Studies investigating Escherichia coli strain diversity and demographics in human hosts are frequently inconsistent regarding sampling effort and methodology while current strain typing methods are often expensive or laborious. To rectify these inconsistencies, sampling effort was investigated by comparing the diversity of 15-isolate collections to 100-isolate collections from 3 human subjects. Temporal variation in E. coli strain diversity was also studied by collecting 15 isolates once every 6 months. Additionally, strain identification and diversity collected by different sampling methods (fecal swabs vs. anal swabs collected at different times around defecation) were compared to identify any inherent biases in sampling method. This study employed pyroprinting, a new inexpensive and simple strain typing method using pyrosequencing, to generate DNA fingerprints (or pyroprints) based on the Intergenic Transcribed Spacer sequences in the ribosomal RNA operon to differentiate E. coli strains. Differences in strain diversity were apparent when comparing sampling efforts. The sampling effort investigation suggested that certain subjects hosted very large and highly diverse E. coli strain populations such that even 100 isolates may not fully represent E. coli strain populations in human hosts. Instead, the sampling effort required to accurately represent strain demographics may depend on strain richness and evenness within each host. The temporal investigation yielded similar or greater strain abundance and diversity compared to other typing methods in the literature suggesting pyroprinting is a similarly discriminating tool. When agglomerated over time or by subject, no significant differences in diversity were observed between subjects or between sampling methods despite visible differences in strain richness and evenness.
","abstract_html":"<p>Studies investigating <em>Escherichia coli</em> strain diversity and demographics in human hosts are frequently inconsistent regarding sampling effort and methodology while current strain typing methods are often expensive or laborious. To rectify these inconsistencies, sampling effort was investigated by comparing the diversity of 15-isolate collections to 100-isolate collections from 3 human subjects. Temporal variation in <em>E. coli</em> strain diversity was also studied by collecting 15 isolates once every 6 months. Additionally, strain identification and diversity collected by different sampling methods (fecal swabs vs. anal swabs collected at different times around defecation) were compared to identify any inherent biases in sampling method. This study employed pyroprinting, a new inexpensive and simple strain typing method using pyrosequencing, to generate DNA fingerprints (or pyroprints) based on the Intergenic Transcribed Spacer sequences in the ribosomal RNA operon to differentiate <em>E. coli</em> strains. Differences in strain diversity were apparent when comparing sampling efforts. The sampling effort investigation suggested that certain subjects hosted very large and highly diverse <em>E. coli</em> strain populations such that even 100 isolates may not fully represent <em>E. coli</em> strain populations in human hosts. Instead, the sampling effort required to accurately represent strain demographics may depend on strain richness and evenness within each host. The temporal investigation yielded similar or greater strain abundance and diversity compared to other typing methods in the literature suggesting pyroprinting is a similarly discriminating tool. When agglomerated over time or by subject, no significant differences in diversity were observed between subjects or between sampling methods despite visible differences in strain richness and evenness.</p>","abstract_has_math":false,"creators":["Neal, Emily R."],"institution":null,"degree_name":"MS in Biological Sciences","degree_level":null,"degree_discipline":"Biological Sciences","degree_department":null,"school":null,"contributors":["Michael Black"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2013,"date_issued":"2013-06-01T07:00:00Z","date_published":"2013-06-01T07:00:00Z","updated_at":"2026-07-24T01:32:50Z","subjects":["Escherichia coli","strain diversity","sampling effort","Environmental Microbiology and Microbial Ecology"],"languages":[],"rights":[],"rights_urls":[],"identifier_entries":[{"key":"dc:identifier","label":"Identifier","values":["10.15368/theses.2013.135"],"render_values":[{"text":"10.15368/theses.2013.135","href":"https://doi.org/10.15368/theses.2013.135","code":true}]}]},"links":{"outbound_url":"https://digitalcommons.calpoly.edu/theses/984","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Michael Black"]},{"key":"dc:creator","label":"Author","values":["Neal, Emily R."]