About

Sarah Ho is the CVM Director of Student Engagement at the College of Veterinary Medicine at NC State University. Her role involves fostering student development and engagement within the college community. The page emphasizes the college's focus on student achievement, well-being, and extracurricular growth, but does not provide specific details about her research focus, background, or key contributions.

Research topics

• Computational biology
• Biology
• Genetics

Selected publications

• The development of non-destructive sampling methods of parchment skins for genetic species identification

  PLoS ONE · 2024 · 5 citations

  • Computer Science
  • Evolutionary biology
  • Computational biology

  Parchment, the skins of animals prepared for use as writing surfaces, offers a valuable source of genetic information. Many have clearly defined provenance, allowing for the genetic findings to be evaluated in temporal and spatial context. While these documents can yield evidence of the animal sources, the DNA contained within these aged skins is often damaged and fragmented. Previously, genetic studies targeting parchment have used destructive sampling techniques and so the development and validation of non-destructive sampling methods would expand opportunities and facilitate testing of more precious documents, especially those with historical significance. Here we present genetic data obtained by non-destructive sampling of eight parchments spanning the 15th century to the modern day. We define a workflow for enriching the mitochondrial genome (mtGenome), generating next-generation sequencing reads to permit species identification, and providing interpretation guidance. Using sample replication, comparisons to destructively sampled controls, and by establishing authentication criteria, we were able to confidently assign full/near full mtGenome sequences to 56.3% of non-destructively sampled parchments, each with greater than 90% of the mtGenome reference covered. Six of eight parchments passed all four established thresholds with at least one non-destructive sample, highlighting promise for future studies.

  PublisherOA PDFDOI

• Pseudo-pac site sequences used by phage P22 in generalized transduction of <i>Salmonella</i>

  bioRxiv (Cold Spring Harbor Laboratory) · 2024 · 1 citations

  • Biology
  • Genetics
  • Computational biology

  pseudo-pac sites in this study could be applied to other phage-host systems.

  DOI

• Effects of danofloxacin dosing regimen on gastrointestinal pharmacokinetics and fecal microbiome in steers

  Scientific Reports · 2021 · 8 citations

  • Medicine
  • Biology
  • Pharmacology

  Fluoroquinolones are a class of antimicrobial commonly used in human medicine, and deemed critical by the World Health Organization. Nonetheless, two formulations are approved for the treatment of respiratory disease in beef cattle. The objective of this study was to determine the gastrointestinal pharmacokinetics and impact on enteric bacteria of cattle when receiving one of the two dosing regimens (high: 40 mg/kg SC once or low: 20 mg/kg IM q48hr) of danofloxacin, a commonly utilized synthetic fluoroquinolone in veterinary medicine. Danofloxacin was administered to 12 steers (age 7 months) fitted with intestinal ultrafiltration devices at two different dosing regimens to assess the gastrointestinal pharmacokinetics, the shifts in the gastrointestinal microbiome and the development of resistant bacterial isolates. Our results demonstrated high intestinal penetration of danofloxacin for both dosing groups, as well as, significant differences in MIC values for E. coli and Enterococcus between dosing groups at selected time points over a 38 day period. Danofloxacin treatment consistently resulted in the Euryarchaeota phyla decreasing over time, specifically due to a decrease in Methanobrevibacter. Although microbiome differences were minor between dosing groups, the low dose group had a higher number of isolates with MIC values high enough to cause clinically relevant resistance. This information would help guide veterinarians as to appropriate dosing schemes to minimize the spread of antimicrobial resistance.

  PublisherOA PDFDOI

• Perspectives and Benefits of High-Throughput Long-Read Sequencing in Microbial Ecology

  Applied and Environmental Microbiology · 2021 · 196 citations

  • Computer Science
  • Computational biology
  • Biology

  Short-read, high-throughput sequencing (HTS) methods have yielded numerous important insights into microbial ecology and function. Yet, in many instances short-read HTS techniques are suboptimal, for example, by providing insufficient phylogenetic resolution or low integrity of assembled genomes. Single-molecule and synthetic long-read (SLR) HTS methods have successfully ameliorated these limitations. In addition, nanopore sequencing has generated a number of unique analysis opportunities, such as rapid molecular diagnostics and direct RNA sequencing, and both Pacific Biosciences (PacBio) and nanopore sequencing support detection of epigenetic modifications. Although initially suffering from relatively low sequence quality, recent advances have greatly improved the accuracy of long-read sequencing technologies. In spite of great technological progress in recent years, the long-read HTS methods (PacBio and nanopore sequencing) are still relatively costly, require large amounts of high-quality starting material, and commonly need specific solutions in various analysis steps. Despite these challenges, long-read sequencing technologies offer high-quality, cutting-edge alternatives for testing hypotheses about microbiome structure and functioning as well as assembly of eukaryote genomes from complex environmental DNA samples.

