Gut microbiome modifications over time when removing in-feed antibiotics from the prophylaxis of post-weaning diarrhea in piglets
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ABSTRACT:
PROVIDER: PRJEB45296 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR7815500_1.fastq.gz | Fastqsanger.gz | |||
| ERR7815500_2.fastq.gz | Fastqsanger.gz | |||
| ERR7815510_1.fastq.gz | Fastqsanger.gz | |||
| ERR7815510_2.fastq.gz | Fastqsanger.gz | |||
| ERR7815520_1.fastq.gz | Fastqsanger.gz |
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Project description:Post-weaning diarrhea (PWD) in pigs has mainly an infectious basis and control strategies are centred on antibiotics added to the diet. Given concerns on the spread of multi-resistant bacteria, it is necessary to develop alternative prophylactic approaches to control PWD in piglets. The most promising alternative strategies are based on substances that act indirectly on the bacteria by stimulating the immune system or by improving gut health. The aim of this study was to evaluate the effect on the gut microbiota of feed supplemented with a mixture of essential oils (garlic and oregano) in weaning piglets, compared to traditional PWD management (in-feed antibiotics) and to a control group without any diet supplementation. The study involved 197 piglets from 18 litters in a single farm. The piglets were followed from birth to day 58 of age and were weaned at day 26. During the experimental period, the animals were monitored for weight and growth, average daily gain, morbidity and mortality. For the metataxonomics analysis, rectal samples were collected from 17 piglets from the three experimental groups at 4 different time-points (days 1, 12, 26 and 58). Results revealed that the gut microbiota in pre- and post-weaning piglets was dominated by the phyla Firmicutes (51%), Bacteroidetes (25%) and Proteobacteria (16%), which together make up for over 90% of the entire piglet core gut microbiota. The core microbiota comprised 10 taxa before weaning and 43 taxa after weaning, with 7 taxa overlapping between timepoints: two of them (Prevotella 9, p-value = 0.00095; Solobacterium p-value = 0.00821) were significantly more abundant after weaning. All alpha diversity indexes were significantly different between pre- and post-weaning, while only Shannon and Simpson diversity and equitability were significantly different between treatments. Based on the matrix of Bray-Curtis dissimilarities, samples showed clear clustering per timepoint (before and after weaning, p-value < 0.001) and between treatments by timepoint (p-value = 0.0086). The oil-diet group showed a consistently higher F:B ratio at all timepoints. These results show that the pig gut microbiota changes significantly with weaning, and suggest that the use of essential oils as feed supplementation to control PWD does not seem to alter sgnificantly the microbiota nor the growth parameters of piglets, however modifications of specific taxa may occur.
| S-EPMC8901073 | biostudies-literature
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:MicroRNAs (miRNAs) in serum are very stable and specific. Moreover, serum miRNAs are non-destructive and convenient. Studies have shown that the changes of serum miRNAs are closely relative to the pathological stresses and diseases. Our previous studies suggested that weaning stress induced the abnormal miRNA transcriptome in the intestine of piglets. In this project, we will further screen serum miRNA expression in piglets induced by weaning stress using miRNA microarray. Microarrays containing 422 porcine unique miRNA probes were employed to identify differences in the expression patterns of the miRNA between weaning piglets at 4 d after weaning and suckling piglets at the same days old. A total of 115 differentally expressed miRNAs were found,therein 63 miRNAs upregulated and 52 miRNA downregulated; 64 miRNAs are statistically significant but have low signals (signal < 500);122 miRNAs are not statistically significant (p > 0.01); the remaining 132 miRNAs have not detected signals.
