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and you may need to create a new Wiley Online Library account. Look for organically grown and sourced protein powders from the United States. 4A). Appl Microbiol Biotechnol. Length and direction of vectors indicate the strength and direction of the relationship. Similarly, the MRG‐like ORFs were first annotated using BLASTP against BacMet v.2.0 database at an E‐value ≤ 10−5. >> Table S10. /ModDate (D:20070813183756+02'00') endobj Bacterial Epidemiology and Antimicrobial Resistance Research Unit, United States Department of Agriculture, Athens, GA, 30605 USA, Department of Biological Sciences, Auburn University, Auburn, AL, 36849 USA, Institute of Bioinformatics, University of Georgia, Athens, GA, 30602 USA, Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA, 30329 USA, Savannah River Ecology Laboratory, University of Georgia, PO Drawer E, Aiken, SC, 29802 USA, Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, 30602 USA, Odum School of Ecology, University of Georgia, Athens, GA, 30602 USA. Neither the United States Government, nor any agency thereof, nor any of their employees makes any warranty, express or implied or assumes any legal liability or responsibility for the accuracy, completeness or usefulness of any information, apparatus, product or process disclosed or represents that its use would not infringe privately owned rights. The relative abundance and diversity of ARGs and MRGs was significantly higher at Tim’s Branch, a site with historic heavy metal and radionuclide contamination, compared to the reference site. Kos V, Budie B, Hudnik V, Lobnik F, Zupan M (1996) Determination of heavy metal concentrations in plants exposed to different degrees of pollution using ICP-AES. We further examined van clusters detected in our dataset using publicly available RefSeq proteins on https://www.ncbi.nlm.nih.gov/. Learn more. /Contents 56 0 R /Parent 6 0 R Several unclassified genera in the family Acidobacteriaceae possessed resistance genes for antimicrobial/biocide efflux (44%), Cu (12%), Zn (12%), As (9%), Fe (5%), Ni (5%), cobalt‐nickel (3%) and several others. According to the World Health Organization’s (WHO) 2014 report, the world is at the brink of a post‐antibiotic era, characterized by a significant reduction in the effectiveness of antibiotics and other antimicrobial agents, in addition to more frequent antibiotic treatment failures. /Type /Catalog Notably, our results were particularly interesting with respect to vancomycin, a ‘last resort’ broad‐spectrum antibiotic rarely used in hospital settings. The ARG‐like ORFs from the HMM results were extracted from the original protein sequences of ORFs predicted in the contigs using Seqkit v0.12.0 (https://bioinf.shenwei.me/seqkit/usage/). /Rotate 0 We used PICRUSt results to assign samples in three categories based on the expected resistance categories: ‘Low’, ‘Medium’ and ‘High’. PCC 6803. endobj /Resources 75 0 R Moreover, several studies have reported on the co‐selection of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) in a variety of contaminated environments. /MediaBox [0 0 595 842] Please check your email for instructions on resetting your password. /Contents 68 0 R /G12 27 0 R The relative abundance of ARG types was lowest at Ash Basin’s ranging from 0.34 to 0.43 ARG genes per 16S rRNA copy; whereas they were higher at Pond B where they ranged between 0.37 and 0.57 ARG genes per 16S rRNA copy (Table S7). Two KOs related to ARGs and MRGs , emrB (K07644) and cusS (K07644) respectively, were significantly enriched in soils from Ash Basins and Pond B compared to Upper Three Runs. These studies have also demonstrated how such genes can be enriched and disseminated in various animal models, sediment, bodies of water and even the human gut (Cesare et al., 2016; Fang et al., 2016; Henriques et al., 2016; Ju et al., 2016; Zhao et al., 2018).
Deblur uses error profiles to denoise Illumina data and is capable of differentiating amplicons by a single base pair. PICRUSt predicted metagenome contributions of soil samples. Bacmet Ids, genes, and antibiotic, biocide, or metal type. FREE Shipping on your first order shipped by Amazon. Table S13.
