Associations between Escherichia coli O157 shedding and the faecal microbiota of dairy cows
Open accessAbstract
AIMS: Dairy cattle shed pathogenic Escherichia coli O157 (O157) in faeces, playing a role in human exposure. We aimed to measure faecal microbial communities in early lactation dairy cattle, and model outcomes with O157 shedding metrics. METHODS AND RESULTS: Daily faecal samples were collected from 40 cattle on two Colorado dairies for five consecutive days, and characterized for O157. 16S rRNA gene sequencing was used to measure sample-level microbial communities. Alpha-diversity metrics were associated with O157 outcomes via regression modelling, adjusting for confounders. Differential abundance of taxa were identified between O157(+) and O157(-) samples and between shedding days of individuals, using matched Wilcoxon rank-sum tests, zero-inflated Gaussian (ZIG) regression and negative binomial regression. After removing an outlier, multi-day and intermittently shedding cows had lower average richness compared to those that never shed. ZIG modelling revealed Bacillus coagulans to be more abundant in O157(-) samples, while Moryella were more abundant in O157(+) samples. Negative binomial models and Wilcoxon tests revealed no differentially abundant taxa between O157(+) vs O157(-) samples, or between shedding days of individuals. CONCLUSIONS: Microbial diversity and some taxa may be influenced by or affect O157 shedding by dairy cattle. SIGNIFICANCE AND IMPACT OF THE STUDY: If future work corroborates these findings, dairy cow microbial community changes may be used to guide on-farm strategies that mitigate O157 dissemination, protecting the human food chain.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Differences in both the mucosa-associated microbiota of the rectoanal junction and fecal microbiota of cattle influence the shedding of the human pathogen Escherichia coli O157 in cattle feces.
“Recently, differences in both the mucosa-associated microbiota of the rectoanal junction and fecal microbiota of cattle have been shown to influence the shedding of the human pathogen Escherichia coli O157 in cattle feces (Stenkamp-Strahm et al., 2018; Wang et al., 2018).”
From Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present, and future (2018) · cites this paper as Stenkamp-Strahm et al., 2018
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
R: A Language and Environment for Statistical Computing
R Core Team (2000) · doi:10.32614/r.manuals · Cited by 355,706 · see citing works
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
Benjamini, Y., & Hochberg, Y. (1995) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1995.tb02031.x · Cited by 109,482 · see citing works
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Love, M. I., Huber, W., & Anders, S. (2014) · Genome Biology · doi:10.1186/s13059-014-0550-8 · Cited by 95,106 · see citing works
QIIME allows analysis of high-throughput community sequencing data
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., et al. (2010) · Nature Methods · doi:10.1038/nmeth.f.303 · Cited by 34,887 · see citing works
phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
McMurdie, P. J., & Holmes, S. (2013) · PLoS ONE · doi:10.1371/journal.pone.0061217 · Cited by 21,013 · see citing works
Search and clustering orders of magnitude faster than BLAST
Edgar, R. C. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq461 · Cited by 20,617 · see citing works
Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
