Gut Microbiota Composition and Diversity in Different Commercial Swine Breeds in Early and Finishing Growth Stages.
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ABSTRACT:
SUBMITTER: Ma J
PROVIDER: S-EPMC9264831 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Subclinical doses of antimicrobials are commonly used in the swine industry to control infectious diseases and growth performance. Accumulating evidence suggests that swine administered with antibiotics are susceptible to disease development due to disruption of the beneficial gut microbial community, which is associated with host immune regulation, nutrient digestion, and colonization resistance against pathogens. In this study, we found that finishing swine administered with lincomycin showed gut dysbiosis and increased diarrhea incidence compared with control swine. 16S rRNA amplicon sequencing was used to analyze the gut microbiota in finishing swine administered with lincomycin. The relative abundance of detrimental microbes, such as species of Clostridium, Aerococcus, Escherichia-Shigella, and Corynebacterium was increased in the feces of lincomycin-administered finishing swine, but that of bacteria associated with fiber degradation, such as species of Treponema, Succinivibrio, Fibrobacter, and Cellulosilyticum was decreased. Moreover, administration of lincomycin significantly increased the enrichment of metabolic pathways related to pathogenicity and deficiency of polysaccharide degradation. These results suggest that lincomycin treatment could cause severe disruption of the commensal microbiota in finishing swine.
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Project description:BackgroundFeed efficiency is a crucial parameter in swine production, given both its economic and environmental impact. The gut microbiota plays an essential role in nutrient digestibility and is, therefore, likely to affect feed efficiency. This study aimed to characterize feed efficiency, fatness traits, and gut microbiome composition in three major breeds of domesticated swine and investigate a possible link between feed efficiency and gut microbiota composition.ResultsAverage daily feed intake (ADFI), average daily gain (ADG), feed conversion ratio (FCR), residual feed intake (RFI), backfat, loin depth, and intramuscular fat of 615 pigs belonging to the Duroc (DR), Landrace (LR), and Large White (LW) breeds were measured. Gut microbiota composition was characterized by 16S rRNA gene sequencing. Orthogonal contrasts between paternal line (DR) and maternal lines (LR+LW) and between the two maternal lines (LR versus LW) were performed. Average daily feed intake and ADG were statistically different with DR having lower ADFI and ADG compared to LR and LW. Landrace and LW had a similar ADG and RFI, with higher ADFI and FCR for LW. Alpha diversity was higher in the fecal microbial communities of LR pigs than in those of DR and LW pigs for all time points considered. Duroc communities had significantly higher proportional representation of the Catenibacterium and Clostridium genera compared to LR and LW, while LR pigs had significantly higher proportions of Bacteroides than LW for all time points considered. Amplicon sequence variants from multiple genera (including Anaerovibrio, Bacteroides, Blautia, Clostridium, Dorea, Eubacterium, Faecalibacterium, Lactobacillus, Oscillibacter, and Ruminococcus) were found to be significantly associated with feed efficiency, regardless of the time point considered.ConclusionsIn this study, we characterized differences in the composition of the fecal microbiota of three commercially relevant breeds of swine, both over time and between breeds. Correlations between different microbiome compositions and feed efficiency were established. This suggests that the microbial community may contribute to shaping host productive parameters. Moreover, our study provides important insights into how the intestinal microbial community might influence host energy harvesting capacity. A deeper understanding of this process may allow us to modulate the gut microbiome in order to raise more efficient animals. Video Abstract.
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Project description:Triatoma rubrofasciata (T. rubrofasciata), one kind of triatomine insects, is the vector of Trypanosoma cruzi (T. cruzi), which lead to American trypanosomiasis. Although the gut microbiome may play an essential role in the development and susceptibility of triatomine, there is limited research on the gut microbiota of T. rubrofasciata. To elucidate the effect of the vector's developmental stages and environmental conditions on the gut microbiome, we employed 16S rRNA gene sequencing to profile the gut bacterial community diversity and composition of T. rubrofasciata. Significant shifts were observed in the overall gut microbe diversity and composition across the development of T. rubrofasciata and specific bacteria were detected in different stages. Serratia and Burkholderia-Caballeronia-Paraburkholderia were dominant in the 1st nymphal stage, while the abundance of Staphylococcus was low in the 1st nymphal stage. Oceanicaulis were undetectable in the adult stage and Odoribacter peaked in the 2nd nymphal stage. Moreover, Staphylococcus was correlated negatively with Serratia. Likewise, the total gut microbiota diversity and composition of T. rubrofasciata differentiated significantly by environmental conditions. The ingestion of a bloodmeal increased alpha diversity of gut bacterial communities, and Staphylococcus was more abundant in laboratory-reared bugs whereas Enterococcus enriched in wild-caught bugs. Furthermore, Pantoea was negatively correlated with Staphylococcus, and positively related to Bacillus only. The phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) algorithm showed obvious metagenomic functional differences by environmental conditions, and Chagas disease relevant pathway was enriched in wild-caught T. rubrofasciata.
