Environmental metagenome from CAVES
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ABSTRACT:
PROVIDER: PRJNA610730 | ENA |
REPOSITORIES: ENA
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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.
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Project description:BACKGROUND:Nowadays, not only are single genomes commonly analyzed, but also metagenomes, which are sets of, DNA fragments (reads) derived from microbes living in a given environment. Metagenome analysis is aimed at extracting crucial information on the organisms that have left their traces in an investigated environmental sample.In this study we focus on the MetaSUB Forensics Challenge (organized within the CAMDA 2018 conference) which consists in predicting the geographical origin of metagenomic samples. Contrary to the existing methods for environmental classification that are based on taxonomic or functional classification, we rely on the similarity between a sample and the reference database computed at a reads level. RESULTS:We report the results of our extensive experimental study to investigate the behavior of our method and its sensitivity to different parameters. In our tests, we have followed the protocol of the MetaSUB Challenge, which allowed us to compare the obtained results with the solutions based on taxonomic and functional classification. CONCLUSIONS:The results reported in the paper indicate that our method is competitive with those based on taxonomic classification. Importantly, by measuring the similarity at the reads level, we avoid the necessity of using large databases with annotated gene sequences. Hence our main finding is that environmental classification of metagenomic data can be proceeded without using large databases required for taxonomic or functional classification. REVIEWERS:This article was reviewed by Eran Elhaik, Alexandra Bettina Graf, Chengsheng Zhu, and Andre Kahles.
| S-EPMC6854650 | biostudies-literature