Changes in the Ileal, but Not Fecal, Microbiome in Response to Increased Dietary Protein Level and Enterotoxigenic Escherichia coli Exposure in Pigs

Impact of including two types of destoned olive cakes in pigs' diets on fecal bacterial composition and study of the relationship between fecal microbiota, feed efficiency, gut fermentation, and gaseous emissions

The microbial population in the pig's gastrointestinal tract can be influenced by incorporating fibrous by-products into the diets. This study investigated the impact of including two types of dried olive cake (OC) in pigs' diets on fecal bacterial composition. The correlation between fecal microbiota and growth performance, nutrient digestibility, gut fermentation pattern and slurry gas emissions was also evaluated. Thirty male Pietrain x (Landrace x Large white) pigs (47.9 ± 4.21 kg) were assigned to three groups: a control group (C), a group fed a diet with 20% partially defatted OC (20PDOC), and a group fed a diet with 20% cyclone OC (20COC) for 21 days. Fecal samples collected before and after providing the experimental diets were analyzed for the V3-V4 region of the 16S rRNA gene. Pigs were weighed, and feed intake was recorded throughout the study. Potential ammonia and methane emissions from slurry were measured. No significant differences in alpha diversity indexes were found. The taxonomic analysis revealed that Firmicutes and Bacteroidota phyla were dominant at the phylum level across all groups. Differential abundance analysis using ALDEx showed significant differences among groups for various bacteria at the phylum, genus, and species levels at the end of the experiment. Pigs from 20PDOC and 20COC groups exhibited increased abundances of health-promoting bacteria, such as Plactomycetota at the phylum level and Allisonella and an unidentified genus from the Eggerthellaceae family at the genus level. These changes influenced short-chain fatty acids' (SCFA) concentration in slurries, leading to greater acetic, butyric, caproic and heptanoic acids in OC-fed groups, especially 20COC pigs. A volatility analysis revealed significant positive correlations (p < 0.05) between Uncultured_Bacteroidales and Unculured_Selenomonadaceae and energy digestibility. Monoglobus and Desulfovibrio showed a positive significant (p < 0.05) correlation with total SCFA, indicating a high impact on gut fermentation. However, growth performance parameters and potential gas emission displayed no significant correlations with a specific bacterial genus. In conclusion, our results suggest that OC inclusion into pig diets could positively modulate and contribute to the gut microbiota's favorable composition and functionality. Also, nutrient digestibility and gut fermentation patterns can be associated with specific microbial populations.

The Effect of Maternal Probiotic or Synbiotic Supplementation on Sow and Offspring Gastrointestinal Microbiota, Health, and Performance

The increasing prevalence of antimicrobial-resistant pathogens has prompted the reduction in antibiotic and antimicrobial use in commercial pig production. This has led to increased research efforts to identify alternative dietary interventions to support the health and development of the pig. The crucial role of the GIT microbiota in animal health and performance is becoming increasingly evident. Hence, promoting an improved GIT microbiota, particularly the pioneer microbiota in the young pig, is a fundamental focus. Recent research has indicated that the sow's GIT microbiota is a significant contributor to the development of the offspring's microbiota. Thus, dietary manipulation of the sow's microbiota with probiotics or synbiotics, before farrowing and during lactation, is a compelling area of exploration. This review aims to identify the potential health benefits of maternal probiotic or synbiotic supplementation to both the sow and her offspring and to explore their possible modes of action. Finally, the results of maternal sow probiotic and synbiotic supplementation studies are collated and summarized. Maternal probiotic or synbiotic supplementation offers an effective strategy to modulate the sow's microbiota and thereby enhance the formation of a health-promoting pioneer microbiota in the offspring. In addition, this strategy can potentially reduce oxidative stress and inflammation in the sow and her offspring, enhance the immune potential of the milk, the immune system development in the offspring, and the sow's feed intake during lactation. Although many studies have used probiotics in the maternal sow diet, the most effective probiotic or probiotic blends remain unclear. To this extent, further direct comparative investigations using different probiotics are warranted to advance the current understanding in this area. Moreover, the number of investigations supplementing synbiotics in the maternal sow diet is limited and is an area where further exploration is warranted.

