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Updated: Sep 17, 2025
Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq
Published on: March 12, 2021
Multi-omics integration identifies key biomarkers in retinopathy of prematurity through 16S rRNA sequencing and
Linlin Guo1, Ruoming Wang2, Liping Han3
1The Second Department of Radiotherapy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
Insights
Changes in infant gut bacteria and metabolites are linked to retinopathy of prematurity (ROP). This study identified specific microbial and metabolic signatures associated with ROP, offering potential diagnostic and therapeutic targets.
Area of Science:
- Neonatal research
- Microbiome studies
- Ophthalmology
Background:
- The gut microbiome plays a role in neonatal conditions, including retinopathy of prematurity (ROP).
- Understanding the gut's influence on ROP pathogenesis is crucial for developing new interventions.
Purpose of the Study:
- To identify key intestinal microbiota and metabolites in infants with ROP.
- To examine the relationship between gut microbiota, metabolites, and ROP development.
Main Methods:
- Collected fecal samples from infants with and without ROP at two time points (weeks 2 and 4).
- Performed 16S rRNA sequencing for microbial analysis and non-targeted metabolomic analysis.
- Utilized combined analysis of sequencing and metabolomic data.
Main Results:
- At week 4, ROP infants showed significantly altered gut microbial diversity (higher alpha-diversity, lower Simpson index).
- Key bacterial genera associated with ROP included Bifidobacterium, Staphylococcus, and Klebsiella.
- Metabolomic analysis revealed significant alterations in pathways like steroid hormone biosynthesis and PPAR signaling, with combined analysis showing high diagnostic accuracy (AUC 0.9958).
Conclusions:
- Characteristic changes in intestinal flora and metabolites are associated with ROP.
- These findings suggest potential microbial and metabolic targets for ROP diagnosis and therapy.
Background:
The gut microbiome is increasingly recognized for its role in the pathogenesis of neonatal conditions commonly associated with retinopathy of prematurity (ROP). This study aimed to identify key intestinal microbiota and metabolites in ROP and examine their relationships.
Methods:
Fecal samples were collected from infants with and without ROP at weeks 2 (T1) and 4 (T2) for 16S rRNA sequencing. At T2, additional fecal samples underwent non-targeted metabolomic analyses. A combined analysis of the 16S rRNA sequencing and metabolomics data was performed.
Results:
No significant differences in α-diversity indexes were observed between the ROP and non-ROP at T1. However, at T2, the Chao, ACE, and Shannon indices were significantly higher, whereas the Simpson index was lower in ROP compared to non-ROP. At the phylum level, the dominant phyla at T2 included Pseudomonadota, Bacillota, Actinomycetota, Bacteroidota, and Verrucomicrobiota. LEfSe analysis of T2 showed that Bifidobacterium, Rhodococcus, Staphyloococcus, Caulobacter, Sphingomonas, Aquabacterium, and Klebsiella as key genera associated with ROP. Metabolomic analysis identified 382 differentially accumulated metabolites, which were enriched in steroid hormone biosynthesis; the PPAR signaling pathway; linoleic acid metabolism; histidine metabolism; and alanine, aspartate, and glutamate metabolism. Additionally, the AUC of the combined analysis exceeded that of differential bacterial communities (0.9958) alone.
Conclusion:
This study revealed characteristic changes in the intestinal flora and metabolites in ROP, which provide promising targets/pathways for ROP diagnosis and therapy.
