Recent Publications by IM Students and Faculty - March 2021
Below are recent publications by IM students, faculty, and affiliates. Would you like your research showcased? Send your paper to email@example.com in time for the next edition!
Bold Indicates ISU faculty and affiliates
^Indicates publications by IM students
1. Yim-im, W., Huang, H., Park, J., Wang, C., Calzada, G., Gauger, P., Harmon, K., Main, R., Zhang, J. (2021). Comparison of ZMAC and MARC-145 Cell Lines for Improving Porcine Reproductive and Respiratory Syndrome Virus Isolation from Clinical Samples. Journal of Clinical Microbiology 59(3), e01757-01720. doi: 10.1128/jcm.01757-20.
Abstract: The MARC-145 cell line is commonly used to isolate porcine reproductive and respiratory syndrome virus (PRRSV) for diagnostics, research, and vaccine production, but it yields frustratingly low success rates of virus isolation (VI). The ZMAC cell line, derived from porcine alveolar macrophages, has become available, but its utilization for PRRSV VI from clinical samples has not been evaluated. This study compared PRRSV VI results in ZMAC and MARC-145 cells from 375 clinical samples (including 104 lung, 140 serum, 90 oral fluid, and 41 processing fluid samples). The PRRSV VI success rate was very low in oral fluids and processing fluids regardless of whether ZMAC cells or MARC-145 cells were used. Success rates of PRRSV VI from lung and serum samples were significantly higher in ZMAC than in MARC-145 cells. Lung and serum samples with threshold cycle (CT) values of <30 had better VI success. PRRSV-2 in genetic lineages 1 and 8 was isolated more successfully in ZMAC cells than in MARC-145 cells, whereas PRRSV-2 in genetic lineage 5 was isolated in the two cell lines with similar success rates. For samples with positive VI in both ZMAC and MARC-145 cells, 14 of 23 PRRSV-2 isolates had similar titers in the two cell lines. A total of 51 of 95 (53.7%) ZMAC-obtained PRRSV-2 or PRRSV-1 isolates grew in MARC-145 cells, and all 46 (100%) MARC-145-obtained isolates grew in ZMAC cells. In summary, ZMAC cells allow better isolation of a wide range of PRRSV field strains; however, not all of the ZMAC-obtained PRRSV isolates grow in MARC-145 cells. This report provides important guidelines to improve isolation of PRRSV from clinical samples for further characterization and/or for producing autogenous vaccines.
News: Read about the project here https://www.news.iastate.edu/news/2021/03/02/newprrscellline
2. ^Anderson, C.J., ^Koester, L.R., and Schmitz-Esser, S. (2021). Rumen Epithelial Communities Share a Core Bacterial Microbiota: A Meta-Analysis of 16S rRNA Gene Illumina MiSeq Sequencing Datasets. Frontiers in Microbiology 12(539). doi: 10.3389/fmicb.2021.625400.
Abstract: In this meta-analysis, 17 rumen epithelial 16S rRNA gene Illumina MiSeq amplicon sequencing data sets were analyzed to identify a core rumen epithelial microbiota and core rumen epithelial OTUs shared between the different studies included. Sequences were quality-filtered and screened for chimeric sequences before performing closed-reference 97% OTU clustering, and de novo 97% OTU clustering. Closed-reference OTU clustering identified the core rumen epithelial OTUs, defined as any OTU present in ≥ 80% of the samples, while the de novo data was randomly subsampled to 10,000 reads per sample to generate phylum- and genus-level distributions and beta diversity metrics. 57 core rumen epithelial OTUs were identified including metabolically important taxa such as Ruminococcus, Butyrivibrio, and other Lachnospiraceae, as well as sulfate-reducing bacteria Desulfobulbus and Desulfovibrio. Two Betaproteobacteria OTUs (Neisseriaceae and Burkholderiaceae) were core rumen epithelial OTUs, in contrast to rumen content where previous literature indicates they are rarely found. Two core OTUs were identified as the methanogenic archaea Methanobrevibacter and Methanomethylophilaceae. These core OTUs are consistently present across the many variables between studies which include different host species, geographic region, diet, age, farm management practice, time of year, hypervariable region sequenced, and more. When considering only cattle samples, the number of core rumen epithelial OTUs expands to 147, highlighting the increased similarity within host species despite geographical location and other variables. De novo OTU clustering revealed highly similar rumen epithelial communities, predominated by Firmicutes, Bacteroidetes, and Proteobacteria at the phylum level which comprised 79.7% of subsampled sequences. The 15 most abundant genera represented an average of 54.5% of sequences in each individual study. These abundant taxa broadly overlap with the core rumen epithelial OTUs, with the exception of Prevotellaceae which were abundant, but not identified within the core OTUs. Our results describe the core and abundant bacteria found in the rumen epithelial environment and will serve as a basis to better understand the composition and function of rumen epithelial communities.
3. Schmitz-Esser, S., ^Anast, J.M., and ^Cortes, B.W. (2021). A Large-Scale Sequencing-Based Survey of Plasmids in Listeria monocytogenes Reveals Global Dissemination of Plasmids. Frontiers in Microbiology 12(510). doi: 10.3389/fmicb.2021.653155.
Abstract: The food-borne pathogen Listeria monocytogenes is known for its capacity to cope with multiple stress conditions occurring in food and food production environments (FPEs). Plasmids can provide benefits to their host strains, and it is known that various Listeria strains contain plasmids. However, the current understanding of plasmid frequency and function in L. monocytogenes strains remains rather limited. To determine the presence of plasmids among L. monocytogenes strains and their potential contribution to stress survival, a comprehensive dataset was established based on 1,921 published genomes from strains representing 14 L. monocytogenes sequence types (STs). Our results show that an average of 54% of all L. monocytogenes strains in the dataset contained a putative plasmid. The presence of plasmids was highly variable between different STs. While some STs, such as ST1, ST2, and ST4, contained few plasmid-bearing strains (<15% of the strains per ST), other STs, such as ST121, ST5, ST8, ST3, and ST204, possessed a higher proportion of plasmid-bearing strains with plasmids found in >71% of the strains within each ST. Overall, the sizes of plasmids analyzed in this study ranged from 4 to 170 kbp with a median plasmid size of 61 kbp. We also identified two novel groups of putative Listeria plasmids based on the amino acid sequences of the plasmid replication protein, RepA. We show that highly conserved plasmids are shared among Listeria strains which have been isolated from around the world over the last few decades. To investigate the potential roles of plasmids, nine genes related to stress-response were selected for an assessment of their abundance and conservation among L. monocytogenes plasmids. The results demonstrated that these plasmid genes exhibited high sequence conservation but that their presence in plasmids was highly variable. Additionally, we identified a novel transposon, Tn7075, predicted to be involved in mercury-resistance. Here, we provide the largest plasmid survey of L. monocytogenes to date with a comprehensive examination of the distribution of plasmids among L. monocytogenes strains. Our results significantly increase our knowledge about the distribution, composition, and conservation of L. monocytogenes plasmids and suggest that plasmids are likely important for the survival of L. monocytogenes in food and FPEs.