High amylose to amylopectin ratios in nitrogen-free diets decrease the ileal endogenous amino acid losses of broiler chickens

This study explored the variation of ileal endogenous amino acid (IEAA) losses and its influencing factors in chickens offered nitrogen-free diets (NFD) containing different ratios of amylose to amylopectin (AM/AP). A total of 252 broiler chickens at 28 d old were randomly allocated into 7 treatment groups for a 3-d trial. The dietary treatments included a basal diet (control), a NFD containing corn starch (CS), and 5 NFD with AM/AP ratios of 0.20, 0.40, 0.60, 0.80, and 1.00, respectively. As the AM/AP ratio increased, the IEAA losses of all AAs, starch digestibility and maltase activity linearly decreased (P < 0.05), but the DM digestibility linearly and quadratically decreased (P < 0.05). Compared with the control, the NFD increased the number of goblet cells and its regulatory genes mucin-2 and krüppel-like factor 4 (KLF-4) while decreasing serum glucagon and thyroxine concentrations, ileal villus height, and crypt depth (P < 0.05). Additionally, NFD with lower AM/AP ratios (0.20 and 0.40) decreased the ileal microbiota species richness (P < 0.05). In all NFD groups, the number of Proteobacteria increased whereas the abundance of Firmicutes dropped (P < 0.05). However, the broilers in the AM/AP 0.60 group were closer to the digestive physiological state of chickens fed the control diet, with no significant change in maltase activity and mucin-2 expression (P < 0.05). In conclusion, increasing AM/AP ratio in a NFD decreased the IEAA losses and the apparent ileal digestibility of starch but inevitably resulted in malnutrition and disruption of gut microbiota homeostasis. This study recommends AM/AP in NFD at 0.60 to measure IEAA of broiler chickens.

Multispecies probiotic supplementation in diet with reduced crude protein levels altered the composition and function of gut microbiome and restored microbiome-derived metabolites in growing pigs

Both crude protein (CP) and probiotics can modulate the gut microbiome of the host, thus conferring beneficial effects. However, the benefits of low CP diet supplemented with multispecies probiotics on gut microbiome and its metabolites have not been investigated in pigs. Thus, we investigated the combinatory effects of low CP diet supplemented with multispecies probiotics on gut microbiome composition, function, and microbial metabolites in growing pigs. In total, 140 6 week-old piglets (Landrace × Yorkshire × Duroc) were used in this study. The pigs were divided into four groups with a 2 × 2 factorial design based on their diets: normal-level protein diet (16% CP; NP), low-level protein diet (14% CP; LP), NP with multispecies probiotics (NP-P), and LP with multispecies probiotics (LP-P). After the feeding trial, the fecal samples of the pigs were analyzed. The fecal scores were improved by the probiotic supplementation, especially in LP-P group. We also observed a probiotic-mediated alteration in the gut microbiome of pigs. In addition, LP-P group showed higher species richness and diversity compared with other groups. The addition of multispecies probiotics in low CP diet also enhanced gut microbiota metabolites production, such as short-chain fatty acids (SCFAs) and polyamines. Correlation analysis revealed that Oscillospiraceae UCG-002, Eubacterium coprostanoligenes, Lachnospiraceae NK4A136 group, and Muribaculaceae were positively associated with SCFAs; and Prevotella, Eubacterium ruminantium, Catenibacterium, Alloprevotella, Prevotellaceae NK3B31 group, Roseburia, Butyrivibrio, and Dialister were positively correlated with polyamines. Supplementation with multispecies probiotics modulated the function of the gut microbiome by upregulating the pathways for protein digestion and utilization, potentially contributing to enriched metabolite production in the gut. The results of this study demonstrate that supplementation with multispecies probiotics may complement the beneficial effects of low CP levels in pig feed. These findings may help formulate sustainable feeding strategies for swine production.

Antibacterial plant combinations prevent postweaning diarrhea in organically raised piglets challenged with enterotoxigenic Escherichia coli F18

