Salmonella enterica Serovar Typhimurium Exploits Inflammation to Modify Swine Intestinal Microbiota

Rise of the guardians: Gut microbial maneuvers in bacterial infections

AIMS

Bacterial infections are one of the major causes of mortality globally. The gut microbiota, primarily comprised of the commensals, performs an important role in maintaining intestinal immunometabolic homeostasis. The current review aims to provide a comprehensive understanding of how modulation of the gut microbiota influences opportunistic bacterial infections.

MATERIALS AND METHODS

Primarily centered around mechanisms related to colonization resistance, nutrient, and metabolite-associated factors, mucosal immune response, and commensal-pathogen reciprocal interactions, we discuss how gut microbiota can promote or prevent bacterial infections.

KEY FINDINGS

Opportunistic infections can occur directly due to obligate pathogens or indirectly due to the overgrowth of opportunistic pathobionts. Gut microbiota-centered mechanisms of altered intestinal immunometabolic and metabolomic homeostasis play a significant role in infection promotion and prevention. Depletion in the population of commensals, increased abundance of pathobionts, and overall decrease in gut microbial diversity and richness caused due to prolonged antibiotic use are risk factors of opportunistic bacterial infections, including infections from multidrug-resistant spp. Gut commensals can limit opportunistic infections by mechanisms including the production of antimicrobials, short-chain fatty acids, bile acid metabolism, promoting mucin formation, and maintaining immunological balance at the mucosa. Gut microbiota-centered strategies, including the administration of probiotics and fecal microbiota transplantation, could help attenuate opportunistic bacterial infections.

SIGNIFICANCE

The current review discussed the gut microbial population and function-specific aspects contributing to bacterial infection susceptibility and prophylaxis. Collectively, this review provides a comprehensive understanding of the mechanisms related to the dual role of gut microbiota in bacterial infections.

Impact of Early Weaning on Development of the Swine Gut Microbiome

Considering that pigs are naturally weaned between 12 and 18 weeks of age, the common practice in the modern swine industry of weaning as early as between two and four weeks of age increases challenges during this transition period. Indeed, young pigs with an immature gut are suddenly separated from the sow, switched from milk to a diet consisting of only solid ingredients, and subjected to a new social hierarchy from mixing multiple litters. From the perspective of host gut development, weaning under these conditions causes a regression in histological structure as well as in digestive and barrier functions. While the gut is the main center of immunity in mature animals, the underdeveloped gut of early weaned pigs has yet to contribute to this function until seven weeks of age. The gut microbiota or microbiome, an essential contributor to the health and nutrition of their animal host, undergoes dramatic alterations during this transition, and this descriptive review aims to present a microbial ecology-based perspective on these events. Indeed, as gut microbial communities are dependent on cross-feeding relationships, the change in substrate availability triggers a cascade of succession events until a stable composition is reached. During this process, the gut microbiota is unstable and prone to dysbiosis, which can devolve into a diseased state. One potential strategy to accelerate maturation of the gut microbiome would be to identify microbial species that are critical to mature swine gut microbiomes, and develop strategies to facilitate their establishment in early post-weaning microbial communities.

Raw potato starch diet supplement in weaned pigs could reduce Salmonella Typhimurium infection by altering microbiome composition and improving immune status

Backgorund

Salmonella enterica serovar Typhimurium (ST) is one of the causative agents of gastroenteritis in pigs. Pigs fed a diet supplemented with raw potato starch (RPS) have improved gut health by the alteration of the microbiota composition and production of short-chain fatty acids (SCFAs). This study aimed to evaluate the effects of RPS supplementation in reducing infection severity and fecal shedding in ST-infected pigs.

Methods

The weaned experimental pigs were divided into two groups: CON (n = 6) fed a corn/soybean-based diet and TRT (n = 6) supplemented with 5% RPS. After 21 d, the pigs were inoculated with ST, and their body weight, clinical signs, and fecal shedding of ST were monitored for 14 d. At 14 d post-inoculation (dpi), the jejunum, cecum, ileum, and colon tissues were collected from euthanized pigs, and histopathological lesions and cytokine gene expression were compared. Additionally, blood samples at 2 dpi were analyzed for gene ontology enrichment. Moreover, the gutmicrobiome was analyzed using 16S rRNA metagenomic sequencing, and the SCFA concentration was measured using gas chromatography.

Results

The average daily weight gain was significantly higher in TRT than in CON during the ST infection period; however, histopathological lesion scores were significantly lower in TRT than in CON. The relative abundance of nine genera of butyrate- and acetate-producing bacteria significantly increased in TRT compared with that of only two acetate-producing bacteria in CON. Among the genes involved in the immune response, IL-18 expression level was significantly lower in the jejunum and colon in TRT than in CON. Furthermore, Reg3γ expression was significantly different in the cecum and colon of both groups.

Conclusion

The diet supplemented with RPS in weaned pigs could result in predominance of butyrate- and acetate-producing bacteria, reducing the severity of ST infection by improving the immune status.

Timing and delivery route effects of cecal microbiome transplants on Salmonella Typhimurium infections in chickens: potential for in-hatchery delivery of microbial interventions

BACKGROUND

Exposure to microbes early in life has long-lasting effects on microbial community structure and function of the microbiome. However, in commercial poultry settings chicks are reared as a single-age cohort with no exposure to adult birds which can have profound effects on microbiota development and subsequent pathogen challenge. Microbiota manipulation is a proven and promising strategy to help reduce pathogen load and transmission within broiler flocks. However, administration of microbiota transplant products in a hatchery setting may prove challenging. Effective administration strategies are dependent on key factors, such as; the age of chicks receiving interventions and mode of delivery. This study aimed to assess these two aspects to provide supporting evidence towards microbiome manipulation strategies for use in commercial hatcheries.

RESULTS

Manipulation of the microbiota between 4 and 72 h of hatch markedly reduced faecal shedding and colonisation with the foodborne pathogen Salmonella enterica serovar Typhimurium (ST4/74). Administration of transplant material via spray or gel drop delivery systems had minimal effect on the protection conferred with fewer birds in transplant groups shown to shed ST4/74 in the faeces compared to PBS-gavaged control birds. Analysis of the microbiome following transplantation demonstrated that all transplant groups had higher diversity and species richness than non-transplant groups during the first week of life and the early stages of infection with ST47/4.The relative abundance of the bacterium Faecalibacterium prausnitzii was significantly higher in CMT groups compared to PBS controls. The presence of F. prausnitzii was also shown to increase in PBS-challenged birds compared to unchallenged birds potentially indicating a role of this bacterium in limiting Salmonella infections.

CONCLUSIONS

This study demonstrated that administration of microbiome transplants, using methods that would align with hatchery practices, effectively reduced colonisation and shedding of Salmonella in chickens. Age of chicks at microbiome administration had limited effect on the diversity and composition of the microbiome and conferred protection against Salmonella infections. Traditional hatchery delivery systems, such as spray or gel-drop, are sufficient to transfer donor material, alter the microbiome and confer protection against Salmonella. This study helps highlight the opportunity for use of microbiome modification methods within the hatchery.