Alpha diversity indices for MRGs (BacMet). When examining ARG subtypes, Shannon indexes ranged from 4.33 and 4.50, and we observed a significantly higher diversity of antimicrobial/biocide efflux resistance genes at Tim’s Branch compared to the reference site (P < 0.05; Fig. The macrolide‐lincosoamide‐streptogramin resistance gene, macB, is part a drug efflux system in the ATP‐binding cassette (ABC) family of transporters. /BitsPerComponent 8 High‐quality reads for the 24 selected samples were de novo assembled using the default k‐mer size using Spades v.3.9.0 (Bankevich et al., 2012). endobj Relative position of soil samples in the biplot is based on log transformed Bray Curtis dissimilarities.
/Count 13 /Parent 6 0 R PROKKA v.1.14 was also used to functionally annotate the predicted ORFs, using the SARGfam HMM profile as input (Seemann, 2014). Reads that mapped to the assembly, were counted using the prokkagff2gtf and htseq‐count scripts (Anders et al., 2015). /Author <4779F5726569204CE1737A6CF3> Briefly, the fastq reads were quality trimmed to obtain clean reads, ARG reads and 16S rRNA genes were extracted from all the samples, then ARG reads were identified and annotated using a BLASTX approach by searching the combined ARG databases of CARD (The Comprehensive Antibiotic Resistance Database) and ResFinder (Zankari et al., 2012; McArthur et al., 2013). Trace elements were log‐transformed, when necessary, to meet assumptions of normality. Multidrug efflux pumps are typically chromosomally encoded and are conserved across the majority, if not all, strains of bacterial species (Blanco et al., 2016). /ProcSet [/PDF /Text /ImageB /ImageC /ImageI] In examining MRG types, we found that SRS soils contained a diverse collection of genes associated with copper, arsenic, iron, nickel, zinc, molybdenum resistance and multi‐metal resistance. /Filter /FlateDecode Bray–Curtis distances between samples (beta‐diversity) were computed and visualized using PRIMER 7.0 software with PERMANOVA + add‐on (Primer‐E, United Kingdom) as several distance‐based plots (Bray and Curtis, 1957). /A [8 0 R] These categories encompassed a percentage range of 0.05% to 0.15% corresponding to the proportion of genes detected relative to number of 16S rRNA sequences. Vectors indicate the weight and direction of those edaphic properties or heavy metals that were best predictors of soil bacterial composition as suggested by the results of the distance‐based linear model (distLM).
Alpha diversity indices for ARGs (SARGfam). /Parent 6 0 R << The Savannah River Site (SRS, 33°00′N and 81°41W) is an approximately 800 km2 former nuclear weapons production facility situated along the Savannah River in the upper coastal plain of South Carolina near Aiken, SC (Fig. All 80 samples (20 samples per site) were placed on ice until eventual storage at −20°C. Heat map of variations of AB‐MRG‐like contigs contained in the top 30 AB‐MRG types. This is particularly concerning given that unlike antibiotics, heavy metals do not degrade in the environment and can exert long‐standing and widespread co‐selection pressure (Baker‐Austin et al., 2006). Table S18. /Type /Page Instead, we observed that while soil communities were similarly structured, being predominated by Proteobacteria (27.24% ± 0.02%), Acidobacteria (22.00% ± 0.04%) and Actinobacteria (14.83% ± 0.02%), among others, there was a higher abundance and diversity of taxa in samples from the reference site (Upper Three Runs) compared with samples from Ash Basins, Tim’s Branch and Pond B. If your protein powder is whey, casein or otherwise cow-based, select a product that comes from grass-fed cows. /P [84 0 R]
The prevalence and dissemination of antimicrobial resistance is a serious global public health concern that cannot be understated. 16 0 obj endobj The software Prodigal v.2.60 was used to predict ORFs within contigs (Hyatt et al., 2010). << In this study, we collected soils from four locations with habitats consisting of mixed hardwood and pine forest; three contaminated sites, and a reference site located on the SRS (Fig. Please enable it to take advantage of the complete set of features! Cobalt was more influential in community structure in Tim’s Branch soils, while Zn and Pb were larger factors in Ash Basin soils.