Metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1058714 | ENA |
REPOSITORIES: ENA
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Project description:Transcriptional profiling of Day 30 embryos (D30E) was performed. First parity sows were submitted to an ovulation-induction protocol, intermittent suckling (IS), during lactation. IS consisted of 8 h/d separation from their litters during the last 7d of a 28d lactation. During separation, sows received boar exposure. There were 3 treatments: control (C28, n=19), where piglets were weaned at D28 of lactation and were bred after weaning and two IS treatments: sows were either bred at their first induced estrus during lactation (IS21FE, n=18), or were “skipped” and bred at their second estrus (IS21SE, n= 17) which occurred after final weaning at D28. Sows were slaughtered and embryos were collected on D30 of gestation for DNA PCR sexing. Later, D30E from the same sex with similar weight were pooled for further microarray investigation.
2015-09-16 | GSE73020 | GEO
Project description:Transcriptional profiling of Day 30 embryos (D30E) was performed. First parity sows were submitted to an ovulation-induction protocol, intermittent suckling (IS), during lactation. IS consisted of 8 h/d separation from their litters during the last 7d of a 28d lactation. During separation, sows received boar exposure. There were 3 treatments: control (C28, n=19), where piglets were weaned at D28 of lactation and were bred after weaning and two IS treatments: sows were either bred at their first induced estrus during lactation (IS21FE, n=18), or were “skipped” and bred at their second estrus (IS21SE, n= 17) which occurred after final weaning at D28. Sows were slaughtered and embryos were collected on D30 of gestation for DNA PCR sexing. Later, D30E from the same sex with similar weight were pooled for further microarray investigation. Stimulating lactational oestrus then two mating strategies were applied to primiparous sows. For the microarray experiment, three biological replicates (three sows) were chosen from each treatment group comparing control (C28) to either IS21FE or IS21SE. A pool of females and males D30E were chosen and pooled separately for each comparison.
2015-09-16 | E-GEOD-73020 | biostudies-arrayexpress
Project description:Seminal plasma (SP) promotes sperm survival and fertilizing capacity, but also potentially affects embryo development presumably via specific signaling to the internal genital tract. This study evaluated how heterologous SP, infused shortly before post-cervical artificial insemination (AI) affected the transcriptional pattern of the pig endometrium and embryo development rates. Post-weaning estrus sows (n= 34) received 40-mL intrauterine infusions of either heterologous pooled SP or BTS (Control) 30 minutes before AI of semen extended to 10% of homologous SP. Embryos (all sows) and endometrium samples (3 sows/group) were removed by laparotomy at day 6 after SP or BTS infusions to morphologically evaluate embryo developmental staging and the endometrial transcriptome via microarrays (PORGENE 1.0 ST GeneChip array, Affymetrix), validated by qPCR. Embryo viability was equal between groups (~93%), but embryos were significantly (P<0.05) more advanced (full/peri-hatching blastocysts) in the SP-treated group compared to control. A total of 1,604 endometrium transcripts were differentially expressed in the SP group compared to controls. An enrichment analysis depicted an overrepresentation of genes and pathways associated with immune response, cytokine signaling, cell cycle, cell adhesion, and hormone response, among others. SP-infusions prior to AI positive impacted pre-implantation embryo development by altering endometrial genes and pathways potentially involved in embryo development.
2019-10-31 | E-MTAB-7989 | biostudies-arrayexpress
Project description:We demonstrated that a maternal antibiotic treatment can change intestinal development of the offspring piglets permanently by showing that maternal gestational antibiotic treatment affects intestinal development in offspring piglets for a period of at least seven weeks after the antibiotic treatment in the sows was finished. It was shown that immediately after birth the piglets from amoxicillin treated sows, showed upregulation of genes involved in processes related to ‘tight junctions’ and ‘immunoglobulins’. In addition, these piglets had significantly lower number of goblet cells. Together, this may lead to a gut wall that is more rapidly closed in piglets from amoxicillin treated sows, affecting the uptake of immunoglobulins and the intestinal development. Later in life, around weaning, gene expression and morphological data indicate that the crypts of piglets from amoxicillin treated sows deepen around weaning as an effect of the amoxicillin treatment which in combination with the upregulation of genes involved in cell cycle processes, ribosomal activity and protein degradation might imply that the intestinal development, the subsequent differentiation of cells or the timing of these processes was delayed by the maternal antibiotic treatment.