Neglected gut microbiome: interactions of the non-bacterial gut microbiota with enteric pathogens

A diverse array of commensal microorganisms inhabits the human intestinal tract. The most abundant and most studied members of this microbial community are undoubtedly bacteria. Their important role in gut physiology, defense against pathogens, and immune system education has been well documented over the last decades. However, the gut microbiome is not restricted to bacteria. It encompasses the entire breadth of microbial life: viruses, archaea, fungi, protists, and parasitic worms can also be found in the gut. While less studied than bacteria, their divergent but important roles during health and disease have become increasingly more appreciated. This review focuses on these understudied members of the gut microbiome. We will detail the composition and development of these microbial communities and will specifically highlight their functional interactions with enteric pathogens, such as species of the family Enterobacteriaceae. The interactions can be direct through physical interactions, or indirect through secreted metabolites or modulation of the immune response. We will present general concepts and specific examples of how non-bacterial gut communities modulate bacterial pathogenesis and present an outlook for future gut microbiome research that includes these communities.

Weaning stress and intestinal health of piglets: A review

Weaning is considered to be one of the most critical periods in pig production, which is related to the economic benefits of pig farms. However, in actual production, many piglets are often subjected to weaning stress due to the sudden separation from the sow, the changes in diet and living environment, and other social challenges. Weaning stress often causes changes in the morphology and function of the small intestine of piglets, disrupts digestion and absorption capacity, destroys intestinal barrier function, and ultimately leads to reduced feed intake, increased diarrhea rate, and growth retardation. Therefore, correctly understanding the effects of weaning stress on intestinal health have important guiding significance for nutritional regulation of intestinal injury caused by weaning stress. In this review, we mainly reviewed the effects of weaning stress on the intestinal health of piglets, from the aspects of intestinal development, and intestinal barrier function, thereby providing a theoretical basis for nutritional strategies to alleviate weaning stress in mammals in future studies.

High-throughput sequencing-based metagenomic and transcriptomic analysis of intestine in piglets infected with salmonella

Salmonella enterica serovar Typhimurium isolate HJL777 is a virulent bacterial strain in pigs. The high rate of salmonella infection are at high risk of non-typhoidal salmonella gastroenteritis development. Salmonellosis is most common in young pigs. We investigated changes in gut microbiota and biological function in piglets infected with salmonella via analysis of rectal fecal metagenome and intestinal transcriptome using 16S rRNA and RNA sequencing. We identified a decrease in Bacteroides and increase in harmful bacteria such as Spirochaetes and Proteobacteria by microbial community analysis. We predicted that reduction of Bacteroides by salmonella infection causes proliferation of salmonella and harmful bacteria that can cause an intestinal inflammatory response. Functional profiling of microbial communities in piglets with salmonella infection showed increasing lipid metabolism associated with proliferation of harmful bacteria and inflammatory responses. Transcriptome analysis identified 31 differentially expressed genes. Using gene ontology and Innate Immune Database analysis, we identified that BGN, DCN, ZFPM2 and BPI genes were involved in extracellular and immune mechanisms, specifically salmonella adhesion to host cells and inflammatory responses during infection. We confirmed alterations in gut microbiota and biological function during salmonella infection in piglets. Our findings will help prevent disease and improve productivity in the swine industry.

High Dietary Intake of Rye Affects Porcine Gut Microbiota in a Salmonella Typhimurium Infection Study

Bacterial fermentation of undigested carbohydrates in the hindgut has considerable potential for the stimulation or inhibition of the growth of distinct bacteria within microbiota. The aim of the present study was to evaluate whether high levels of rye affect porcine gut microbiota composition with subsequent effects on the load of Salmonella Typhimurium, an intestinal pathogen with zoonotic relevance. Therefore, forty-two 25-day-old piglets were allocated to two groups and fed a diet containing either 69% wheat or 69% rye for 35 days. One week after introducing the two different diets, the piglets were experimentally infected with Salmonella Typhimurium. The microbiota composition of cecal and fecal samples of the piglets were evaluated 28 days after infection. In the cecum, promoted growth of Bifidobacterium, several lactic acid bacteria and Faecalibacterium prausnitzii were seen in pigs fed the diet containing 69% rye. Bacterial species belonging to the genera Bifidobacterium and Catenisphaera were associated with differing bacterial counts of Salmonella Typhimurium detected in the cecal contents of all piglets in both feeding groups via cultural cultivation. The high intake of rye instead of wheat seems to promote the growth of beneficial intestinal bacteria accompanied by impaired growth conditions for the foodborne pathogen Salmonella Typhimurium.

Short Chain Fatty Acids and Bacterial Taxa Associated with Reduced Salmonella enterica serovar I 4,[5],12:i:- Shedding in Swine Fed a Diet Supplemented with Resistant Potato Starch

Salmonella enterica serovar I 4,[5],12:i:- is a foodborne pathogen of concern because many isolates are multidrug-resistant (resistant to ≥3 antimicrobial classes) and metal tolerant. In this study, three in-feed additives were individually tested for their ability to reduce Salmonella I 4,[5],12:i:- shedding in swine: resistant potato starch (RPS), high amylose corn starch, and a fatty acid blend, compared with a standard control diet over 21 days. Only RPS-fed pigs exhibited a reduction in Salmonella fecal shedding, different bacterial community compositions, and different cecal short chain fatty acid (SCFA) profiles relative to control animals. Within the RPS treatment group, pigs shedding the least Salmonella tended to have greater cecal concentrations of butyrate, valerate, caproate, and succinate. Additionally, among RPS-fed pigs, several bacterial taxa (Prevotella_7, Olsenella, and Bifidobacterium, and others) exhibited negative relationships between their abundances of and the amount of Salmonella in the feces of their hosts. Many of these same taxa also had significant positive associations with cecal concentrations of butyrate, valerate, caproate, even though they are not known to produce these SCFAs. Together, these data suggest the RPS-associated reduction in Salmonella shedding may be dependent on the establishment of bacterial cross feeding interactions that result in the production of certain SCFAs. However, directly feeding a fatty acid mix did not replicate the effect. RPS supplementation could be an effective means to reduce multidrug-resistant (MDR) S. enterica serovar I 4,[5],12:i:- in swine, provided appropriate bacterial communities are present in the gut. IMPORTANCE Prebiotics, such as resistant potato starch (RPS), are types of food that help to support beneficial bacteria and their activities in the intestines. Salmonella enterica serovar I 4,[5],12:i:- is a foodborne pathogen that commonly resides in the intestines of pigs without disease, but can make humans sick if unintentionally consumed. Here we show that in Salmonella inoculated pigs, feeding them a diet containing RPS altered the colonization and activity of certain beneficial bacteria in a way that reduced the amount of Salmonella in their feces. Additionally, within those fed RPS, swine with higher abundance of these types of beneficial bacteria had less Salmonella I 4,[5],12:i:- in their feces. This work illustrates likely synergy between the prebiotic RPS and the presence of certain gut microorganisms to reduce the amount of Salmonella in the feces of pigs and therefore reduce the risk that humans will become ill with MDR Salmonella serovar I 4,[5],12:i:-.

