{"id":{"repo_id":"vt","oai_identifier":"oai:vtechworks.lib.vt.edu:10919/49676"},"canonical_url":"https://search.dev.ndltd.org/etd/vt/oai:vtechworks.lib.vt.edu:10919/49676","repository":{"repo_id":"vt","name":"Virginia Tech","base_url":"https://vtechworks.lib.vt.edu/oai/request"},"display":{"title":"Metagenomic Analysis of Antibiotic Resistance Genes in the Fecal Microbiome Following Therapeutic and Prophylactic Antibiotic Administration in Dairy Cows","abstract":"The use of antibiotics in dairy cattle has the potential to stimulate the development and subsequent fecal dissemination of antibiotic resistance genes (ARGs) in bacteria. The objectives were to use metagenomic techniques to evaluate the effect of antibiotic treatment on ARG prevalence in the fecal microbiome of the dairy cow and to determine the temporal excretion pattern of ARGs. Twelve Holstein cows were assigned to one of four antibiotic treatments: control, pirlimycin, ceftiofur, or cephapirin. Fecal samples were collected on d -1, 1, 3, 5, 7, 14, 21, and 28. Samples were freeze-dried and subjected to DNA extraction followed by Illumina paired-end HiSeq sequencing and quantitative polymerase chain reaction (qPCR). Illumina sequences were analyzed using MG-RAST and the Antibiotic Resistance Gene Database (ARDB) via BLAST. Abundance of ampC, ermB, tetO, tetW, and 16S rRNA genes were determined using qPCR. All data were statistically analyzed with PROC GLIMMIX in SAS. Antibiotic treatment resulted in a shift in bacterial cell functions. Sequences associated with 'resistance to antibiotics and toxic compounds' were higher in ceftiofur-treated cows than control cows. Ceftiofur-treated cows had a higher abundance of 𝛽-lactam and multidrug resistance sequences than control cows. There was no effect of treatment or day on fecal tetO and ermB excretion. The relative abundances of tetW and ampC were higher on d 3 post-treatment than d 5 and d 28. In conclusion, antibiotic use in dairy cattle shifted bacterial cell functions and temporarily increased antibiotic resistance in the fecal microbiome.","abstract_html":"The use of antibiotics in dairy cattle has the potential to stimulate the development and subsequent fecal dissemination of antibiotic resistance genes (ARGs) in bacteria. The objectives were to use metagenomic techniques to evaluate the effect of antibiotic treatment on ARG prevalence in the fecal microbiome of the dairy cow and to determine the temporal excretion pattern of ARGs. Twelve Holstein cows were assigned to one of four antibiotic treatments: control, pirlimycin, ceftiofur, or cephapirin. Fecal samples were collected on d -1, 1, 3, 5, 7, 14, 21, and 28. Samples were freeze-dried and subjected to DNA extraction followed by Illumina paired-end HiSeq sequencing and quantitative polymerase chain reaction (qPCR). Illumina sequences were analyzed using MG-RAST and the Antibiotic Resistance Gene Database (ARDB) via BLAST. Abundance of ampC, ermB, tetO, tetW, and 16S rRNA genes were determined using qPCR. All data were statistically analyzed with PROC GLIMMIX in SAS. Antibiotic treatment resulted in a shift in bacterial cell functions. Sequences associated with 'resistance to antibiotics and toxic compounds' were higher in ceftiofur-treated cows than control cows. Ceftiofur-treated cows had a higher abundance of 𝛽-lactam and multidrug resistance sequences than control cows. There was no effect of treatment or day on fecal tetO and ermB excretion. The relative abundances of tetW and ampC were higher on d 3 post-treatment than d 5 and d 28. In conclusion, antibiotic use in dairy cattle shifted bacterial cell functions and temporarily increased antibiotic resistance in the fecal microbiome.","abstract_has_math":false,"creators":["Caudle, Lindsey Renee"],"institution":"Virginia Tech","degree_name":"Master of Science","degree_level":"masters","degree_discipline":"Dairy Science","degree_department":"Dairy Science","school":null,"contributors":[],"advisors":[],"committee_chairs":["Knowlton, Katharine F."],"committee_members":["Strickland, Michael","Pruden, Amy","Akers, Robert Michael"],"year":2014,"date_issued":"2014-07-24","date_published":"2014-07-24","updated_at":"2026-07-22T22:19:48Z","subjects":["shotgun metagenomic sequencing","antibiotic resistance","dairy cow"],"languages":[],"rights":["In Copyright"],"rights_urls":["http://rightsstatements.org/vocab/InC/1.0/"],"identifier_entries":[{"key":"dc:identifier.other","label":"Dc Identifier Other","values":["vt_gsexam:3509"],"render_values":[{"text":"vt_gsexam:3509","href":null,"code":true}]}]},"links":{"outbound_url":"http://hdl.handle.net/10919/49676","outbound_label":"Handle","outbound_source":"dc:identifier.uri"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.committeechair","label":"Committee Chair","values":["Knowlton, Katharine F."]