Dataset Information

Development of the Tonsil Microbiome in Pigs and Effects of Stress on the Microbiome.

ABSTRACT: Tonsils, lympho-epithelial tissues located at the junction of the oropharynx and nasopharynx, play a key role in surveillance, colonization, and persistence of inhaled and ingested pathogens. In pigs, the tonsils are a reservoir for numerous bacteria and viruses, including host-specific pathogens and potential zoonotic pathogens as well as commensal organisms. However, there are no in depth studies of the development of the tonsillar microbiome in pigs, or any mammal, over time. The goal of this study was to follow the development of the tonsil microbiome in healthy pigs from birth to market weight. Samples were collected using tonsil brushes from 16 piglets (4 each from 4 sows) at newborn, 1, 2, 3, and 4 weeks of age, and from 8 of those piglets at 6, 8, 10, 12, 16, and 19 weeks of age. Bacterial DNA was isolated from each sample and 16S rDNA genes were amplified and sequenced. Sequence analysis showed that members of the Streptococcaceae, Pasteurellaceae, and Moraxellaceae were present at all time points and represent the three most abundant families identified. Other community members appeared transiently or increased or decreased significantly with disruption events or stress. We observed four significant shifts in the tonsil community that coincided with well-defined disruption events: weaning plus addition of Carbadox plus movement to the nursery at week 3, removal of Carbadox and addition of Tylan at week 5, removal of Tylan and habitat change at week 9, and habitat change at week 16. Weaning triggered a bloom of Streptococcaeae and decrease of Moraxellaceae. The shift from Carbadox to Tylan led to reduction in Proteobacteria and Streptococcaceae but an increase in other Firmicutes, accompanied by a dramatic increase in community richness. Cessation of Tylan coincided with a return to a less rich community, and a bloom in Clostridiales. The final shift in habitat was accompanied by a decrease in Clostridiales and increase in Proteobacteria. The tonsillar microbiome of older pigs resembled the previously described mature core tonsillar microbiome. This study demonstrates a temporal succession in the development of the pig tonsillar microbiome, and significant community shifts that correlate with disruption events.

SUBMITTER: Pena Cortes LC

PROVIDER: S-EPMC6156429 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Development of the Tonsil Microbiome in Pigs and Effects of Stress on the Microbiome.

Pena Cortes Luis Carlos LC LeVeque Rhiannon M RM Funk Julie A JA Marsh Terence L TL Mulks Martha H MH

Frontiers in veterinary science 20180919

Tonsils, lympho-epithelial tissues located at the junction of the oropharynx and nasopharynx, play a key role in surveillance, colonization, and persistence of inhaled and ingested pathogens. In pigs, the tonsils are a reservoir for numerous bacteria and viruses, including host-specific pathogens and potential zoonotic pathogens as well as commensal organisms. However, there are no in depth studies of the development of the tonsillar microbiome in pigs, or any mammal, over time. The goal of this ...[more]

PMID: 30283792

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Project description:Introduction: Methoxychlor (MXC) is an organochlorine pesticide (OCP) that was formerly used worldwide as an insecticide against pests and mosquitoes. However, MXC is not biodegradable and has lipophilic characteristics; thus, it accumulates in organisms and affects reproductive function. MXC, as an estrogenic compound, promotes oxidative stress, induces oxidative stress damage to ovarian follicles, and causes miscarriages and stillbirths in females. In this research endeavor, our primary objective was to explore the ramifications of MXC regarding the developmental processes occurring during the initial stages of embryogenesis in pigs. Methods: In this study, we counted the blastocyst rate of early embryos cultured in vitro. We also examined the reactive oxygen species level, glutathione level, mitochondrial membrane potential, mitochondrial copy number and ATP level in four-cell stage embryos. Finally, apoptosis and DNA damage in blastocyst cells, as well as pluripotency-related and apoptosis-related genes in blastocyst cells were detected. The above experiments were used to evaluate the changes of MXC damage on early parthenogenetic embryo development. Results and Discussion: The results showed that early embryos exposed to MXC had a significantly lower cleavage rate, blastocyst rate, hatching rate, and total cell count compared with the control group. It was also of note that MXC not only increased the levels of reactive oxygen species (ROS), but also decreased the mitochondrial membrane potential (ΔΨm) and mitochondrial copy number during the development of early embryos. In addition, after MXC treatment, blastocyst apoptosis and DNA damage were increased, decreased cell proliferation, and the expression of pluripotency-related genes SOX2, NANOG, and OCT4 was down-regulated, while the expression of apoptosis-related genes BAX/BCL-2 and Caspase9 was up-regulated. Our results clearly show that MXC can have deleterious effects on the developmental processes of early porcine embryos, establishing the toxicity of MXC to the reproductive system. In addition, the study of this toxic effect may lead to greater concern about pesticide residues in humans and the use of safer pesticides, thus potentially preventing physiological diseases caused by chemical exposure.