The Game for Three: Salmonella–Host–Microbiota Interaction Models

Colonization of the gastrointestinal (GI) tract by enteric pathogens occurs in a context strongly determined by host-specific gut microbiota, which can significantly affect the outcome of infection. The complex gameplay between the trillions of microbes that inhabit the GI tract, the host, and the infecting pathogen defines a specific triangle of interaction; therefore, a complete model of infection should consider all of these elements. Many different infection models have been developed to explain the complexity of these interactions. This review sheds light on current knowledge, along with the strengths and limitations of in vitro and in vivo models utilized in the study of Salmonella–host–microbiome interactions. These models range from the simplest experiment simulating environmental conditions using dedicated growth media through in vitro interaction with cell lines and 3-D organoid structure, and sophisticated “gut on a chip” systems, ending in various animal models. Finally, the challenges facing this field of research and the important future directions are outlined.

Potential of a fucoidan-rich Ascophyllum nodosum extract to reduce Salmonella shedding and improve gastrointestinal health in weaned pigs naturally infected with Salmonella

BACKGROUND

Dietary supplementation with a fucoidan-rich Ascophyllum nodosum extract (ANE), possessing an in vitro anti-Salmonella Typhimurium activity could be a promising on-farm strategy to control Salmonella infection in pigs. The objectives of this study were to: 1) evaluate the anti-S. Typhimurium activity of ANE (containing 46.6% fucoidan, 18.6% laminarin, 10.7% mannitol, 4.6% alginate) in vitro, and; 2) compare the effects of dietary supplementation with ANE and Zinc oxide (ZnO) on growth performance, Salmonella shedding and selected gut parameters in naturally infected pigs. This was established post-weaning (newly weaned pig experiment) and following regrouping of post-weaned pigs and experimental re-infection with S. Typhimurium (challenge experiment).

RESULTS

In the in vitro assay, increasing ANE concentrations led to a linear reduction in S. Typhimurium counts (P <  0.05). In the newly weaned pig experiment (12 replicates/treatment), high ANE supplementation increased gain to feed ratio, similar to ZnO supplementation, and reduced faecal Salmonella counts on d 21 compared to the low ANE and control groups (P <  0.05). The challenge experiment included thirty-six pigs from the previous experiment that remained on their original dietary treatments (control and high ANE groups with the latter being renamed to ANE group) apart from the ZnO group which transitioned onto a control diet on d 21 (ZnO-residual group). These dietary treatments had no effect on performance, faecal scores, Salmonella shedding or colonic and caecal Salmonella counts (P > 0.05). ANE supplementation decreased the Enterobacteriaceae counts compared to the control. Enterobacteriaceae counts were also reduced in the ZnO-residual group compared to the control (P <  0.05). ANE supplementation decreased the expression of interleukin 22 and transforming growth factor beta 1 in the ileum compared to the control (P <  0.05).

CONCLUSIONS

ANE supplementation was associated with some beneficial changes in the composition of the colonic microbiota, Salmonella shedding, and the expression of inflammatory genes associated with persistent Salmonella infection.

Current knowledge and perspectives of potential impacts of Salmonella enterica on the profile of the gut microbiota

In the past decade, the initial studies of the gut microbiota started focusing on the correlation of the composition of the gut microbiota and the health or diseases of the host, and there are extensive literature reviews pertaining to this theme. However, little is known about the association between the microbiota, the host, and pathogenic bacteria, such as Salmonella enterica, which is among the most important foodborne pathogens and identified as the source of multiple outbreaks linked to contaminated foods causing salmonellosis. Secretion systems, flagella, fimbriae, endotoxins, and exotoxins are factors that play the most important roles in the successful infection of the host cell by Salmonella. Infections with S. enterica, which is a threat to human health, can alter the genomic, taxonomic, and functional traits of the gut microbiota. The purpose of this review is to outline the state of knowledge on the impacts of S. enterica on the intestinal microbiota and highlight the need to identify the gut bacteria that could contribute to salmonellosis.

Salmonella enterica Serovar Typhimurium Temporally Modulates the Enteric Microbiota and Host Responses To Overcome Colonization Resistance in Swine

Salmonella enterica serovar Typhimurium is a prevalent incitant of enteritis in human beings and nonhuman animals. It has been proposed that host defense responses incited by Salmonella allow the bacterium to overcome colonization resistance. Piglets (n = 24) were orally inoculated with S. enterica serovar Typhimurium DT104 or buffer alone, and the host and microbial responses were temporally examined at the acute (2 days postinoculation [dpi]), subacute (6 dpi), and recovery (10 dpi) stages of salmonellosis. At the acute stage of disease, body temperatures were elevated, and feed consumption and weight gain were reduced. The densities of Salmonella associated with the gut mucosa decreased over time, with higher densities of the bacterium in the ileum and the large intestine. Moreover, substantive histopathological changes were observed as a function of time, with prominent epithelial injury and neutrophil infiltration observed at 2 dpi. Correspondingly, a variety of host metrics were temporally affected in piglets with salmonellosis (e.g., TNFα, IFNγ, PR39, βD2, iNOS, IL8, REGIIIγ). The enteric microbiota was characterized using culture-independent and -dependent methods in concert, and taxon- and location-specific changes to the microbiota were observed in infected piglets. Bacteroides spp. (e.g., Bacteroides uniformis, Bacteroides fragilis), Streptococcus spp. (e.g., Streptococcus gallolyticus), and various Gammaproteobacteria were highly associated with inflamed tissues, while bacteria within the Ruminococcaceae and Veillonellaceae families were mainly associated with healthy mucosae. In conclusion, the study findings showed that S Typhimurium incited temporal and spatial modifications to the swine autochthonous microbiota, and to host defense responses, that were consistent with overcoming colonization resistance to incite salmonellosis in swine.IMPORTANCE Limited information is available on host and enteric microbiota responses incited by Salmonella enterica serovar Typhimurium in swine and on possible mechanisms by which the bacterium overcomes colonization resistance to incite salmonellosis. Temporal characterization of a variety of host metrics in piglets (e.g., physiological, histopathological, and immunological) showed the importance of studying the progression of salmonellosis. A number of host responses integrally associated with disease development were identified. Utilization of next-generation sequence analysis to characterize the enteric microbiota was found to lack sufficient resolution; however, culture-dependent and -independent methods in combination identified taxon- and location-specific changes to bacterial communities in infected piglets. The study identified bacterial and host responses associated with salmonellosis, which will be beneficial in understanding colonization resistance and in the development of effective alternatives to antibiotics to mitigate salmonellosis.