Wang, Q., Garrity, G. M., Tiedje, J. M., & Cole, J. R. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.00062-07 · Cited by 19,770 · see citing works
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
Price, M. N., Dehal, P. S., & Arkin, A. P. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009490 · Cited by 14,894 · see citing works
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
DeSantis, T. Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E. L., Keller, K., Huber, T., Dalevi, D., Hu, P., & Andersen, G. L. (2006) · Applied and Environmental Microbiology · doi:10.1128/aem.03006-05 · Cited by 10,891 · see citing works
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Huntley, J., Fierer, N., Owens, S. M., Betley, J., Fraser, L., Bauer, M., et al. (2012) · The ISME Journal · doi:10.1038/ismej.2012.8 · Cited by 8,839 · see citing works
McDonald, D. T., Price, M. N., Goodrich, J. K., Nawrocki, E. P., DeSantis, T. Z., Probst, A. J., Andersen, G. L., Knight, R. D., & Hugenholtz, P. (2011) · The ISME Journal · doi:10.1038/ismej.2011.139 · Cited by 5,010 · see citing works
The human microbiome: at the interface of health and disease
Cho, I., & Blaser, M. J. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3182 · Cited by 3,449 · see citing works
PyNAST: a flexible tool for aligning sequences to a template alignment
Caporaso, J. G., Bittinger, K. L., Bushman, F. D., DeSantis, T. Z., Andersen, G. L., & Knight, R. D. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp636 · Cited by 3,374 · see citing works
Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible
McMurdie, P. J., & Holmes, S. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003531 · Cited by 2,894 · see citing works
Differential abundance analysis for microbial marker-gene surveys
Paulson, J. N., Stine, O. C., Bravo, H. C., & Pop, M. (2013) · Nature Methods · doi:10.1038/nmeth.2658 · Cited by 2,393 · see citing works
Normalization and microbial differential abundance strategies depend upon data characteristics
Weiss, S. J., Xu, Z. Z., Peddada, S. D., Amir, A., Bittinger, K. L., González, A., Lozupone, C., Zaneveld, J., Vázquez‐Baeza, Y., Birmingham, A., et al. (2017) · Microbiome · doi:10.1186/s40168-017-0237-y · Cited by 2,123 · see citing works
Recent Advances in Understanding Enteric Pathogenic Escherichia coli
Croxen, M. A., Law, R. J., Scholz, R., Keeney, K. M., Wlodarska, M., & Finlay, B. B. (2013) · Clinical Microbiology Reviews · doi:10.1128/cmr.00022-13 · Cited by 1,578 · see citing works
Microbiota-mediated colonization resistance against intestinal pathogens
Buffie, C. G., & Pamer, E. G. (2013) · Nature reviews. Immunology · doi:10.1038/nri3535 · Cited by 1,564 · see citing works
Paton, A. W., & Paton, J. C. (1998) · Journal of Clinical Microbiology · doi:10.1128/jcm.36.2.598-602.1998 · Cited by 1,215 · see citing works
Lactic Acid Permeabilizes Gram-Negative Bacteria by Disrupting the Outer Membrane
Alakomi, H.-L., Skyttä, E., Saarela, M., Mattila-Sandholm, T., Latva-Kala, K., & Helander, I. M. (2000) · Applied and Environmental Microbiology · doi:10.1128/aem.66.5.2001-2005.2000 · Cited by 1,093 · see citing works
Indole as an intercellular signal in microbial communities
Lee, J.-H., & Lee, J. (2010) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.2009.00204.x · Cited by 1,059 · see citing works
The Earth Microbiome project: successes and aspirations
Gilbert, J. A., Jansson, J. K., & Knight, R. D. (2014) · BMC Biology · doi:10.1186/s12915-014-0069-1 · Cited by 879 · see citing works
Gut Microbiota Orchestrates Energy Homeostasis during Cold
