D-SPF 16S
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1243748 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:D-SPF small intestine 16S Raw sequence reads
| PRJNA1280547 | ENA
Project description:The gut microbiota is closely associated with digestion, metabolism, immunity, and host health. The imbalance of the microbial community in livestock directly affects their well-being and, consequently, productivity. The composition and diversity of the gut microbiota are influenced not only by host genetics but also by environmental factors such as the microbial complexity of the rearing environment, feeds, and antibiotics. Here, we focus on the comparison of gut microbial communities in miniature pigs developed for xenotransplantation in specific pathogen-free (SPF) and conventional (non-SPF) facilities. To identify the disparities in gut microbial composition and functionality between these two environments, 16S RNA metagenome sequencing was conducted using fecal samples. The results revealed that the non-SPF pigs had higher gut microbiota diversity than the SPF pigs. The genera Streptococcus and Ruminococcus were more abundant in SPF pigs than in non-SPF pigs. Blautia, Bacteroides, and Roseburia were exclusively observed in SPF pigs, whereas Prevotella was exclusively found in non-SPF pigs. Carbohydrate and nucleotide metabolism, as well as environmental information processing, were predicted to be enriched in SPF pigs. In addition, energy and lipid metabolism, along with processes related to genetic information, cellular communication, and diseases, were predicted to be enriched in non-SPF pigs. This study makes an important contribution to elucidating the impact of environments harboring a variety of microorganisms, including pathogens, on the gut microbiota of miniature pigs. Furthermore, we sought to provide foundational data on the characteristics of the gut microbiota in genetically modified pigs, which serve as source animals for xenotransplantation.
2024-04-22 | GSE264183 | GEO
Project description:Sex-based differences in respiratory disease outcomes are well recognized; however, the immunological mechanisms driving this dimorphism remain incompletely understood. While sex hormones influence immune cell development and function, the role of commensal microbes in shaping sex-specific lung immunity has not been fully defined. In a companion lung immune profiling study, we used single-cell RNA sequencing (scRNA-seq) and flow cytometry to compare male and female mice housed under specific pathogen-free (SPF) or germ-free (GF) conditions. Under SPF conditions, males exhibited a striking myeloid bias with increased monocytes and macrophages, broad upregulation of inflammatory mediators (including S100a8, S100a9, and Il1b), and enrichment of TNF and interferon (IFN) signaling pathways. In contrast, females displayed lymphocyte-skewed profiles with higher frequencies of T cells and natural killer (NK) cells. These sex-based differences in immune composition and inflammatory programs were largely absent in GF mice, consistent with microbial exposure amplifying baseline immunological dimorphism between males and females. The present GEO submission provides 16S rRNA gene amplicon sequencing (V3–V4) from cage-level pooled fecal samples collected from SPF male and SPF female cages to verify microbial colonization status in the SPF cohort. Unsurprisingly, DNA from GF samples fell below the threshold for reliable sequencing, consistent with successful maintenance of germ-free conditions. SPF mice harbored relatively diverse bacterial communities, typical of murine gut microbiota. The companion lung scRNA-seq dataset is available in GEO under accession GSE316448.
2026-09-01 | GSE317154 | GEO
Project description:Morus alba L. Raw protein sequence reads and sequence
2024-02-08 | PXD049451 |
Project description:Mus musculus (C57BL/6 lineage SPF female) fecal Raw sequence reads
| PRJNA1337703 | ENA