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Project description:Fully understanding the dynamic distribution of the gut microbiota in pigs is essential, as gut microorganisms play a fundamental role in physiological processes, immunity, and the metabolism of nutrients by the host. Here, we first summarize the characteristics and the dynamic shifts in the gut microbial community of pigs at different ages based on the results of 63 peer-review publications. Then a meta-analysis based on the sequences from 16 studies with accession numbers in the GenBank database is conducted to verify the characteristics of the gut microbiota in healthy pigs. A dynamic shift is confirmed in the gut microbiota of pigs at different ages and growth phases. In general, Bacteroides, Escherichia, Clostridium, Lactobacillus, Fusobacterium, and Prevotella are dominant in piglets before weaning, then Prevotella and Aneriacter shift to be the predominant genera with Fusobacterium, Lactobacillus, and Miscellaneous as comparative minors in postweaned pigs. A number of 19 bacterial genera, including Bacteroides, Prevotella, and Lactobacillus can be found in more than 90% of pigs and three enterotypes can be identified in all pigs at different ages, suggesting there is a "core" microbiota in the gut of healthy pigs, which can be a potential target for nutrition or health regulation. The "core" members benefit the growth and gut health of the host. These findings help to define an "optimal" gut microbial profile for assessing, or improving, the performance and health status of pigs at different growth stages. IMPORTANCE The ban on feed antibiotics by more and more countries, and the expected ban on ZnO in feed supplementation from 2022 in the EU, urge researchers and pig producers to search for new alternatives. One possible alternative is to use the so-called "next-generation probiotics (NGPs)" derived from gastrointestinal tract. In this paper, we reveal that a total of 19 "core" bacterial genera including Bacteroides, Prevotella, and Lactobacillus etc., can be found in more than 90% of healthy pigs across different ages. These identified genera may probably be the potential candidates of NGPs or the potential target of microflora regulation. Adding substrates preferred by these target microbes will help to increase the abundance of specific symbiotic species and benefit the gut health of pigs. Further research targeting these "core" microbes and the dynamic distribution of microbiota, as well as the related function is of great importance in swine production.
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Project description:BackgroundThe apple snail, Pomacea canaliculata, is one of the world's 100 worst invasive alien species and vector of some pathogens relevant to human health.MethodsOn account of the importance of gut microbiota to the host animals, we compared the communities of the intestinal microbiota from P. canaliculata collected at different developmental stages (juvenile and adult) and different sexes by using high-throughput sequencing.ResultsThe core bacteria phyla of P. canaliculata gut microbiota included Tenericutes (at an average relative abundance of 45.7 %), Firmicutes (27.85 %), Proteobacteria (11.86 %), Actinobacteria (4.45 %), and Cyanobacteria (3.61 %). The female group possessed the highest richness values, whereas the male group possessed the lowest bacterial richness and diversity compared with the female and juvenile group. Both the developmental stages and sexes had important effects on the composition of the intestinal microbiota of P. canaliculata. By LEfSe analysis, microbes from the phyla Proteobacteria and Actinobacteria were enriched in the female group, phylum Bacteroidetes was enriched in the male group, family Mycoplasmataceae and genus Leuconostoc were enriched in the juvenile group. PICRUSt analysis predicted twenty-four metabolic functions in all samples, including general function prediction, amino acid transport and metabolism, transcription, replication, recombination and repair, carbohydrate transport and metabolism, etc. CONCLUSIONS: This study provided a general understanding of the diversity characteristics of intestinal microbial communities of P. canaliculata, and indicated that developmental stage and gender could both influence the intestinal microbes of P. canaliculata. Further study may focus on the interaction between the gut microbiota and their host.