Chevalier, C., Stojanović, O., Colin, D. J., Suarez-Zamorano, N., Tarallo, V., Veyrat-Durebex, C., Rigo, D., Fabbiano, S., Stevanović, A., Hagemann, S., et al. (2015) · Cell · doi:10.1016/j.cell.2015.11.004 · Cited by 829 · see citing works
March, S. B., & Ratnam, S. (1986) · Journal of Clinical Microbiology · doi:10.1128/jcm.23.5.869-872.1986 · Cited by 572 · see citing works
Rideout, J. R., He, Y., Navas-Molina, J. A., Walters, W. A., Ursell, L. K., Gibbons, S. M., Chase, J., McDonald, D. T., Gonzalez, A., Robbins‐Pianka, A., et al. (2014) · PeerJ · doi:10.7717/peerj.545 · Cited by 550 · see citing works
Mao, S., Zhang, M., Liu, J., & Zhu, W. (2015) · Scientific Reports · doi:10.1038/srep16116 · Cited by 532 · see citing works
Sekirov, I., Tam, N. M., Jogova, M., Robertson, M. L., Li, Y., Lupp, C., & Finlay, B. B. (2008) · Infection and Immunity · doi:10.1128/iai.00319-08 · Cited by 483 · see citing works
Majowicz, S. E., Scallan, E., Jones‐Bitton, A., Sargeant, J. M., Stapleton, J. E., Angulo, F. J., Yeung, D. H., & Kirk, M. (2014) · Foodborne Pathogens and Disease · doi:10.1089/fpd.2013.1704 · Cited by 431 · see citing works
Fate of Escherichia coli O157:H7 in Manure-Amended Soil
Jiang, X., Morgan, J., & Doyle, M. P. (2002) · Applied and Environmental Microbiology · doi:10.1128/aem.68.5.2605-2609.2002 · Cited by 363 · see citing works
Community structures of fecal bacteria in cattle from different animal feeding operations
Shanks, O. C., Kelty, C. A., Archibeque, S., Jenkins, M., Newton, R. J., McLellan, S. L., Huse, S. M., & Sogin, M. L. (2011) · Applied and Environmental Microbiology · doi:10.1128/aem.02988-10 · Cited by 359 · see citing works
Bansal, T., Englert, D. L., Lee, J., Hegde, M., Wood, T. K., & Jayaraman, A. (2007) · Infection and Immunity · doi:10.1128/iai.00630-07 · Cited by 358 · see citing works
Wang, G., Clark, C. G., & Rodgers, F. G. (2002) · Journal of Clinical Microbiology · doi:10.1128/jcm.40.10.3613-3619.2002 · Cited by 341 · see citing works
Enterohemorrhagic E. coli (EHEC) pathogenesis
Nguyen, Y., & Sperandio, V. (2012) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2012.00090 · Cited by 315 · see citing works
Longitudinal Study ofEscherichia coliO157:H7 Dissemination on Four Dairy Farms in Wisconsin
Shere, J. A., Bartlett, K. J., & Kaspar, C. W. (1998) · Applied and Environmental Microbiology · doi:10.1128/aem.64.4.1390-1399.1998 · Cited by 297 · see citing works
Jewell, K. A., McCormick, C. A., Odt, C. L., Weimer, P. J., & Suen, G. (2015) · Applied and Environmental Microbiology · doi:10.1128/aem.00720-15 · Cited by 281 · see citing works
Antagonistic activity of probiotic lactobacilli and bifidobacteria against entero- and uropathogens
Hütt, P., Shchepetova, J., Lõivukene, K., Kullisaar, T., & Mikelsaar, M. (2006) · Journal of Applied Microbiology · doi:10.1111/j.1365-2672.2006.02857.x · Cited by 259 · see citing works
A fifteen month study of Escherichia coli O157:H7 in a dairy herd
MECHIE, S. C., Chapman, P. A., & Siddons, C. A. (1997) · Epidemiology and Infection · doi:10.1017/s0950268896007194 · Cited by 246 · see citing works
Brashears, M. M., Galyean, M. L., Loneragan, G. H., Mann, J. E., & Killinger, K. (2003) · Journal of Food Protection · doi:10.4315/0362-028x-66.5.748 · Cited by 226 · see citing works
Microbial succession in the gastrointestinal tract of dairy cows from 2 weeks to first lactation
Dill‐McFarland, K. A., Breaker, J. D., & Suen, G. (2017) · Scientific Reports · doi:10.1038/srep40864 · Cited by 207 · see citing works
Thorsen, J., Brejnrod, A., Mortensen, M. S., Rasmussen, M. A., Stokholm, J., Al‐Soud, W. A., Sørensen, S. J., Bisgaard, H. F., & Waage, J. (2016) · Microbiome · doi:10.1186/s40168-016-0208-8 · Cited by 197 · see citing works
