Human oral metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA184695 | ENA |
REPOSITORIES: ENA
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Project description:Bacterial community development in experimental gingivitis
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Project description:Comparison of microbiome of periodontitis, gingivitis, and healthy
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Project description:Metagenome data from soil samples were collected at 0 to 10cm deep from 2 avocado orchards in Channybearup, Western Australia, in 2024. Amplicon sequence variant (ASV) tables were constructed based on the DADA2 pipeline with default parameters.
2025-06-15 | GSE298403 | GEO
Project description:Subgingival microbiome in college students with dental plaque-induced gingivitis, and their change and stability before and after intervention
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Project description:Oral polymorphonuclear neutrophils (oPMNs) are essential for the maintenance of oral health. Functionally active oPMNs have been described in oral health, gingivitis and periodontitis. Interestingly, recent evidence showed that oPMNs from chronic periodontitis patients have a similar functional and reactivity pattern compared to oPMNs from healthy subjects. However, it remains unknown whether oPMNs respond to the initiation and resolution of gingival inflammation. Therefore, this study aimed to evaluate the oPMNs’ transcriptional responses during the initiation and resolution of an experimentally induced gingivitis. Oral rinses were obtained from 8 subjects at 4 different time points during the experiment for the isolation of oPMNs; day 0 (baseline), day 9 (during gingivitis challenge), day 14 (end of the challenge) and day 21 (resolution). Transcriptome of oPMNs was determined by RNAsequencing. Differentially expressed genes (DEGs) was selected at P<0.01 level, and evaluated for pathway regulation at different time points using Ingenuity Pathway Analysis suite. During the gingivitis challenge, dental plaque levels and gingival bleeding levels were significantly increased at day 14 compared to baseline. Transcriptome analysis indicate four major clusters of DEGs, which consisted of a group of 256 initial response DEGs (day 9 only), 221 late response DEGs (day 14 only), 53 persistent response DEGs (consistent at day 9 and day 14), and a group of 524 DEGs showing response only after the gingivitis challenge (day 21 only). Pathway analysis of the initial response DEGs showed their involvement in many immune regulatory pathways (interleukin signaling, reactive oxygen species processes and granulocyte adhesion and diapedesis). Late responding DEGs mainly showed activation of signaling pathways and phagosome formation as part of the phagocytosis process, whereas DEGs at day 21 were involved in epithelial adherence signaling and other miscellaneous related signaling pathways. This study showed that oPMNs have specific expression profiles during the development and resolution of experimental gingivitis. Even though, the specific observed pathways were not identical within each time point, the altered pathways indicate PMN responses in general and suggests an immunomodulatory role for the oPMNs. The oPMNs may therefore play a co-controlling part in the initiation and resolution of gingival inflammation.
2020-09-01 | GSE118304 | GEO
Project description:Comparison of microbiome of periodontitis, gingivitis, and healthy at pre- and post-treatment
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Project description:Dietary intake of fruits and vegetables (FV) has been inversely associated with lower risk of ulcerative colitis. A pig model was used to evaluate the impact of feeding FV on the host response to dextran sulfate sodium (DSS)-induced colitis. Methods: Six-week-old pigs were fed a grower diet alone or supplemented with lyophilized FV equivalent to the half (half-FV) or full (full-FV) daily levels recommended for humans by the Dietary Guidelines for Americans (DGA). Pigs were fed a 1) grower diet alone (negative control), 2) grower diet and orally treated with 4% DSS for 10 days to induce colitis (positive control), 3) half-FV diet treated with 4% DSS or 4) full-FV diet treated with 4% DSS. Pigs were monitored for the development of clinical signs of colitis. Proximal colon (PC) contents and mucosa (PCM) were collected for gut metagenome, tissue transcriptome and histopathological analysis. Results: Pigs fed the full-FV diet did not exhibit diarrhea, showed less fecal occult blood (FOB), PCM crypt hyperplasia but with no differential expressed genes (DEG) or changes in PC microbiome diversity (p < 0.05). Pigs within the half-FV group exhibited increased group FOB and DEG associated with tissue remodeling, crypt and goblet cell hyperplasia in the PCM and no changes in PC microbiome diversity and two pigs exhibiting diarrhea (p < 0.05). Pigs within the DSS positive control group exhibited a reduced DEG involved with intestinal immune response and PC microbiome diversity with altered metagenome, increased group PCM erosion and FOB with persistent diarrhea in one pig (p < 0.05) Conclusions: Overall, our results showed that pigs fed a three-week full-FV supplemented diet, were resistant to DSS-induced colitis with a differential dose-dependent protective effect on host intestinal tissue and gut metagenome when exposed to an inflammatory challenge.
2026-04-01 | GSE317287 | GEO