},{"key":"dc:contributor.committeemember","label":"Committee Member","values":["Strickland, Michael","Pruden, Amy","Akers, Robert Michael"]},{"key":"dc:contributor.department","label":"Department","values":["Dairy Science"]},{"key":"dc:creator","label":"Author","values":["Caudle, Lindsey Renee"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.accessioned","label":"Dc Date Accessioned","values":["2014-07-25T08:00:23Z"]},{"key":"dc:date.available","label":"Dc Date Available","values":["2014-07-25T08:00:23Z"]},{"key":"dc:date.issued","label":"Date","values":["2014-07-24"]},{"key":"dc:publisher","label":"Institution","values":["Virginia Tech"]},{"key":"dc:type","label":"Dc Type","values":["Thesis"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Dairy Science"]},{"key":"thesis:degree_level","label":"Degree Level","values":["masters"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Master of Science"]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["Virginia Polytechnic Institute and State University"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["shotgun metagenomic sequencing","antibiotic resistance","dairy cow"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:rights","label":"Dc Rights","values":["In Copyright"]},{"key":"dc:rights.uri","label":"Rights URI","values":["http://rightsstatements.org/vocab/InC/1.0/"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.other","label":"Dc Identifier Other","values":["vt_gsexam:3509"]},{"key":"dc:identifier.uri","label":"Identifier URI","values":["http://hdl.handle.net/10919/49676"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["The use of antibiotics in dairy cattle has the potential to stimulate the development and subsequent fecal dissemination of antibiotic resistance genes (ARGs) in bacteria. The objectives were to use metagenomic techniques to evaluate the effect of antibiotic treatment on ARG prevalence in the fecal microbiome of the dairy cow and to determine the temporal excretion pattern of ARGs. Twelve Holstein cows were assigned to one of four antibiotic treatments: control, pirlimycin, ceftiofur, or cephapirin. Fecal samples were collected on d -1, 1, 3, 5, 7, 14, 21, and 28. Samples were freeze-dried and subjected to DNA extraction followed by Illumina paired-end HiSeq sequencing and quantitative polymerase chain reaction (qPCR). Illumina sequences were analyzed using MG-RAST and the Antibiotic Resistance Gene Database (ARDB) via BLAST. Abundance of ampC, ermB, tetO, tetW, and 16S rRNA genes were determined using qPCR. All data were statistically analyzed with PROC GLIMMIX in SAS. Antibiotic treatment resulted in a shift in bacterial cell functions. Sequences associated with 'resistance to antibiotics and toxic compounds' were higher in ceftiofur-treated cows than control cows. Ceftiofur-treated cows had a higher abundance of 𝛽-lactam and multidrug resistance sequences than control cows. There was no effect of treatment or day on fecal tetO and ermB excretion. The relative abundances of tetW and ampC were higher on d 3 post-treatment than d 5 and d 28. In conclusion, antibiotic use in dairy cattle shifted bacterial cell functions and temporarily increased antibiotic resistance in the fecal microbiome."]},{"key":"dc:description.degree","label":"Dc Description Degree","values":["Master of Science"]},{"key":"dc:format.medium","label":"Dc Format Medium","values":["ETD"]},{"key":"dc:title","label":"Title","values":["Metagenomic Analysis of Antibiotic Resistance Genes in the Fecal Microbiome Following Therapeutic and Prophylactic Antibiotic Administration in Dairy Cows"]}]}],"canonical_facts":{"dc:contributor.committeechair":["Knowlton, Katharine F."],"dc:contributor.committeemember":["Strickland, Michael","Pruden, Amy","Akers, Robert Michael"],"dc:contributor.department":["Dairy Science"],"dc:creator":["Caudle, Lindsey Renee"],"dc:date.accessioned":["2014-07-25T08:00:23Z"],"dc:date.available":["2014-07-25T08:00:23Z"],"dc:date.issued":["2014-07-24"],"dc:description.abstract":["The use of antibiotics in dairy cattle has the potential to stimulate the development and subsequent fecal dissemination of antibiotic resistance genes (ARGs) in bacteria. The objectives were to use metagenomic techniques to evaluate the effect of antibiotic treatment on ARG prevalence in the fecal microbiome of the dairy cow and to determine the temporal excretion pattern of ARGs. Twelve Holstein cows were assigned to one of four antibiotic treatments: control, pirlimycin, ceftiofur, or cephapirin. Fecal samples were collected on d -1, 1, 3, 5, 7, 14, 21, and 28. Samples were freeze-dried and subjected to DNA extraction followed by Illumina paired-end HiSeq sequencing and quantitative polymerase chain reaction (qPCR). Illumina sequences were analyzed using MG-RAST and the Antibiotic Resistance Gene Database (ARDB) via BLAST. Abundance of ampC, ermB, tetO, tetW, and 16S rRNA genes were determined using qPCR. All data were statistically analyzed with PROC GLIMMIX in SAS. Antibiotic treatment resulted in a shift in bacterial cell functions. Sequences associated with 'resistance to antibiotics and toxic compounds' were higher in ceftiofur-treated cows than control cows. Ceftiofur-treated cows had a higher abundance of 𝛽-lactam and multidrug resistance sequences than control cows. There was no effect of treatment or day on fecal tetO and ermB excretion. The relative abundances of tetW and ampC were higher on d 3 post-treatment than d 5 and d 28. In conclusion, antibiotic use in dairy cattle shifted bacterial cell functions and temporarily increased antibiotic resistance in the fecal microbiome."],"dc:description.degree":["Master of Science"],"dc:format.medium":["ETD"],"dc:identifier.other":["vt_gsexam:3509"],"dc:identifier.uri":["http://hdl.handle.net/10919/49676"],"dc:publisher":["Virginia Tech"],"dc:rights":["In Copyright"],"dc:rights.uri":["http://rightsstatements.org/vocab/InC/1.0/"],"dc:subject":["shotgun metagenomic sequencing","antibiotic resistance","dairy cow"],"dc:title":["Metagenomic Analysis of Antibiotic Resistance Genes in the Fecal Microbiome Following Therapeutic and Prophylactic Antibiotic Administration in Dairy Cows"],"dc:type":["Thesis"],"thesis:degree_discipline":["Dairy Science"],"thesis:degree_level":["masters"],"thesis:degree_name":["Master of Science"],"thesis:institution_name":["Virginia Polytechnic Institute and State University"]},"updated_at":"2026-07-22T22:19:48Z"}