, NE) - NEMEIRR Sustainable intensification of high-yielding production systems may help meet increasing demands for food, fuel, and fiber worldwide. Specifically, corn stover is being removed by producers for livestock purposes, and stover is also targeted as a primary 2nd generation biofuel feedstock. The NEMEIRR experimental objectives are to quantify how stover removal (no removal, moderate removal, high removal) and tillage management (no-till, disk) affect crop yields, soil organic carbon, soil greenhouse gas emissions, and other soil responses (microbial community structure, function; soil health). This experiment is conducted in a fully irrigated continuous corn system in the western Corn Belt, and soil and plant measurements have been taken since study establishment in 2001.

        Data from: Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation

          We describe a method that adds long-read sequencing to a mix of technologies used to assemble a highly complex cattle rumen microbial community, and provide a comparison to short read-based methods. Long-read alignments and Hi-C linkage between contigs support the identification of 188 novel virus-host associations and the determination of phage life cycle states in the rumen microbial community. The long-read assembly also identifies 94 antimicrobial resistance genes, compared to only seven alleles in the short-read assembly.

          Data from: Chondroitin sulfate disaccharides modified the structure and function of the murine gut microbiome under healthy and stressed conditions

            Chondroitin sulfate (CS) has been widely used for medical and nutraceutical purposes due to its roles in maintaining tissue structural integrity. We investigated if CS disaccharides may act as a bioactive compound and modulate gut microbial composition in mice. Our data show that CS disaccharides supplementation for 16 days significantly reduced blood LPS in the mice experiencing exhaustive exercise stress. CS disaccharides partially restored total fecal short-chain fatty acids from the level significantly repressed in mice under the stress. Our findings demonstrated that CS was likely butyrogenic and resulted in a significant increase in fecal butyrate concentration. CS disaccharides had a profound impact on gut microbial composition, affecting the abundance of 13.6% and 7.3% Operational Taxonomic Units in fecal microbial communities in healthy and stressed mice, respectively. CS disaccharides reduced the prevalence of inflammatory Proteobacteria. Together, our findings demonstrated that CS may ameliorate stress-induced intestinal inflammation. Furthermore, CS significantly increased intestinal *Bacteroides acidifaciens* population, indirectly exerting its immunomodulatory effect on the intestine. CS disaccharides had a significant impact on a broad range of biological pathways under stressed condition, such as ABC transporters, two-component systems, and carbohydrate metabolism. Our results will facilitate the development of CS as a bioactive nutraceutical.

            myPhyloDB

              myPhyloDB is an open-source software package aimed at developing a user-friendly web-interface for accessing and analyzing all of your laboratory's microbial ecology data (currently supported project types: soil, air, water, microbial, and human-associated). The storage and handling capabilities of myPhyloDB archives users' raw sequencing files, and allows for easy selection of any combination of projects/samples from all of your projects using the built-in SQL database. The data processing capabilities of myPhyloDB are also flexible enough to allow the upload, storage, and analysis of pre-processed data or raw (454 or Illumina) data files using the built-in versions of Mothur and R.