# High Resolution Characterization of Gut Microbiome and its Response to Antibiotics

> **NIH NIH R01** · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · 2020 · $499,878

## Abstract

Antibiotics use has reached enormous proportions around the world. A well-known consequence of antibiotic
use is the development of bacterial antibiotic resistance. The impact of antibiotics on host and microbial
function, on the other hand, has not been well recognized until recently. The intestinal microbiota aids the host
in metabolic and immunological development and provides beneficial functions such as vitamin production and
pathogen displacement. Dysbiosis of gut microbiota is not only associated with higher risk to pathogenic
microbes, but linked to a large number of complex diseases such as cancers and brain disorders. Despite of
the rapid progresses being made, significant challenges still arise in the study of complex microbiomes,
essentially stemming from the presence of highly similar bacterial species and strains with complex genomes.
A fundamental limitation of all existing metagenomics methods, represented by the widely used 16S rRNA
sequencing and whole metagenome shotgun sequencing, is that they provides insufficient discriminative power
to distinguish among closely related species and strains with high sequence similarity, or confidently map
mobile genetic elements (such as plasmids) to their host genomes. This limitation often leads to fragmented
pictures (large number of short contigs) at a limited resolution that prevents an in-depth characterization of the
effect of antibiotics on gut microbiome. In this project, we will build on a highly innovative method we recently
prototyped for high resolution metagenomic analysis based on long-read Single Molecule Real Time (SMRT)
sequencing, and apply the novel methods to perform in-depth characterization of metagenomic changes and
transmission of mobile genetic elements in response to different types of antibiotics. We expect this study to
uncover novel biological insights, undetectable by previous methods, into the complex genomic dynamics of
microbiomes in response to antibiotics, and provide a novel and general method to help high resolution
characterization of microbiomes.

## Key facts

- **NIH application ID:** 9929625
- **Project number:** 5R01GM128955-03
- **Recipient organization:** ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI
- **Principal Investigator:** Gang Fang
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $499,878
- **Award type:** 5
- **Project period:** 2018-09-06 → 2021-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9929625

## Citation

> US National Institutes of Health, RePORTER application 9929625, High Resolution Characterization of Gut Microbiome and its Response to Antibiotics (5R01GM128955-03). Retrieved via AI Analytics 2026-05-26 from https://api.ai-analytics.org/grant/nih/9929625. Licensed CC0.

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