Early Salmonella Typhimurium infection in pigs disrupts Microbiome composition and functionality principally at the ileum mucosa

Abstract

Salmonella is a major foodborne pathogen which successfully infects animal species for human consumption such as swine. The pathogen has a battery of virulence factors which it uses to colonise and persist within the host. The host microbiota may play a role in resistance to, and may also be indirectly responsible from some of the consequences of, Salmonella infection. To investigate this, we used 16S rRNA metagenomic sequencing to determine the changes in the gut microbiota of pigs in response to infection by Salmonella Typhimurium at three locations: ileum mucosa, ileum content and faeces. Early infection (2 days post-infection) impacted on the microbiome diversity at the mucosa, reflected in a decrease in representatives of the generally regarded as desirable genera (i.e., Bifidobacterium and Lactobacillus). Severe damage in the epithelium of the ileum mucosa correlated with an increase in synergistic (with respect to Salmonella infection; Akkermansia) or opportunistically pathogenic bacteria (Citrobacter) and a depletion in anaerobic bacteria (Clostridium spp., Ruminococcus, or Dialliser). Predictive functional analysis, together with metabolomic analysis revealed changes in glucose and lipid metabolism in infected pigs. The observed changes in commensal healthy microbiota, including the growth of synergistic or potentially pathogenic bacteria and depletion of beneficial or competing bacteria, could contribute to the pathogen’s ability to colonize the gut successfully. The findings from this study could be used to form the basis for further research aimed at creating intervention strategies to mitigate the effects of Salmonella infection.

Effects of Thymol and Thymol α-D-Glucopyranoside on Intestinal Function and Microbiota of Weaned Pigs

“…However, these genera were hardly detected in our samples, while the most abundant genus was undoubtedly Lactobacillus (>97%). This is in agreement with the results of Argüello et al (2018) [63] who found Lactobacillus levels of about 60% in 5 week-old piglets. Lactobacilli might have been stimulated by the lactose present in the diet (4%), as these bacteria are able to use the simple milk sugar for their energy production [66].…”

“…Proteobacteria was the second most abundant phylum in our samples, after Firmicutes. This observation is largely in agreement with the literature, although the reported relative abundances of these phyla fluctuate with values roughly ranging between 60% and 95% for Firmicutes and between 2% and 30% for Proteobacteria [62][63][64][65]. A variety of factors might explain the discrepancy between studies, such as differences in diets, antimicrobial use, age of the animals, breed, and environment [34].…”

“…Indeed, clear differences exist between the microbial communities of the small and large intestine. The jejunum and ileum show a lower bacterial diversity and an enrichment of Firmicutes relative to the large intestinal contents [62] and feces [63]. Proteobacteria was the second most abundant phylum in our samples, after Firmicutes.…”

The Influence of Ketosis on the Rectal Microbiome of Chinese Holstein Cows

“…3A). It is also dominant in pigs (Argüello et al, 2018), and plays a protective role in cirrhotic human patients (Argüello et al, 2018). The abundance of Ruminococcaceae remarkably reduced in chronic heart failure human patients compared to the controls at the genus level (Luedde et al, 2017).…”

Prevention of enteric bacterial infections and modulation of gut microbiota composition with conjugated linoleic acids producingLactobacillusin mice

“…A balanced gut microbial ecosystem serves as the crucial defense against colonization and infection with enteric pathogens [14,48,49]. Salmonella infection could have negatively impact on gut intestinal microbiome composition by diminishing the abundances of Firmicutes including Lactobacillus and Bifidobacterium, and simultaneously favoring the dominance of Proteobacteria inducing follow-up opportunistic infections [50–52]. In our study, we observed the raised abundances of Salmonella and Enterobacter with overall reduced bacterial species diversity following ST challenge in mice, whereas LC + mcra pre-administration successfully prevented the negative shifting of gut microbiota composition induced by ST infection.…”