Coagulin, a bacteriocin-like inhibitory substance produced by Bacillus coagulans I4
Hyronimus, Marrec, C. L., & Urdaci, M. C. (1998) · Journal of Applied Microbiology · doi:10.1046/j.1365-2672.1998.00466.x · Cited by 189 · see citing works
Indole signalling contributes to the stable maintenance of Escherichia coli multicopy plasmids
Chant, E. L., & Summers, D. (2006) · Molecular Microbiology · doi:10.1111/j.1365-2958.2006.05481.x · Cited by 182 · see citing works
Cobbold, R. N., Hancock, D. D., Rice, D. H., Berg, J., Stilborn, R., Hovde, C. J., & Besser, T. E. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.01742-06 · Cited by 170 · see citing works
Schmidt, H., Scheef, J., Huppertz, H., et al. (1999) · Journal of Clinical Microbiology · doi:10.1128/jcm.37.11.3491-3496.1999 · Cited by 127 · see citing works
Peterson, R. E., Klopfenstein, T. J., Erickson, G. E., Folmer, J., Hinkley, S., Moxley, R. A., & Smith, D. R. (2007) · Journal of Food Protection · doi:10.4315/0362-028x-70.2.287 · Cited by 126 · see citing works
High levels of background flora inhibits growth of Escherichia coli O157:H7 in ground beef
Vold, L., Holck, A. L., Wasteson, Y., et al. (2000) · International Journal of Food Microbiology · doi:10.1016/s0168-1605(00)00215-4 · Cited by 115 · see citing works
Hirakawa, H., Kodama, T., Takumi-Kobayashi, A., Honda, T., & Yamaguchi, A. (2009) · Microbiology · doi:10.1099/mic.0.020420-0 · Cited by 101 · see citing works
Robinson, S. E., Wright, E. J., Hart, C. A., et al. (2004) · Journal of Applied Microbiology · doi:10.1111/j.1365-2672.2004.02390.x · Cited by 98 · see citing works
Carrothers, J. M., York, M. A., Brooker, S. L., Lackey, K. A., Williams, J. E., Shafii, B., Price, W. J., Settles, M. L., McGuire, M. A., & McGuire, M. K. (2015) · Journal of Nutrition · doi:10.3945/jn.115.211110 · Cited by 97 · see citing works
Factors Associated with Shiga Toxin-Producing Escherichia coli Shedding by Dairy and Beef Cattle
Venegas-Vargas, C., Henderson, S. T., Khare, A., Mosci, R. E., Lehnert, J. D., Singh, P., Ouellette, L., Norby, B., Funk, J. A., Rust, S. R., et al. (2016) · Applied and Environmental Microbiology · doi:10.1128/aem.00829-16 · Cited by 81 · see citing works
Menrath, A., Wieler, L. H., Heidemanns, K., Semmler, T., Fruth, A., & Kemper, N. (2010) · Gut Pathogens · doi:10.1186/1757-4749-2-7 · Cited by 75 · see citing works
Xu, Y., Dugat‐Bony, É., Zaheer, R., Selinger, L. J., Barbieri, R., Munns, K. D., McAllister, T. A., & Selinger, L. B. (2014) · PLoS ONE · doi:10.1371/journal.pone.0098115 · Cited by 59 · see citing works
Moryella indoligenes gen. nov., sp. nov., an anaerobic bacterium isolated from clinical specimens
Carlier, J., K'ouas, G., & Han, X. Y. (2007) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijs.0.64705-0 · Cited by 58 · see citing works
Similarity of the ruminal bacteria across individual lactating cows
Jami, E., & Mizrahi, I. (2012) · Anaerobe · doi:10.1016/j.anaerobe.2012.04.003 · Cited by 57 · see citing works
Ayaz, N. D., Gençay, Y. E., & Erol, İ. (2014) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2014.01.002 · Cited by 52 · see citing works
Cernicchiaro, N., Pearl, D. L., McEwen, S. A., Harpster, L., Homan, H. J., Linz, G. M., & LeJeune, J. T. (2012) · Zoonoses and Public Health · doi:10.1111/j.1863-2378.2012.01457.x · Cited by 47 · see citing works
Cobbaut, K., Berkvens, D. L., Houf, K., et al. (2009) · Journal of Food Protection · doi:10.4315/0362-028x-72.9.1848 · Cited by 45 · see citing works