Enrofloxacin Shifts Intestinal Microbiota and Metabolic Profiling and Hinders Recovery from Salmonella enterica subsp. enterica Serovar Typhimurium Infection in Neonatal Chickens

Enrofloxacin is an important antibiotic used for prevention and treatment of Salmonella infection in poultry in many countries. However, oral administration of enrofloxacin may lead to the alterations in the microbiota and metabolome in the chicken intestine, thereby reducing colonization resistance to the Salmonella infection. To study the effect of enrofloxacin on Salmonella in the chicken cecum, we used different concentrations of enrofloxacin to feed 1-day-old chickens, followed by oral challenge with Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium). We then explored the distribution pattern of S. Typhimurium in cecum contents in vivo and analyzed the microbial community structure of cecum contents using microbial 16S amplicon sequencing. Untargeted metabolomics was used to explore the gut metabolome on day 14. Faecalibacterium and Anaerostipes, which are closely related to the chicken intestinal metabolome, were screened using a multi-omics technique. The abundance of S. Typhimurium was significantly higher in the enrofloxacin-treated group than in the untreated group, and S. Typhimurium persisted longer. Moreover, the cecal colony structures of the three groups exhibited different characteristics, with Lactobacillus reaching its highest abundance on day 21. Notably, S. Typhimurium infection is known to affect the fecal metabolome of chickens differently. Thus, our results suggested that enrofloxacin and Salmonella infections completely altered the intestinal microbiota and metabolism of chickens.IMPORTANCE In this study, we examined the effects of S. Typhimurium infection and enrofloxacin treatment on the microbiota and metabolite synthesis in chicken cecum, in order to identify target metabolites that may promote S. Typhimurium colonization and aggravate inflammation and to evaluate the important microbiota that may be associated with these metabolites. Our findings may facilitate the use of antibiotics to prevent S. Typhimurium infection.

Butyrate-mediated autophagy inhibition limits cytosolic Salmonella Infantis replication in the colon of pigs treated with a mixture of Lactobacillus and Bacillus

Probiotics as an effective and safe strategy for controlling Salmonella infection are much sought after, while autophagy is a central issue in eliminating intracellular pathogens of intestinal epithelial cells. In this study, an animal model of colitis has been developed by infecting weaned pigs orally with a strain of Salmonella Infantis in order to illuminate the potential efficacy of a mixture of Lactobacillus and Bacillus (CBB-MIX) in the resistance to Salmonella infection by regulating butyrate-mediated autophagy. We found that CBB-MIX alleviated S. Infantis-induced colitis and tissue damage. Autophagy markers ATG5, Beclin-1, and the LC3-II/I ratio were significantly enhanced by S. Infantis infection, while treatment with CBB-MIX suppressed S. Infantis-induced autophagy. Additionally, S. Infantis-induced colonic microbial dysbiosis was restored by this treatment, which also preserved the abundance of the butyrate-producing bacteria and the butyrate concentration in the colon. A Caco-2 cell model of S. Infantis infection showed that butyrate had the same effect as the CBB-MIX in restraining S. Infantis-induced autophagy activation. Further, the intracellular S. Infantis load assay indicated that butyrate restricted the replication of cytosolic S. Infantis rather than that in Salmonella-containing vacuoles. Suppression of autophagy by knockdown of ATG5 also attenuated S. Infantis-induced cell injury. Moreover, hyper-replication of cytosolic S. Infantis in Caco-2 cells was significantly decreased when autophagy was inhibited. Our data demonstrated that Salmonella may benefit from autophagy for cytosolic replication and butyrate-mediated autophagy inhibition reduced the intracellular Salmonella load in pigs treated with a probiotic mixture of Lactobacillus and Bacillus.

The Systemic Zinc Homeostasis Was Modulated in Broilers Challenged by Salmonella

Salmonella challenge leads to systemic responses that induce the hypozincaemia in mice, which is considered a vital strategy against Salmonella invasion. However, it is not yet known if this phenomenon occurs in broilers. To investigate the change in zinc homeostasis of broilers against Salmonella challenge, 1-day-old male broilers were fed with the basal diet for 7 days. Afterwards, broilers were orally inoculated with either 0 or 0.5 × 108 CFU Salmonella Typhimurium (ST). The serum and selected tissues of Salmonella-challenged and non-challenged broilers were collected at 1, 3 and 7 days post-challenge for zinc homeostasis analysis. Our results showed that Salmonella challenge results in hypozincaemia (serum zinc decrease and liver zinc increase) via modulating the systemic zinc homeostasis of broilers. A profound, zinc transporter-mediated zinc absorption and redistribution affecting zinc homeostasis provided a mechanistic explanation for this phenomenon. In addition, we found that the zinc importers Zip5, Zip10, Zip11, Zip12, Zip13 and Zip14 were mainly downregulated in Salmonella-challenged broilers to reduce zinc absorption in the duodenum, while the Zip14 mRNA expression was upregulated to redistribute zinc into the liver. Collectively, these findings reveal that broilers counteract Salmonella infection via modulating their systemic zinc homeostasis.

Identification of single-nucleotide variants associated with susceptibility to Salmonella in pigs using a genome-wide association approach

BACKGROUND

Salmonella enterica serovars are a major cause of foodborne illness and have a substantial impact on global human health. In Canada, Salmonella is commonly found on swine farms and the increasing concern about drug use and antimicrobial resistance associated with Salmonella has promoted research into alternative control methods, including selecting for pig genotypes associated with resistance to Salmonella. The objective of this study was to identify single-nucleotide variants in the pig genome associated with Salmonella susceptibility using a genome-wide association approach. Repeated blood and fecal samples were collected from 809 pigs in 14 groups on farms and tonsils and lymph nodes were collected at slaughter. Sera were analyzed for Salmonella IgG antibodies by ELISA and feces and tissues were cultured for Salmonella. Pig DNA was genotyped using a custom 54 K single-nucleotide variant oligo array and logistic mixed-models used to identify SNVs associated with IgG seropositivity, shedding, and tissue colonization.

RESULTS

Variants in/near PTPRJ (p = 0.0000066), ST6GALNAC3 (p = 0.0000099), and DCDC2C (n = 3, p < 0.0000086) were associated with susceptibility to Salmonella, while variants near AKAP12 (n = 3, p < 0.0000358) and in RALGAPA2 (p = 0.0000760) may be associated with susceptibility.

CONCLUSIONS

Further study of the variants and genes identified may improve our understanding of neutrophil recruitment, intracellular killing of bacteria, and/or susceptibility to Salmonella and may help future efforts to reduce Salmonella on-farm through genetic approaches.

Effect of flavophospholipol on fecal microbiota in weaned pigs challenged with Salmonella Typhimurium

BACKGROUND

The heightened prevalence of Salmonella Typhimurium remains a public health and food safety concern. Studies have reported antibiotic, flavophospholipol, may have the ability to reduce Salmonella in swine, as well as alter the gut microbiota in favour of beneficial bacteria by inhibiting pathogenic bacteria. Thus, the objective of this study was to investigate the fecal microbiota of weaned pigs receiving in-feed flavophospholipol and challenged with Salmonella Typhimurium.