2016-09-21 | GSE69920 | GEO
Project description:BackgroundPost weaning diarrhoea (PWD) causes piglet morbidity and mortality at weaning and is a major driver for antimicrobial use worldwide. New regulations in the EU limit the use of in-feed antibiotics (Ab) and therapeutic zinc oxide (ZnO) to prevent PWD. New approaches to control PWD are needed, and understanding the role of the microbiota in this context is key. In this study, shotgun metagenome sequencing was used to describe the taxonomic and functional evolution of the faecal microbiota of the piglet during the first two weeks post weaning within three experimental groups, Ab, ZnO and no medication, on commercial farms using antimicrobials regularly in the post weaning period.ResultsDiversity was affected by day post weaning (dpw), treatment used and diarrhoea but not by the farm. Microbiota composition evolved towards the dominance of groups of species such as Prevotella spp. at day 14dpw. ZnO inhibited E. coli overgrowth, promoted higher abundance of the family Bacteroidaceae and decreased Megasphaera spp. Animals treated with Ab exhibited inconsistent taxonomic changes across time points, with an overall increase of Limosilactobacillus reuteri and Megasphaera elsdenii. Samples from non-medicated pigs showed virulence-related functions at 7dpw, and specific ETEC-related virulence factors were detected in all samples presenting diarrhoea. Differential microbiota functions of pigs treated with ZnO were related to sulphur and DNA metabolism, as well as mechanisms of antimicrobial and heavy metal resistance, whereas Ab treated animals exhibited functions related to antimicrobial resistance and virulence.ConclusionAb and particularly ZnO maintained a stable microbiota composition and functionality during the two weeks post weaning, by limiting E. coli overgrowth, and ultimately preventing microbiota dysbiosis. Future approaches to support piglet health should be able to reproduce this stable gut microbiota transition during the post weaning period, in order to maintain optimal gut physiological and productive conditions.
| S-EPMC11022352 | biostudies-literature
Project description:ObjectiveThe aim of this study was to examine shifts in the composition of the bacterial population in the intestinal tracts (ITs) of weaning piglets by antibiotic treatment using high-throughput sequencing.MethodsSixty 28-d-old weaning piglets were randomly divided into two treatment groups. The Control group was treated with a basal diet without antibiotics. The Antibiotic group's basal diet contained colistin sulfate at a concentration of 20 g per ton and bacitracin zinc at a concentration of 40 g per ton. All of the pigs were fed for 28 days. Then, three pigs were killed, and the luminal contents of the jejunum, ileum, cecum, and colon were collected for DNA extraction and high-throughput sequencing.ResultsThe results showed that the average daily weight gain of the antibiotic group was significantly greater (p<0.05), and the incidence of diarrhea lower (p>0.05), than the control group. A total of 812,607 valid reads were generated. Thirty-eight operational taxonomic units (OTUs) that were found in all of the samples were defined as core OTUs. Twenty-one phyla were identified, and approximately 90% of the classifiable sequences belonged to the phylum Firmicutes. Forty-two classes were identified. Of the 232 genera identified, nine genera were identified as the core gut microbiome because they existed in all of the tracts. The proportion of the nine core bacteria varied at the different tract sites. A heat map was used to understand how the numbers of the abundant genera shifted between the two treatment groups.ConclusionAt different tract sites the relative abundance of gut microbiota was different. Antibiotics could cause shifts in the microorganism composition and affect the composition of gut microbiota in the different tracts of weaning piglets.