2019-07-29 | GSE115178 | GEO
Project description:Gut microbiome research is rapidly moving towards the functional characterization of the microbiota by means of shotgun meta-omics. Here, we selected a cohort of healthy subjects from an indigenous and monitored Sardinian population to analyze their gut microbiota using both shotgun metagenomics and shotgun metaproteomics. We found a considerable divergence between genetic potential and functional activity of the human healthy gut microbiota, in spite of a quite comparable taxonomic structure revealed by the two approaches. Investigation of inter-individual variability of taxonomic features revealed Bacteroides and Akkermansia as remarkably conserved and variable in abundance within the population, respectively. Firmicutes-driven butyrogenesis (mainly due to Faecalibacterium spp.) was shown to be the functional activity with the higher expression rate and the lower inter-individual variability in the study cohort, highlighting the key importance of the biosynthesis of this microbial by-product for the gut homeostasis. The taxon-specific contribution to functional activities and metabolic tasks was also examined, giving insights into the peculiar role of several gut microbiota members in carbohydrate metabolism (including polysaccharide degradation, glycan transport, glycolysis and short-chain fatty acid production). In conclusion, our results provide useful indications regarding the main functions actively exerted by the gut microbiota members of a healthy human cohort, and support metaproteomics as a valuable approach to investigate the functional role of the gut microbiota in health and disease.
2017-07-19 | PXD005780 | Pride
Project description:Purpose: Using a C57BL6/J mouse model of diet-induced obesity, we observed that mannose supplementation of high fat diet-fed mice prevents weight gain, lowers adiposity, reduces liver steatosis, and improves glucose tolerance and insulin sensitivity. Mannose increases Bacteroidetes to Firmicutes ratio of the gut microbiota, a signature previously associated with the lean phenotype. These beneficial effects of mannose are observed when supplementation is started early (3 weeks post weaning) but are lost when started later in life (8 weeks post weaning). We profiled transcriptomes of gut microbiota from high fat diet mice supplemented with or without mannose to understand the functional differences of supplementation at 3 weeks post weaning and 8 weeks post weaning. Method: Mice were weaned on high fat diet (HFD) or high fat diet with 2% mannose in drinking water (HFDM). RNA from each mouse for each diet group was isolated individually using Ambion RiboPure Bacteria kit (ThermoFisher Scientific). 1 mg cecal RNA each from 8 mice/diet group was pooled to generate 1 pool/diet for library preparation. The quality of total RNA was assessed by the Agilent Bioanalyzer Nano chip (Agilent Technologies). Total RNA was Ribo-depleted using Ribo-Zero Gold rRNA kit (Epidemiology) (Illumina). RNA-Seq library was constructed from the recovered non-ribosomal RNAs using Truseq Stranded total RNA library preparation kit (Illumina) as per the instructions. Multiplexed libraries were pooled and single-end 50-bp sequencing was performed using an Illumina Hiseq 1500. Results: The comparison of transcriptome profiles of mice supplemented with mannose at 3 weeks post weaning and 8 weeks post weaning shows mannose reduced transcript abundance for glycosyl hydrolases and carbohydrate metabolism when supplied at 3 weeks post weaning. Conclusion: The beneficial effects of mannose in responsive mice (3 weeks post weaning) are at least in part due to reduced energy harvest by gut microbes.