Project description:Antibiotics are widely used in pig farming across the world which has led to concerns about the potential impact on human health through the selection of antibiotic resistant pathogenic bacteria. This worry has resulted in the development of a production scheme known as pigs Raised Without Antibiotics (RWA), in which pigs are produced in commercial farms, but are ear-tagged as RWA until slaughter unless they receive treatment, thus allowing the farmer to sell the pigs either as premium priced RWA or as conventional meat. Development of antibiotic resistance in pig farming has been studied in national surveys of antibiotic usage and resistance, as well as in experimental studies of groups of pigs, but not in individual pigs followed longitudinally in a commercial pig farm. In this study, a cohort of RWA designated pigs were sampled at 10 time points from birth until slaughter along with pen-mates treated with antibiotics at the same farm. From these samples, the microbiome, determined using 16S sequencing, and the resistome, as determined using qPCR for 82 resistance genes, was investigated, allowing us to examine the difference between RWA pigs and antibiotic treated pigs. We furthermore included 176 additional pigs from six different RWA farms which were sampled at the slaughterhouse as an endpoint to substantiate the cohort as well as for evaluation of intra-farm variability. The results showed a clear effect of age in both the microbiome and resistome composition from early life up until slaughter. As a function of antibiotic treatment, however, we observed a small but significant divergence between treated and untreated animals in their microbiome composition immediately following treatment, which disappeared before 8 weeks of age. The effect on the resistome was evident and an effect of treatment could still be detected at week 8. In animals sampled at the slaughterhouse, we observed no difference in the microbiome or the resistome as a result of treatment status but did see a strong effect of farm origin. Network analysis of co-occurrence of microbiome and resistome data suggested that some resistance genes may be transferred through mobile genetic elements, so we used Hi-C metagenomics on a subset of samples to investigate this. We conclude that antibiotic treatment has a differential effect on the microbiome vs. the resistome and that although resistance gene load is increased by antibiotic treatment load, this effect disappears before slaughter. More studies are needed to elucidate the optimal way to rear pigs without antibiotics.

Project description:BackgroundThe tonsil of the soft palate in pigs is the colonization site of both commensal and pathogenic microbial agents. Streptococcus suis infections are a significant economic problem in the swine industry. The development of S. suis disease remains poorly understood. The purpose of this study was to identify whether the tonsillar microbiota profile in nursery pigs is altered with S. suis disease. Here, the dynamics of the tonsillar microbiota from 20 healthy pigs and 43 diseased pigs with S. suis clinical signs was characterized.ResultsBased on the presence or absence of S. suis in the systemic sites, diseased pigs were classified into confirmed (n = 20) or probable (n = 23) group, respectively. Microbiota composition was assessed using the V3-V4 hypervariable region of the 16S rRNA, and results were analyzed to identify the diversity of the tonsillar microbiota. The taxonomic composition of the tonsil microbiota proved to be highly diverse between individuals, and the results showed statistically significant microbial community structure among the diagnosis groups. The confirmed group had the lowest observed species richness while the probable group had higher phylogenetics diversity level compared to the healthy group. Un-weighted Unifrac also demonstrated that the probable group had a higher beta diversity than both the healthy and the confirmed group. A Dirichlet-multinomial mixture (DMM) model-based clustering method partitioned the tonsil microbiota into two distinct community types that did not correspond with disease status. However, there was an association between Streptococcus suis serotype 2 and DMM community type 1 (p = 0.03). ANCOM-BC identified 24 Streptococcus amplicon sequence variants (ASVs) that were differentially abundant between the DMM community types.ConclusionsThis study provides a comprehensive analysis of the structure and membership of the tonsil microbiota in nursery pigs and uncovers differences and similarities across varying S. suis disease status. While the overall abundance of Streptococcus was not different among the diagnosis groups, the unique profile of DMM community type 1 and the observed correlation with S. suis serotype 2 could provide insight into potential tonsillar microbiota involvement in S. suis disease.

Dataset Information

Development of the Tonsil Microbiome in Pigs and Effects of Stress on the Microbiome.

Publications

Development of the Tonsil Microbiome in Pigs and Effects of Stress on the Microbiome.

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