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.available","label":"Dc Date Available","values":["2013-07-24T07:00:00Z"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Biological Sciences"]},{"key":"thesis:degree_name","label":"Degree Name","values":["MS in Biological Sciences"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Escherichia coli","strain diversity","sampling effort","Environmental Microbiology and Microbial Ecology"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://digitalcommons.calpoly.edu/theses/984","10.15368/theses.2013.135"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["Studies investigating Escherichia coli strain diversity and demographics in human hosts are frequently inconsistent regarding sampling effort and methodology while current strain typing methods are often expensive or laborious. To rectify these inconsistencies, sampling effort was investigated by comparing the diversity of 15-isolate collections to 100-isolate collections from 3 human subjects. Temporal variation in E. coli strain diversity was also studied by collecting 15 isolates once every 6 months. Additionally, strain identification and diversity collected by different sampling methods (fecal swabs vs. anal swabs collected at different times around defecation) were compared to identify any inherent biases in sampling method. This study employed pyroprinting, a new inexpensive and simple strain typing method using pyrosequencing, to generate DNA fingerprints (or pyroprints) based on the Intergenic Transcribed Spacer sequences in the ribosomal RNA operon to differentiate E. coli strains. Differences in strain diversity were apparent when comparing sampling efforts. The sampling effort investigation suggested that certain subjects hosted very large and highly diverse E. coli strain populations such that even 100 isolates may not fully represent E. coli strain populations in human hosts. Instead, the sampling effort required to accurately represent strain demographics may depend on strain richness and evenness within each host. The temporal investigation yielded similar or greater strain abundance and diversity compared to other typing methods in the literature suggesting pyroprinting is a similarly discriminating tool. When agglomerated over time or by subject, no significant differences in diversity were observed between subjects or between sampling methods despite visible differences in strain richness and evenness.
"]},{"key":"dc:title","label":"Title","values":["Escherichia coli Strain Diversity in Humans: Effects of Sampling Effort and Methodology"]}]}],"canonical_facts":{"dc:contributor":["Michael Black"],"dc:creator":["Neal, Emily R."],"dc:date.available":["2013-07-24T07:00:00Z"],"dc:description.abstract":["Studies investigating Escherichia coli strain diversity and demographics in human hosts are frequently inconsistent regarding sampling effort and methodology while current strain typing methods are often expensive or laborious. To rectify these inconsistencies, sampling effort was investigated by comparing the diversity of 15-isolate collections to 100-isolate collections from 3 human subjects. Temporal variation in E. coli strain diversity was also studied by collecting 15 isolates once every 6 months. Additionally, strain identification and diversity collected by different sampling methods (fecal swabs vs. anal swabs collected at different times around defecation) were compared to identify any inherent biases in sampling method. This study employed pyroprinting, a new inexpensive and simple strain typing method using pyrosequencing, to generate DNA fingerprints (or pyroprints) based on the Intergenic Transcribed Spacer sequences in the ribosomal RNA operon to differentiate E. coli strains. Differences in strain diversity were apparent when comparing sampling efforts. The sampling effort investigation suggested that certain subjects hosted very large and highly diverse E. coli strain populations such that even 100 isolates may not fully represent E. coli strain populations in human hosts. Instead, the sampling effort required to accurately represent strain demographics may depend on strain richness and evenness within each host. The temporal investigation yielded similar or greater strain abundance and diversity compared to other typing methods in the literature suggesting pyroprinting is a similarly discriminating tool. When agglomerated over time or by subject, no significant differences in diversity were observed between subjects or between sampling methods despite visible differences in strain richness and evenness.
"],"dc:identifier":["https://digitalcommons.calpoly.edu/theses/984","10.15368/theses.2013.135"],"dc:subject":["Escherichia coli","strain diversity","sampling effort","Environmental Microbiology and Microbial Ecology"],"dc:title":["Escherichia coli Strain Diversity in Humans: Effects of Sampling Effort and Methodology"],"thesis:degree_discipline":["Biological Sciences"],"thesis:degree_name":["MS in Biological Sciences"]},"updated_at":"2026-07-24T01:32:50Z"}