2018-11-06 | GSE110794 | GEO
Project description:Early-weaning-induced stress causes diarrhea, thereby reduces growth performance of piglets. Gut bacterial dysbiosis emerges as a leading cause of post-weaning diarrhea. The present study was aimed to investigate the effect of capsulized fecal microbiota transportation (FMT) on gut bacterial community, immune response and gut barrier function of weaned piglets. Thirty-two were randomly divided into two groups fed with basal diet for 21 days. Recipient group was inoculated orally with capsulized fecal microbiota of health Tibetan pig daily morning during whole period of trial, while control group was given orally empty capsule. The results showed that the F/G ratio, diarrhea ratio, diarrhea index, and histological damage score of recipient piglets were significantly decreased. FMT treatment also significantly increased the colon length of piglets. Furthermore, the relative abundances of Firmicutes, Euryarchaeota, Tenericutes, Lactobacillus, Methanobrevibacter and Sarcina in colon of recipient piglets were increased, and the relative abundances of Campylobacter, Proteobacteria, and Melainabacteria were significantly decreased compared with control group.
2019-09-17 | GSE137470 | GEO
Project description:Primiparous sows were randomly allocated to two treatments and were separated from piglets 8h daily from Day 21 of lactation companied with daily boar exposure for oestrus detection until weaning (Day 28). Gene expression of Day 9 embryos were compared between control sows (FE; sows artificially inseminated when in heat during lactation ) and Skip-a-Heat sows (SE; sows in heat during lactation and artificially inseminated on the following oestrus cycle).
2013-12-23 | GSE53576 | GEO
Project description:Intracerebral hemorrhage (ICH) induces alterations in the gut microbiota composition, significantly impacting neuroinflammation post-ICH. However, the impact of gut microbiota absence on neuroinflammation following ICH-induced brain injury remain unexplored. Here, we observed that the gut microbiota absence was associated with reduced neuroinflammation, alleviated neurological dysfunction, and mitigated gut barrier dysfunction post-ICH. In contrast, recolonization of microbiota from ICH-induced SPF mice by transplantation of fecal microbiota (FMT) exacerbated brain injury and gut impairment post-ICH. Additionally, microglia with transcriptional changes mediated the protective effects of gut microbiota absence on brain injury, with Apoe emerging as a hub gene. Subsequently, Apoe deficiency in peri-hematomal microglia was associated with improved brain injury. Finally, we revealed that gut microbiota influence brain injury and gut impairment via gut-derived short-chain fatty acids (SCFA).
2024-05-13 | GSE266602 | GEO
Project description:Background: The etiology of Inflammatory Bowel Disease (IBD) is unclear but involves both genetics and environmental factors, including the gut microbiota. Indeed, exacerbated activation of the gastrointestinal immune system toward the gut microbiota occurs in genetically susceptible hosts and under the influence of the environment. For instance, a majority of IBD susceptibility loci lie within genes involved in immune responses, such as caspase recruitment domain member 9 (Card9). However, the relative impacts of genotype versus microbiota on colitis susceptibility in the context of CARD9 deficiency remain unknown. Results: Card9 gene directly contributes to recovery from dextran sodium sulfate (DSS)-induced colitis by inducing the colonic expression of the cytokine IL-22 and the antimicrobial peptides Reg3 and Reg3 independently of the microbiota. On the other hand, Card9 is required for regulating the microbiota capacity to produce AhR ligands, which leads to the production of IL-22 in the colon, promoting recovery after colitis. In addition, cross-fostering experiments showed that five weeks after weaning, the microbiota transmitted from the nursing mother before weaning had a stronger impact on the tryptophan metabolism of the pups than the pups' own genotype. Conclusions: These results show the role of CARD9 and its effector IL-22 in mediating recovery from DSS-induced colitis in both microbiota-independent and microbiota-dependent manners. Card9 genotype modulates the microbiota metabolic capacity to produce AhR ligands, but this effect can be overridden by the implantation of a WT or healthy microbiota before weaning. It highlights the importance of the weaning reaction occurring between the immune system and microbiota for the host metabolism and immune functions throughout life. A better understanding of the impact of genetics on microbiota metabolism is key to developing efficient therapeutic strategies for patients suffering from complex inflammatory disorders.
2024-05-01 | GSE262585 | GEO