| S-EPMC5205595 | biostudies-literature
Project description:Creep feed provision may ease weaning, hence we determined the impact of providing fibrous creep feed before weaning and adding this feed to the post-weaning diet on piglet behavior and performance. Pre-weaning, litters with on average 12 piglets were given creep feed (CF, n = 12 litters) or not (NF, n = 10 litters). Post-weaning, piglets (n = 8 pens with 4 piglets/treatment) were given a weaner diet (CON) or weaner diet supplemented with creep feed (CS). Behaviors were scored in the home pen at d11, 16, 22 and 27 after birth and at wk 1 and 2 post-weaning. Feed intake, growth and fecal consistency were measured up to d14 post-weaning. A blood sample was taken at d2, 15 and 29 after birth and d2, 5 and 14 post-weaning. CF-piglets consumed on average 397 ± 71 g creep feed before weaning. CF-piglets grew faster in the last week before weaning than NF-piglets (249 ± 7 vs. 236 ± 11 g/d, F (1, 18) = 5.81, P = 0.03). However, CF- and NF-piglets did not differ in weaning weight, within-litter coefficient of variation in weaning weight, behaviors in the farrowing and weaner pen, and haptoglobin concentrations. Creep feed supplementation enhanced feed exploration at wk 2 post-weaning (0.29 ± 0.08 vs. 0.11 ± 0.03%, F (1, 27) = 5.27, P = 0.03), but did not affect other post-weaning behaviors. Pre-weaning creep feed provision and post-weaning creep feed supplementation did not affect overall feed intake, growth, feed efficiency and fecal consistency for the first 14 days post-weaning, neither body weight at d14 post-weaning. Nevertheless, CF-piglets had a lower within-pen coefficient of variation in body weight at d14 post-weaning than NF-piglets (13.6 ± 1.9 vs. 15.1 ± 1.5%, F (1, 26) = 6.89, P = 0.01). In conclusion, pre-weaning creep feed provision and post-weaning creep feed supplementation had no clear effects on piglet behavior and performance.
| S-EPMC7689248 | biostudies-literature
Project description:The weaning process represents a delicate phase for piglets, and is often characterized by lower feed intake, lower weight gain, diarrhea, and ultimately increased mortality. We aimed to determine the effects of RAC supplementation in diets on improving piglet growth and vitality, reducing post-weaning diarrhea, and enhancing gut health. In a 2 × 2 × 2 factorial experiment, we selected forty sows and their piglets. Piglets were followed until seven weeks of age. There were no significant differences found between RAC treated and control piglets until weaning (p = 0.26). However, three weeks after weaning, RAC treated piglets had higher body weight and average daily growth (ADG) than the control piglets (p = 0.003). In addition, the piglets that received RAC after weaning, irrespective of mother or prior creep feed treatment, had lower post-weaning diarrhea (PWD) and fecal myeloperoxidase (MPO) level than control piglets. Gut microbiota analysis in post-weaning piglets revealed that RAC supplementation significantly increased Lachnospiraceae_unclassified, Blautia, Butyricicoccus, Gemmiger and Holdemanella, and decreased Bacteroidales_unclassified. Overall, RAC supplementation to piglets modulated post-weaning gut microbiota, improved growth performance after weaning, reduced post-weaning diarrhea and reduced fecal myeloperoxidase levels. We therefore consider RAC to be a potential natural feed supplement to prevent enteric infections and improve growth performance in weaning piglets.
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Project description:Transcriptional profiling of 25d old piglets comparing control untreated suckling jejunum with weaned piglets' jejunum. The goal was to gain new insight into the interaction between weaning and intestinal function.A keen interest is paid in deciphering expression changes of apoptosis or cell cycle control genes. The statistical analysis of gene ontology revealed that most of these altered genes are metabolic-related enzymes and regulators which may involved in the biological regulation, developmental process, and cellular process. Weaning also causes alterations in various immune response pathways. Results likely indicate that weaning induced cell cycle arrest, enhanced apoptosis, and inhibited cell proliferation.
2014-05-01 | GSE48050 | GEO
Project description:Capsulized fecal microbiota transportation ameliorates post-weaning diarrhea through modulating the gut microbiota in piglets
| PRJNA565690 | ENA
Project description:Sixty crossbred piglets (Duroc*Landrace*Yorkshire) weaned at the age of 21 days were maintained for one week and had free access to feed and water. During this week, all the piglets were scored for the severity of diarrhea. Diarrhea index was scored as follows: 1= hard feces; 2= no scours, feces of normal consistency; 3= mild scours, soft, partially formed feces; 4= moderate scours, loose, semi-liquid feces; 5= watery feces; as previously did Those piglets with a score of 4 or 5 for three continuous days were designated as diarrhea piglets, while those piglets with a score of 1 or 2 for three continuous days were designated as normal piglets..
2022-01-03 | GSE192690 | GEO