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Project description:BackgroundThe interplay between the gut microbiota and feeding behavior has consequences for host metabolism and health. The present study aimed to explore gut microbiota overall influence on feeding behavior traits and to identify specific microbes associated with the traits in three commercial swine breeds at three growth stages. Feeding behavior measures were obtained from 651 pigs of three breeds (Duroc, Landrace, and Large White) from an average 73 to 163 days of age. Seven feeding behavior traits covered the information of feed intake, feeder occupation time, feeding rate, and the number of visits to the feeder. Rectal swabs were collected from each pig at 73 ± 3, 123 ± 4, and 158 ± 4 days of age. DNA was extracted and subjected to 16 S rRNA gene sequencing.ResultsDifferences in feeding behavior traits among breeds during each period were found. The proportion of phenotypic variances of feeding behavior explained by the gut microbial composition was small to moderate (ranged from 0.09 to 0.31). A total of 21, 10, and 35 amplicon sequence variants were found to be significantly (q-value < 0.05) associated with feeding behavior traits for Duroc, Landrace, and Large White across the three sampling time points. The identified amplicon sequence variants were annotated to five phyla, with Firmicutes being the most abundant. Those amplicon sequence variants were assigned to 28 genera, mainly including Christensenellaceae_R-7_group, Ruminococcaceae_UCG-004, Dorea, Ruminococcaceae_UCG-014, and Marvinbryantia.ConclusionsThis study demonstrated the importance of the gut microbial composition in interacting with the host feeding behavior and identified multiple archaea and bacteria associated with feeding behavior measures in pigs from either Duroc, Landrace, or Large White breeds at three growth stages. Our study provides insight into the interaction between gut microbiota and feeding behavior and highlights the genetic background and age effects in swine microbial studies.
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Project description:Recently, interest in the function of pig backfat (BF) has increased in the field of livestock animals, and many transcriptome-based studies using commercial pig breeds have been conducted. However, there is a lack of comprehensive studies regarding the biological mechanisms of Korean native pigs (KNPs) and Yorkshire pig crossbreeds. In this study, therefore, BF samples of F1 crossbreeds of KNPs and Yorkshire pigs were investigated to identify differentially expressed genes (DEGs) and their related terms using RNA-sequencing analysis. DEG analysis identified 611 DEGs, of which 182 were up-regulated and 429 were down-regulated. Lipid metabolism was identified in the up-regulated genes, whereas growth and maturation-related terminologies were identified in the down-regulated genes. LEP and ACTC1 were identified as highly connected core genes during functional gene network analysis. Fat tissue was observed to affect lipid metabolism and organ development due to hormonal changes driven by transcriptional alteration. This study provides a comprehensive understanding of BF contribution to crossbreeds of KNPs and Yorkshire pigs during growth periods.
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Project description:This study investigated the effect of a low protein (LP) diet on growth performance, nitrogen emission, carcass traits, meat quality, and gut microbiota in finishing pigs. Fifty-four barrows (Duroc × Landrace × Yorkshire) were randomly assigned to three treatments with six replicates (pens) of three pigs each. The pigs were fed with either high protein (HP, 16% CP), medium protein (MP, 12% CP), and LP diets (10% CP), respectively. The LP diets did not influence the growth performance, but significantly decreased the plasma urea nitrogen contents and fecal nitrogen emission (P < 0.05). The LP diet significantly decreased the plasma contents of malondialdehyde (MDA) and increased the plasma glutathione (GSH) contents (P < 0.05). The LP diets significantly increased the backfat thickness at the first and last ribs, L* (lightness) value of meat color, and muscle fiber density in the longissimus dorsi (P < 0.05). The messenger RNA (mRNA) expression of fatty acid synthetase (FAS), peroxisome proliferator-activated receptor-gamma (PPARγ), leptin, and acetyl-CoA carboxylase (ACC) was significantly downregulated, while that of carnitine palmitoyltransferase 1 (CPT1) and myosin heavy chain (MYHC) IIx in the longissimus Dorsi muscle was significantly upregulated by LP diets (P < 0.05). The 16S sequencing analysis showed that the abundance of unidentified Bacteria at the phylum level, and Halanaerobium and Butyricicoccusat at the genus level in the colonic digesta were significantly decreased by LP diet (P < 0.05). The LP diet significantly decreased the observed species of α-diversity in both ileal and colonic microbiota (P < 0.05). Spearman correlation analysis identified a significant positive correlation between the abundance of the ileal genera Streptococcus and L* value at 24 and 48 h, and a significant negative correlation between unidentified_Ruminococcasceae in both ileum and colon with L* value at 24 h (P < 0.05). Collectively, the LP diet supplemented with lysine, methionine, threonine, and tryptophan could reduce the fecal nitrogen emission without affecting growth performance and improve meat quality by regulating the antioxidant capacity and gene expression involved in fat metabolism as well as modulating the gut microbiota composition in finishing pigs.
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