King, L. A., Loukiadis, E., Mariani‐Kurkdjian, P., et al. (2014) · Clinical Microbiology and Infection · doi:10.1111/1469-0691.12736 · Cited by 44 · see citing works
Haldar, L., & Gandhi, D. N. (2016) · Veterinary World · doi:10.14202/vetworld.2016.766-772 · Cited by 35 · see citing works
Chopyk, J., Moore, R. M., DiSpirito, Z., Stromberg, Z. R., Lewis, G. L., Renter, D. G., Cernicchiaro, N., Moxley, R. A., & Wommack, K. E. (2016) · Microbiome · doi:10.1186/s40168-016-0155-4 · Cited by 31 · see citing works
Risk factors forEscherichia coliO157 shedding and super-shedding by dairy heifers at pasture
Williams, K., Ward, M. P., Dhungyel, O. P., et al. (2014) · Epidemiology and Infection · doi:10.1017/s0950268814001630 · Cited by 30 · see citing works
Zhao, L., Tyler, P. J., Starnes, J., Bratcher, C. L., Rankins, D. L., McCaskey, T. A., & Wang, L. (2013) · Journal of Applied Microbiology · doi:10.1111/jam.12250 · Cited by 30 · see citing works
Ferreira, M. R. A., Filho, E. G. F., Pinto, J. F. N., et al. (2014) · Tropical Animal Health and Production · doi:10.1007/s11250-014-0541-5 · Cited by 29 · see citing works
Cookson, A. L., Cao, M., Bennett, J., et al. (2010) · Applied and Environmental Microbiology · doi:10.1128/aem.02528-09 · Cited by 14 · see citing works
Stenkamp-Strahm, C. M., McConnel, C. S., Rao, S., et al. (2016) · Epidemiology and Infection · doi:10.1017/s0950268816001928 · Cited by 11 · see citing works
Self-citationPrevalence of Escherichia coli O157 Shedding in Preweaned Calves on Colorado Dairies
Stenkamp-Strahm, C. M., McConnel, C. S., Hyatt, D. R., et al. (2017) · Journal of Food Protection · doi:10.4315/0362-028x.jfp-16-531 · Cited by 6 · see citing works
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
Huws, S. A., Creevey, C. J., Oyama, L. B., Mizrahi, I., Denman, S. E., Popova, M., Muñoz-Tamayo, R., Forano, E., Waters, S. M., Hess, M., et al. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.02161 · Cited by 487 · see citing works
- Authors
- Stenkamp‐Strahm, C., McConnel, C., Magzamen, S., Abdo, Z., & Reynolds, S.
- Affiliations
- College of Veterinary Medicine and Biomedical Sciences Colorado State University Fort Collins CO USA
- Colorado State University (US)
- Venue
- Journal of Applied Microbiology
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-02-08
- Volume
- 124
- Issue
- 3
- Pages
- 881-898
- ISSN
- 1364-5072 (ISSN-L)
- 1365-2672
- PMC
- PMC9491513
- OpenAlex
- W2777585519
- Cited by
- 18
- References
- 66
- Citations by year
- 2025: 3 · 2024: 1 · 2023: 1 · 2022: 3 · 2021: 4 · 2020: 1 · 2019: 2 · 2018: 3
- FWCI
- 1.26
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- Journal of Applied Microbiology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- U.S. Department of Agriculture (CRCFY2015; 1004896, 15‐9200‐0443CA)
- Colorado State University
- Centers for Disease Control and Prevention (5U54OH008085)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Endocrinology › Escherichia coli research studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Agricultural and Biological Sciences › Agronomy and Crop Science › Ruminant Nutrition and Digestive Physiology
- Keywords
- Escherichia coli O157, dairy cattle, fecal microbiota, bacterial shedding, microbial diversity, alpha diversity, Bacillus coagulans, early lactation, zoonotic transmission, 16S rRNA gene sequencing
- MeSH terms
- Gastrointestinal Microbiome, Animals, Cattle, Cattle Diseases, Escherichia coli Infections, Feces, Female, Escherichia coli O157
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