RESULTS

Twenty-one weaned pigs were fed either a diet containing 4 ppm of flavophospholipol (treatment group) or a non-medicated feed (control group) for 36 days post-weaning (Day 1 to Day 36). The pigs were orally challenged with a 2 mL dose of 108 CFU/mL of S. Typhimurium at Day 7 and Day 8. Community bacterial DNA extracted from fecal samples collected at Day 6 (before challenge) and Day 36 (28 days after challenge) were used to assess the fecal microbiota using the V4 region of the 16S rRNA gene with Illumina MiSeq next-generation sequencing. Sequencing data were visualized using mothur and analyzed in JMP and R software. The fecal microbiota of pigs in the treatment group had differences in abundance of phyla (Firmicutes, Proteobacteria) and genera (Lactobacillus, Roseburia, Treponema, unclassified Ruminococcaceae, Blautia, Streptococcus, Megasphaera, Dorea, Sporobacter, Peptococcus, unclassified Firmicutes, Clostridium IV and Campylobacter) when compared to pigs that were controls, 28 days after challenge with Salmonella (P < 0.05). Specifically, results demonstrated a significant increase in phylum Proteobacteria (P = 0.001) and decrease in Firmicutes (P = 0.012) and genus Roseburia (P = 0.003) in the treated pigs suggestive of possible microbial dysbiosis. An increased abundance of genera Lactobacillus (P = 0.012) was also noted in the treated group in comparison to the control.

CONCLUSION

Based on these findings, it is difficult to conclude whether treatment with 4 ppm of flavophospholipol is promoting favorable indigenous bacteria in the pig microbiota as previous literature has suggested.

Interactions between host and gut microbiota in domestic pigs: a review

It is well established that pig gut microbiota plays a critical role in maintaining metabolic homeostasis as well as in a myriad of physiological, neurological and immunological functions; including protection from pathogens and digestion of food materials - some of which would be otherwise indigestible by the pig. A rich and diverse gut microbial ecosystem (balanced microbiota) is the hallmark of good health; while qualitative and quantitative perturbations in the microbial composition can lead to development of various diseases. Alternatively, diseases caused by stressors or other factors have been shown to negatively impact the microbiota. This review focuses primarily on how commensal microorganisms in the gastrointestinal tract of pigs influence biochemical, physiological, immunological, and metabolic processes within the host animal.

Transport to the Slaughterhouse Affects the Salmonella Shedding and Modifies the Fecal Microbiota of Finishing Pigs

Contaminated pork is a significant source of foodborne Salmonellosis. Pork is contaminated at the slaughterhouse and the intestinal content is the predominant source of Salmonella for carcass contamination. The prevalence of Salmonella-positive pigs increases significantly when the time of transport to the slaughterhouse is longer than two hours. The hypothesis behind this study is that transport to the slaughterhouse increases the load of Salmonella in feces and determines a shift of the fecal microbiota in finishing pigs. Fecal samples were collected in a pig herd positive for Salmonella spp., the day before the transport and at the slaughterhouse. Salmonella loads were estimated by the most probable number (MPN) technique, according to the ISO/TS 6579-2:2012/A1. Moreover, the fecal bacteria composition was assessed by sequencing the V3-V4 hypervariable regions of the 16S rRNA gene. Our study showed that the load of Salmonella increases after transport, confirming that this phase of the production chain is a critical point for the control of Salmonella contamination. A lower richness and an increased beta-diversity characterized the fecal microbiota composition of Salmonella-positive animals after transport. In this stage, a natural Salmonella infection causes a disruption of the fecal microbiota as observed in challenge studies.

Mycoplasma hyopneumoniae-Lawsonia intracellularis dual challenge modulates intestinal integrity and function1

Lawsonia intracellularis (LI) and Mycoplasma hyopneumoniae (Mh) are 2 globally distributed pathogens that cause significant morbidity and mortality in grow-finish pigs. However, mechanisms that reduce growth and feed efficiency during LI and Mh infection are poorly defined. We hypothesized that reductions in performance are partially due to declines in intestinal function and integrity; thus, this study aimed to evaluate intestinal function and integrity of pigs during a 21-d Mh and LI dual challenge (MhLI). Littermate pairs of barrows (48.1 ± 6.7 kg BW) were selected; 1 pig from each pair was assigned to either MhLI challenge or nonchallenge treatments (n = 12). Pigs were individually housed, fed a corn-soybean diet, and allowed to acclimate for 21 d prior to inoculation. On days postinoculation (dpi) 0, MhLI pigs were dual inoculated with LI and Mh. On dpi 21, all pigs were euthanized for ileal and colon tissue collection. Formalin-fixed tissues were clinically scored and morphology analyzed, frozen tissues assayed for digestive enzyme activities, and fresh tissues mounted into modified Ussing Chambers to assess active nutrient transport, barrier integrity, and bacterial translocation. Data were analyzed using the Mixed Procedure of SAS with treatment as a fixed effect, age and start BW as covariates, and litter as a random effect. Compared with controls, MhLI pigs had decreased ADG (38%, P < 0.001), ADFI (25%, P < 0.001), and G:F (19%, P = 0.012). The MhLI dual challenge did not alter ileum morphology or transepithelial resistance (P > 0.10); however, ex vivo mucosal to serosal translocation of S. Typhimurium in the colon was increased (60%, P = 0.003) in MhLI pigs compared with controls. Additionally, MhLI pigs had increased ileal glucose transport (30%, P = 0.05) and decreased sucrase activity (30%, P = 0.049) compared with controls. This MhLI challenge antagonized intestinal function and integrity, and this may be a contributing factor to reduced pig performance.

Probiotic Lactobacillus rhamnosus GG Induces Alterations in Ileal Microbiota With Associated CD3-CD19-T-bet+IFNγ+/- Cell Subset Homeostasis in Pigs Challenged With Salmonella enterica Serovar 4,[5],12:i:

Salmonella enterica serovar 4,[5],12:i:- (S. 4,[5],12:i:-) is an emerging foodborne pathogen causing salmonellosis in humans and animals. Probiotic Lactobacillus rhamnosus GG (LGG) is an effective strategy for controlling enteric infections through maintaining gut microbiota homeostasis and regulating the intestinal innate immune response. Here, LGG was orally administrated to newly weaned piglets for 1 week before S. 4,[5],12:i:- challenge. S. 4,[5],12:i:- challenge led to disturbed gut microbiota, characterized by increased levels of Psychrobacter, Chryseobacterium indoltheticum, and uncultured Corynebacteriaceae populations, as well as an aberrant correlation network in Prevotellaceae NK3B31 group-centric species. The beneficial effect of LGG correlated with attenuating the expansion of Prevotellaceae NK3B31 group. Fusobacterium only found in the pigs treated with LGG was positively correlated with Lactobacillus animalis and Propionibacterium. Administration of LGG induced the expansion of CD3^-CD19^-T-bet⁺IFNγ⁺ and CD3^-CD19^-T-bet⁺IFNγ^- cell subsets in the peripheral blood at 24 h after a challenge of S. 4,[5],12:i:-. S. 4,[5],12:i:- infection increased the population of intraepithelial CD3^-CD19^-T-bet⁺IFNγ⁺ and CD3^-CD19^-T-bet⁺IFNγ^- cells in the ileum; however, this increase was attenuated via LGG administration. Correlation analysis revealed that LGG enriched Flavobacterium frigidarium and Facklamia populations, which were negatively correlated with intraepithelial CD3^-CD19^-T-bet⁺IFNγ⁺ and CD3^-CD19^-T-bet⁺IFNγ^- cells in the ileum. The present data suggest that probiotic LGG alters gut microbiota with associated CD3^-CD19^-T-bet⁺IFNγ^+/- cell subset homeostasis in pigs challenged with S. enterica 4,[5],12:i:-. LGG may be used in potential gut microbiota-targeted therapy regimens to regulate the specific immune cell function and, consequently, control enteric infections.

