Single cell transcriptome profiling of immune tissues from germ-free and specific pathogen-free piglet

The commensal microbiota provides immunomodulatory signals during the development, differentiation and activation of immune cells, and is crucial for maintaining host immune homeostasis. However, the systematic effects of commensal microbiota on host immunity based on large animal model at the single-cell level remain to be resolved. Here, we utilized single-cell RNA sequencing (scRNA-seq) to analyze the transcriptome profiling containing 57,720 cells from three important immune tissues [Peyer's patches (PP), mesenteric lymph node (MLN), and spleen] of germ-free (GF) and specific pathogen-free (SPF) piglet. We presented detailed description of the dataset and preliminarily identified the major cell types including immune and non-immune cells, and further annotated the immune cell subsets. This dataset provides a data mining resource for researchers involved in microbe-host interactions, and enables in-depth analysis of cell map alterations caused by the microbiota colonization during early immune development. As the first single-cell transcriptomics dataset for immune tissue of GF and SPF piglet, this provides a valuable data resource for the study of commensal microbe-host immunity regulation.

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Publication Details

Journal
Scientific Data
Published
2025-04-18
DOI
https://doi.org/10.1038/s41597-025-04957-2
Citations
4
Primary Topic
Gut microbiota and health
Type
article
Field-Weighted Citation Impact
3.22

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article

Single cell transcriptome profiling of immune tissues from germ-free and specific pathogen-free piglet

Fanli Kong, Yuchun Ding, Chuang Tang, Mingzhou Li et al.
4 citations
Scientific Data
Gut microbiota and health
3.22
article

Single cell transcriptome profiling of immune tissues from germ-free and specific pathogen-free piglet

Fanli Kong, Yuchun Ding, Chuang Tang, Mingzhou Li, Jideng Ma, Keren Long, Liangpeng Ge, Jing Sun, Li Shen, Yan Liu, Jinwei Zhang, Hao Liang, Junbo Ge, Xiaokai Li, Shuangshuang Chen
article en
4 citations

Abstract

The commensal microbiota provides immunomodulatory signals during the development, differentiation and activation of immune cells, and is crucial for maintaining host immune homeostasis. However, the systematic effects of commensal microbiota on host immunity based on large animal model at the single-cell level remain to be resolved. Here, we utilized single-cell RNA sequencing (scRNA-seq) to analyze the transcriptome profiling containing 57,720 cells from three important immune tissues [Peyer's patches (PP), mesenteric lymph node (MLN), and spleen] of germ-free (GF) and specific pathogen-free (SPF) piglet. We presented detailed description of the dataset and preliminarily identified the major cell types including immune and non-immune cells, and further annotated the immune cell subsets. This dataset provides a data mining resource for researchers involved in microbe-host interactions, and enables in-depth analysis of cell map alterations caused by the microbiota colonization during early immune development. As the first single-cell transcriptomics dataset for immune tissue of GF and SPF piglet, this provides a valuable data resource for the study of commensal microbe-host immunity regulation.

Scientific DataVol. 12(1)
Sun Yat-sen University (CN), Fudan University (CN), Sichuan Agricultural University (CN), Sichuan Animal Science Academy (CN), Chongqing Academy of Animal Science (CN), Zhongshan Hospital (CN), The First Affiliated Hospital, Sun Yat-sen University (CN), Ministry of Science and Technology (LA), Chongqing University of Technology (CN), Ministry of Industry and Information Technology (CN)
National Natural Science Foundation of China, Natural Science Foundation of Chongqing, Centre Scientifique et Technique du Bâtiment
Zero hunger
Openalex Percentile: Top 9%
Gut microbiota and health
3.22
DOIOpen Access PDFOpenAlex
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