  DOI

• Ultra-accurate microbial amplicon sequencing with synthetic long reads

  Microbiome · 2021 · 129 citations

  • Biology
  • Computational biology
  • Genetics

  BACKGROUND: Out of the many pathogenic bacterial species that are known, only a fraction are readily identifiable directly from a complex microbial community using standard next generation DNA sequencing. Long-read sequencing offers the potential to identify a wider range of species and to differentiate between strains within a species, but attaining sufficient accuracy in complex metagenomes remains a challenge. METHODS: Here, we describe and analytically validate LoopSeq, a commercially available synthetic long-read (SLR) sequencing technology that generates highly accurate long reads from standard short reads. RESULTS: LoopSeq reads are sufficiently long and accurate to identify microbial genes and species directly from complex samples. LoopSeq perfectly recovered the full diversity of 16S rRNA genes from known strains in a synthetic microbial community. Full-length LoopSeq reads had a per-base error rate of 0.005%, which exceeds the accuracy reported for other long-read sequencing technologies. 18S-ITS and genomic sequencing of fungal and bacterial isolates confirmed that LoopSeq sequencing maintains that accuracy for reads up to 6 kb in length. LoopSeq full-length 16S rRNA reads could accurately classify organisms down to the species level in rinsate from retail meat samples, and could differentiate strains within species identified by the CDC as potential foodborne pathogens. CONCLUSIONS: The order-of-magnitude improvement in length and accuracy over standard Illumina amplicon sequencing achieved with LoopSeq enables accurate species-level and strain identification from complex- to low-biomass microbiome samples. The ability to generate accurate and long microbiome sequencing reads using standard short read sequencers will accelerate the building of quality microbial sequence databases and removes a significant hurdle on the path to precision microbial genomics. Video abstract.

  DOI

• Evaluation of fecal Lactobacillus populations in dogs with idiopathic epilepsy: a pilot study

  Animal Microbiome · 2020 · 25 citations

  • Biology
  • Physiology
  • Medicine

  BACKGROUND: populations in dogs with idiopathic epilepsy compared to healthy dogs. RESULTS: in culture was not killed by exposure to phenobarbital, potassium bromide, zonisamide, or levetiracetam. CONCLUSIONS: in epilepsy.

  DOI

• Pathogen resistance may be the principal evolutionary advantage provided by the microbiome

  Philosophical Transactions of the Royal Society B Biological Sciences · 2020 · 116 citations

  • Biology
  • Evolutionary biology
  • Ecology

  To survive, plants and animals must continually defend against pathogenic microbes that would invade and disrupt their tissues. Yet they do not attempt to extirpate all microbes. Instead, they tolerate and even encourage the growth of commensal microbes, which compete with pathogens for resources and via direct inhibition. We argue that hosts have evolved to cooperate with commensals in order to enhance the pathogen resistance this competition provides. We briefly describe competition between commensals and pathogens within the host, consider how natural selection might favour hosts that tilt this competition in favour of commensals, and describe examples of extant host traits that may serve this purpose. Finally, we consider ways that this cooperative immunity may have facilitated the adaptive evolution of non-pathogen-related host traits. On the basis of these observations, we argue that pathogen resistance vies with other commensal-provided benefits for being the principal evolutionary advantage provided by the microbiome to host lineages across the tree of life. This article is part of the theme issue 'The role of the microbiome in host evolution'.

  DOI

Frequent coauthors

• Craig Gin

  North Carolina State University

  1 shared

• Jacob Birchfield

  1 shared

• Brendan Cashen

  1 shared

• Manuel Kleiner

  1 shared

• Jessie L. Maier

  North Carolina State University

  1 shared

• Breck A. Duerkop

  University of Colorado Anschutz Medical Campus

  1 shared

• Charlotte Blain

  1 shared

• Emma K. Sheriff

  University of Colorado Anschutz Medical Campus

  1 shared

Awards & honors

• CFEP- Assistant Professor, Microbiomes and Complex Microbial…

Similar researchers at North Carolina State University

• Jonathan Lindseyh-101
• Edward Breitschwerdth-100
• José Alonsoh-94
• Rob Dunnh-94
• Frances S. Liglerh-92