Effects of pulverized oyster mushroom (Pleurotus ostreatus) on diarrhea incidence, growth performance, immunity, and microbial composition in piglets

BACKGROUND

Pleurotus ostreatus mushroom (POM) is an edible mushroom with rich nutritional components and vital pharmacological properties. The present study comprised 100 cross-bred piglets, weaned at 28 days old, who were randomly assigned to four POM diets with five replicates per diet and five piglets per pen.

RESULTS

POM supplementation (P < 0.05) decreased the incidence of diarrhea, and also increased the average daily feed intake and average daily gain of pigs. Fecal acetate, butyrate and propionate increased with the addition of POM. Interleukin-2, immunoglobulin G, immunoglobulin M, tumor necrosis factor-α and immunoglobulin A increased (P < 0.05) with the addition of POM. The 16S rDNA sequencing results showed that the Bacteroidetes and Firmicutes were the dominant microbial strains in the fecal samples, irrespective of POM supplementation. Shannon diversity, whole tree phylogenetic diversity, observed species and Chao1 analysis exhibited significant variation in species richness across the treatments. Principal coordinates analysis showed a significant (P < 0.1) increase in the microbial communities amongst all of the treatment groups.

CONCLUSION

The results of the present study suggest that the supplementation of POM in the diet of piglets might increase feed consumption, gut microbial composition and diversity, as well as short-chain fatty acids synthesis, consequently preventing the occurrence of diarrhea and increasing the growth of piglets. © 2019 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Effects of Astragalus membranaceus fiber on growth performance, nutrient digestibility, microbial composition, VFA production, gut pH, and immunity of weaned pigs

Astragalus membranaceus is an herbaceous perennial plant, growing to about 2 feet tall, with sprawling stems and alternate leaves about 12-24 leaflets. In total, 24 cross bred (Duroc × Landrace × Yorkshire) piglets weaned at 4 weeks with an average body weight of 10.84 ± 1.86 kg, were divided into four groups and randomly assigned to dietary treatments containing different AMSLF levels (0.00%, 2.50%, 5.00%, and 7.50%). The piglets in the control group (0.00% AMSLF) were fed basal diet and other treatment groups were fed basal diet in addition to 2.50%, 5.00%, and 7.50% pulverized AMSLF. The results indicated that supplementation with AMSLF significantly (p < 0.05) decreased diarrheal incidence in piglets. There was significant difference between treatment in terms of ADFI, ADG and FCR. Both 5.00% and 7.50% treatments significantly increased growth performance. The digestibility of gross energy and dry matter increased (p > 0.05) with increasing AMSLF level. The level of blood IL-2 and TNF-α were significantly affected by AMSLF supplementation with 7.50% AMSLF group having higher (p < 0.05) IL-2 and TNF-α levels than the other treatment groups. The 16SrDNA sequencing results from the four treatments showed that the potentially active bacterial microbial population and diversity in pig cecum were dominated by the phyla Bacteriodetes and Firmicutes regardless of the AMSLF supplementation. The Shannon diversity, PD whole tree diversity indices and Chao analyses exhibited significant variability in species richness across the treatments. The principal coordinates analysis (PCoA) showed significant (p < 0.1) differences between bacterial communities in all treatment groups. Results from the current study suggested that AMSLF supplementation increased composition of bacterial microbiota in pig gut. In conclusion, dietary supplements with AMSLF could potentially be used to prevent diarrheal incidence and improved pig production.

Influence of the Intestinal Microbiota on Colonization Resistance to Salmonella and the Shedding Pattern of Naturally Exposed Pigs

Salmonella colonization and infection in production animals such as pigs are a cause for concern from a public health perspective. Variations in susceptibility to natural infection may be influenced by the intestinal microbiota. Using 16S rRNA compositional sequencing, we characterized the fecal microbiome of 15 weaned pigs naturally infected with Salmonella at 18, 33, and 45 days postweaning. Dissimilarities in microbiota composition were analyzed in relation to Salmonella infection status (infected, not infected), serological status, and shedding pattern (nonshedders, single-point shedders, intermittent-persistent shedders). Global microbiota composition was associated with the infection outcome based on serological analysis. Greater richness within the microbiota postweaning was linked to pigs being seronegative at the end of the study at 11 weeks of age. Members of the Clostridia, such as Blautia, Roseburia, and Anaerovibrio, were more abundant and part of the core microbiome in nonshedder pigs. Cellulolytic microbiota (Ruminococcus and Prevotella) were also more abundant in noninfected pigs during the weaning and growing stages. Microbial profiling also revealed that infected pigs had a higher abundance of Lactobacillus and Oscillospira, the latter also being part of the core microbiome of intermittent-persistent shedders. These findings suggest that a lack of microbiome maturation and greater proportions of microorganisms associated with suckling increase susceptibility to infection. In addition, the persistence of Salmonella shedding may be associated with an enrichment of pathobionts such as Anaerobiospirillum. Overall, these results suggest that there may be merit in manipulating certain taxa within the porcine intestinal microbial community to increase disease resistance against Salmonella in pigs. IMPORTANCE Salmonella is a global threat for public health, and pork is one of the main sources of human salmonellosis. However, the complex epidemiology of the infection limits current control strategies aimed at reducing the prevalence of this infection in pigs. The present study analyzes for the first time the impact of the gut microbiota in Salmonella infection in pigs and its shedding pattern in naturally infected growing pigs. Microbiome (16S rRNA amplicon) analysis reveals that maturation of the gut microbiome could be a key consideration with respect to limiting the infection and shedding of Salmonella in pigs. Indeed, seronegative animals had higher richness of the gut microbiota early after weaning, and uninfected pigs had higher abundance of strict anaerobes from the class Clostridia, results which demonstrate that a fast transition from the suckling microbiota to a postweaning microbiota could be crucial with respect to protecting the animals.

The effects of Lawsonia intracellularis, Salmonella enterica serovar Typhimurium and co-infection on IL-8 and TNFα expression in IPEC-J2 cells

Lawsonia intracellularis is among the most important enteric pathogens of swine and has been shown to be a risk factor for increased Salmonella enterica shedding. S. enterica serovar Typhimurium, in addition to being a significant pathogen of swine, also remains one of the most common causes of foodborne illness worldwide. Inflammation and the expression of IL8 and TNFα are an important process in the establishment of S. Typhimurium infection. Yet the effect of L. intracellularis on the expression of these cytokines by enterocytes, the niche both pathogens occupy during infection, is poorly understood. In this study we compared cytokine gene expression between singly and dually infected IPEC-J2 cells, a non-transformed porcine enterocyte cell line. Our results show that L. intracellularis leads to increased expression of IL8 and TNFα and has an additive effect on their expression in co-infection. The increase in expression of inflammatory cytokines may be one mechanism by which L. intracellularis favors S. Typhimurium infection.

Lactobacillus johnsonii L531 reduces pathogen load and helps maintain short-chain fatty acid levels in the intestines of pigs challenged with Salmonella enterica Infantis

In the current study, we screened Lactobacillus strains isolated from the colon of clinically healthy weaned piglets for potential probiotic properties and isolated Lactobacillus. johnsonii L531, which produced high levels of beneficial metabolites (butyric, acetic, and lactic acid) in vitro. We also evaluated the efficacy of this metabolites-producing probiotic in treating Salmonella. Infantis infection. Oral administration of L. johnsonii L531 to newly weaned piglets significantly decreased levels of Salmonella colonization in colonic and jejunal contents, accelerated the clearance of Salmonella in feces after infection, and reduced S. Infantis translocation to the spleen. Pretreatment with SCFAs-promoting probiotic L. johnsonii L531 significantly ameliorated the depletion of SCFAs induced by S. Infantis infection and led to significantly greater weight gain and better feed conversion ratios compared to piglets challenged only with S. Infantis. These data provide further evidence that SCFAs-promoting probiotic L. johnsonii L531 treatment could be a suitable nonantibiotic alternative for controlling Salmonella infection and maintaining metabolic homeostasis, thereby enhancing the gut health of piglets during the critical weaning period.

Piglet gut microbial shifts early in life: causes and effects

The gut microbiome has long been known to play fundamentally important roles in the animal health and the well-being of its host. As such, the establishment and maintenance of a beneficial gut microbiota early in life is crucial in pigs, since early gut colonizers are pivotal in the establishment of permanent microbial community structures affecting the health and growth performance of pigs later in life. Emphasizing this importance of early gut colonizers, it is critical to understand the factors impacting the establishment of the piglet gut microbiome at weaning. Factors include, among others, diet, in-feed antibiotics, probiotics and prebiotic administration. The impact of these factors on establishment of the gut microbiome of piglets at weaning includes effects on piglet gut microbial diversity, structure, and succession. In this review, we thoroughly reviewed the most recent findings on the piglet gut microbiome shifts as influenced by weaning, and how these microbiome changes brought about by various factors that have been shown to affect the development of microbiota in piglets. This review will provide a general overview of recent studies that can help to facilitate the design of new strategies to modulate the gut microbiome in order to enhance gastrointestinal health, growth performance and well-being of piglets.

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

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.

Fecal microbiome of periparturient dairy cattle and associations with the onset of Salmonella shedding

Non-typhoidal Salmonella enterica is a zoonotic pathogen with critical importance in animal and public health. The persistence of Salmonella on farms affects animal productivity and health, and represents a risk for food safety. The intestinal microbiota plays a fundamental role in the colonization and invasion of this ubiquitous microorganism. To overcome the colonization resistance imparted by the gut microbiome, Salmonella uses invasion strategies and the host inflammatory response to survive, proliferate, and establish infections with diverse clinical manifestations. Cattle serve as reservoirs of Salmonella, and periparturient cows have high prevalence of Salmonella shedding; however, little is known about the association between the gut microbiome and the onset of Salmonella shedding during the periparturient period. Thus, the objective of this study was to assess the association between changes in bacterial communities and the onset of Salmonella shedding in cattle approaching parturition. In a prospective cohort study, fecal samples from 98 dairy cows originating from four different farms were collected at four time points relative to calving (-3 wks, -1 wk, +1 wk, +3 wks). All 392 samples were cultured for Salmonella. Sequencing of the V4 region of the 16S rRNA gene using the Illumina platform was completed to evaluate the fecal microbiome in a selected sample subset. Analyses of microbial composition, diversity, and structure were performed according to time points, farm, and Salmonella onset status. Individual cow fecal microbiomes, predominated by Bacteroidetes, Firmicutes, Spirochaetes, and Proteobacteria phyla, significantly changed before and after parturition. Microbial communities from different farms were distinguishable based on multivariate analysis. Although there were significant differences in some bacterial taxa between Salmonella positive and negative samples, our results did not identify differences in the fecal microbial diversity or structure for cows with and without the onset of Salmonella shedding. These data suggest that determinants other than the significant changes in the fecal microbiome influence the periparturient onset of Salmonella shedding in dairy cattle.

Vaccination Against Lawsonia intracellularis Decreases Shedding of Salmonella enterica serovar Typhimurium in Co-Infected Pigs and Alters the Gut Microbiome

Salmonella enterica serovar Typhimurium continues to be a major cause of foodborne illness worldwide and pork can serve as a source of infection. Co-infection of S. enterica with Lawsonia intracellularis, a common intestinal pathogen of swine, has been found as risk factor for increased S. enterica shedding. The objective of this study was to investigate if vaccination against L. intracellularis could lead to decreased S. Typhimurium shedding. To test this hypothesis, pigs were challenged with either S. Typhimurium or S. Typhimurium and L. intracellularis, with and without L. intracellularis vaccination (n = 9 per group). A non-challenged group served as a negative control. Vaccination decreased the shedding of S. Typhimurium in co-infected animals by 2.12 log10 organisms per gram of feces at 7 days post infection. Analysis of the microbiome showed that vaccination led to changes in the abundance of Clostridium species, including Clostridium butyricum, in addition to other compositional changes that may explain the protection mediated against S. Typhimurium. These results indicate that vaccination against L. intracellularis in co-infected herds may provide a new tool to increase food safety by helping to prevent S. enterica without the need for antibiotics.

Salmonella enterica Serovar Typhimurium Strategies for Host Adaptation

Bacterial pathogens must sense and respond to newly encountered host environments to regulate the expression of critical virulence factors that allow for niche adaptation and successful colonization. Among bacterial pathogens, non-typhoidal serovars of Salmonella enterica, such as serovar Typhimurium (S. Tm), are a primary cause of foodborne illnesses that lead to hospitalizations and deaths worldwide. S. Tm causes acute inflammatory diarrhea that can progress to invasive systemic disease in susceptible patients. The gastrointestinal tract and intramacrophage environments are two critically important niches during S. Tm infection, and each presents unique challenges to limit S. Tm growth. The intestinal tract is home to billions of commensal microbes, termed the microbiota, which limits the amount of available nutrients for invading pathogens such as S. Tm. Therefore, S. Tm encodes strategies to manipulate the commensal population and side-step this nutritional competition. During subsequent stages of disease, S. Tm resists host immune cell mechanisms of killing. Host cells use antimicrobial peptides, acidification of vacuoles, and nutrient limitation to kill phagocytosed microbes, and yet S. Tm is able to subvert these defense systems. In this review, we discuss recently described molecular mechanisms that S. Tm uses to outcompete the resident microbiota within the gastrointestinal tract. S. Tm directly eliminates close competitors via bacterial cell-to-cell contact as well as by stimulating a host immune response to eliminate specific members of the microbiota. Additionally, S. Tm tightly regulates the expression of key virulence factors that enable S. Tm to withstand host immune defenses within macrophages. Additionally, we highlight the chemical and physical signals that S. Tm senses as cues to adapt to each of these environments. These strategies ultimately allow S. Tm to successfully adapt to these two disparate host environments. It is critical to better understand bacterial adaptation strategies because disruption of these pathways and mechanisms, especially those shared by multiple pathogens, may provide novel therapeutic intervention strategies.

A comparison of sequencing platforms and bioinformatics pipelines for compositional analysis of the gut microbiome

Background

Advancements in Next Generation Sequencing (NGS) technologies regarding throughput, read length and accuracy had a major impact on microbiome research by significantly improving 16S rRNA amplicon sequencing. As rapid improvements in sequencing platforms and new data analysis pipelines are introduced, it is essential to evaluate their capabilities in specific applications. The aim of this study was to assess whether the same project-specific biological conclusions regarding microbiome composition could be reached using different sequencing platforms and bioinformatics pipelines.

Results

Chicken cecum microbiome was analyzed by 16S rRNA amplicon sequencing using Illumina MiSeq, Ion Torrent PGM, and Roche 454 GS FLX Titanium platforms, with standard and modified protocols for library preparation. We labeled the bioinformatics pipelines included in our analysis QIIME1 and QIIME2 (de novo OTU picking [not to be confused with QIIME version 2 commonly referred to as QIIME2]), QIIME3 and QIIME4 (open reference OTU picking), UPARSE1 and UPARSE2 (each pair differs only in the use of chimera depletion methods), and DADA2 (for Illumina data only). GS FLX+ yielded the longest reads and highest quality scores, while MiSeq generated the largest number of reads after quality filtering. Declines in quality scores were observed starting at bases 150–199 for GS FLX+ and bases 90–99 for MiSeq. Scores were stable for PGM-generated data. Overall microbiome compositional profiles were comparable between platforms; however, average relative abundance of specific taxa varied depending on sequencing platform, library preparation method, and bioinformatics analysis. Specifically, QIIME with de novo OTU picking yielded the highest number of unique species and alpha diversity was reduced with UPARSE and DADA2 compared to QIIME.

Conclusions

The three platforms compared in this study were capable of discriminating samples by treatment, despite differences in diversity and abundance, leading to similar biological conclusions. Our results demonstrate that while there were differences in depth of coverage and phylogenetic diversity, all workflows revealed comparable treatment effects on microbial diversity. To increase reproducibility and reliability and to retain consistency between similar studies, it is important to consider the impact on data quality and relative abundance of taxa when selecting NGS platforms and analysis tools for microbiome studies.

Electronic supplementary material

The online version of this article (10.1186/s12866-017-1101-8) contains supplementary material, which is available to authorized users.

A novel antimicrobial approach based on the inhibition of zinc uptake in Salmonella enterica

In this review we discuss evidences suggesting that bacterial zinc homeostasis represents a promising target for new antimicrobial strategies. The ability of the gut pathogen Salmonella enterica sv Typhimurium to withstand the host responses aimed at controlling growth of the pathogen critically depends on the zinc importer ZnuABC. Strains lacking a functional ZnuABC or its soluble component ZnuA display a dramatic loss of pathogenicity, due to a reduced ability to express virulence factors; withstand the inflammatory response; and compete with other gut microbes. Based on this data, ZnuA was chosen as a candidate for the rational design of novel antibiotics. Through a combination of structural and functional investigations, we have provided a proof of concept of the potential of this approach.

Mechanisms of cross-talk between the diet, the intestinal microbiome, and the undernourished host

Undernutrition remains one of the most pressing global health challenges today, contributing to nearly half of all deaths in children under five years of age. Although insufficient dietary intake and environmental enteric dysfunction are often inciting factors, evidence now suggests that unhealthy gut microbial populations perpetuate the vicious cycle of pathophysiology that results in persistent growth impairment in children. The metagenomics era has facilitated new research identifying an altered microbiome in undernourished hosts and has provided insight into a number of mechanisms by which these alterations may affect growth. This article summarizes a range of observational studies that highlight differences in the composition and function of gut microbiota between undernourished and healthy children; discusses dietary, environmental and host factors that shape this altered microbiome; examines the consequences of these changes on host physiology; and considers opportunities for microbiome-targeting therapies to combat the global challenge of child undernutrition.

Salmonella in Swine: Microbiota Interactions

For the important foodborne pathogen Salmonella enterica to cause disease or persist in pigs, it has evolved an intricate set of interactions between itself, the host, and the indigenous microflora of the host. S. enterica must evade the host's immune system and must also overcome colonization resistance mediated by the pig's indigenous microflora. The inflammatory response against S. enterica provides the bacteria with unique metabolites and is thus exploited by S. enterica for competitive advantage. During infection, changes in the composition of the indigenous microflora occur that have been associated with a breakdown in colonization resistance. Healthy pigs that are low-level shedders of S. enterica also exhibit alterations in their indigenous microflora similar to those in ill animals. Here we review the literature on the interactions that occur between swine, S. enterica, and the indigenous microflora and discuss methods to reduce or prevent colonization of pigs with S. enterica.

Emerging Technologies for Gut Microbiome Research

Understanding the importance of the gut microbiome on modulation of host health has become a subject of great interest for researchers across disciplines. As an intrinsically multidisciplinary field, microbiome research has been able to reap the benefits of technological advancements in systems and synthetic biology, biomaterials engineering, and traditional microbiology. Gut microbiome research has been revolutionized by high-throughput sequencing technology, permitting compositional and functional analyses that were previously an unrealistic undertaking. Emerging technologies, including engineered organoids derived from human stem cells, high-throughput culturing, and microfluidics assays allowing for the introduction of novel approaches, will improve the efficiency and quality of microbiome research. Here, we discuss emerging technologies and their potential impact on gut microbiome studies.

Systemic Concentrations of Short Chain Fatty Acids Are Elevated in Salmonellosis and Exacerbation of Familial Mediterranean Fever

Gut microbiota-produced short chain fatty acids (SCFAs) play an important role in the normal human metabolism and physiology. Although the gradients of SCFAs from the large intestine, where they are largely produced, to the peripheral blood as well as the main routes of SCFA metabolism by different organs are known well for the healthy state, there is a paucity of information regarding how these are affected in disease. In particular, how the inflammation caused by infection or autoinflammatory disease affect the concentration of SCFAs in the peripheral venous blood. In this work, we revealed that diseases caused either by infectious agents (two Salmonella enterica serovars, S. Enteritidis, and S. Typhimurium) or by the exacerbation of an autoinflammatory disease, familial Mediterranean fever (FMF), both result in a significantly elevated systemic concentration of SCFAs. In the case of salmonellosis the concentration of SCFAs in peripheral blood was significantly and consistently higher, from 5- to 20-fold, compared to control. In the case of FMF, however, a significant increase of SCFAs in the peripheral venous blood was detected only in the acute phase of the disease, with a lesser impact in remission. It seems counterintuitive that the dysbiotic conditions, with a reduced number of gut microorganisms, produce such an effect. This phenomenon, however, must be appraised within the context of how the inflammatory diseases affect the normal physiology. We discuss a number of factors that may contribute to the “leak” and persistence of gut-produced SCFAs into the systemic circulation in infectious and autoinflammatory diseases.