Antibiotics and zinc oxide restrictions encourage the search for alternatives to combat intestinal pathogens, including enterotoxigenic Escherichia coli (ETEC), a major cause of postweaning diarrhea (PWD) in pigs. PWD causes important economic losses for conventional and organic farming. This study investigated the effect of dietary supplementation with garlic and apple pomace or blackcurrant on infection indicators and the fecal microbiota of organic-raised piglets challenged with ETEC-F18. For 21 days, 32 piglets (7-weeks-old) were randomly assigned to one of four groups: non-challenge (NC); ETEC-challenged (PC); ETEC-challenged receiving garlic and apple pomace (3 + 3%; GA); ETEC-challenged receiving garlic and blackcurrant (3 + 3%; GB). ETEC-F18 was administered (8 mL; 109 CFU/ml) on days 1 and 2 postweaning. The 1st week, PC had lower average daily gain than those in the NC, GA, and GB groups (P &lt; 0.05). NC pigs showed neither ETEC-F18 shedding nor signs of diarrhea. The PC group had higher diarrhea incidence and lower fecal dry matter than NC (≈5–10 days; 95% sEBCI). The GA and GB groups showed reduced ETEC-F18 and fedA gene shedding, higher fecal dry matter, and lower diarrhea incidence than the PC (≈5–9 days; 95% sEBCI). The NC, GA, and GB had normal hematology values during most of the study, whereas the PC had increased (P &lt; 0.05) red blood cells, hemoglobin, and hematocrit on day 7. Haptoglobin and pig-MAP increased in all groups, peaking on day 7, but PC showed the greatest increase (P &lt; 0.05). The fecal microbiota of PC pigs had reduced α-diversity (day 7; P &lt; 0.05) and higher volatility (days 3–14; P &lt; 0.05). Escherichia, Campylobacter, and Erysipelothrix were more abundant in the PC than in the NC, GB, and GA groups (log2FC &gt; 2; P &lt; 0.05), whereas Catenibacterium, Dialister, and Mitsoukella were more abundant in the NC, GB, and GA than in the PC group (log2FC &gt; 2; P &lt; 0.05). Prevotella and Lactobacillus were more abundant in the GB group (log2FC &gt; 2, P &lt; 0.05). In conclusion, dietary supplementation of GA and GB limited ETEC proliferation, reduced PWD, and beneficially impacted the fecal microbiota's diversity, composition, and stability.

Effects of supplementation of Bacillus amyloliquefaciens on performance, systemic immunity, and intestinal microbiota of weaned pigs experimentally infected with a pathogenic enterotoxigenic E. coli F18

The objective of this study was to investigate the effects of dietary supplementation of Bacillus (B.) amyloliquefaciens on growth performance, diarrhea, systemic immunity, and intestinal microbiota of weaned pigs experimentally infected with F18 enterotoxigenic Escherichia coli (ETEC). A total of 50 weaned pigs (7.41 ± 1.35 kg BW) were individually housed and randomly allotted to one of the following five treatments: sham control (CON-), sham B. amyloliquefaciens (BAM-), challenged control (CON+), challenged B. amyloliquefaciens (BAM+), and challenged carbadox (AGP+). The experiment lasted 28 days, with 7 days of adaptation and 21 days after the first ETEC inoculation. ETEC challenge reduced (P &lt; 0.05) average daily gain (ADG) of pigs. Compared with CON+, AGP+ enhanced (P &lt; 0.05) ADG, while B. amyloliquefaciens supplementation tended (P &lt; 0.10) to increase ADG in pigs from days 0 to 21 post-inoculation (PI). The ETEC challenge increased (P &lt; 0.05) white blood cell (WBC) count on days 7 and 21 PI, while BAM+ pigs tended (P &lt; 0.10) to have low WBC on day 7 PI and had lower (P &lt; 0.05) WBC on day 21 PI compared with CON+. In comparison to AGP+ fecal microbiota, BAM+ had a lower (P &lt; 0.05) relative abundance of Lachnospiraceae on day 0 and Clostridiaceae on day 21 PI, but a higher (P &lt; 0.05) relative abundance of Enterobacyeriaceae on day 0. In ileal digesta, the Shannon index was higher (P &lt; 0.05) in BAM+ than in AGP+. Bray-Curtis PCoA displayed a difference in bacterial community composition in ileal digesta collected from sham pigs vs. ETEC-infected pigs on day 21 PI. Pigs in BAM+ had a greater (P &lt; 0.05) relative abundance of Firmicutes, but a lower (P &lt; 0.05) relative abundance of Actinomycetota and Bacteroidota in ileal digesta than pigs in AGP+. Ileal digesta from AGP+ had a greater (P &lt; 0.05) abundance of Clostridium sensu stricto 1 but lower (P &lt; 0.05) Bifidobacterium than pigs in BAM+. In conclusion, supplementation of B. amyloliquefaciens tended to increase ADG and had limited effects on the diarrhea of ETEC-infected pigs. However, pigs fed with B. amyloliquefaciens exhibit milder systemic inflammation than controls. B. amyloliquefaciens differently modified the intestinal microbiota of weaned pigs compared with carbadox.

Protein Content in the Diet Influences Growth and Diarrhea in Weaning Piglets

The aim of this research has been to assess the effect of the dietary protein level on piglet growth and post-weaning diarrhea (PWD) incidence. Piglet fecal microbiota and feces composition were also assessed. The experiment was carried out on 144 weaned piglets (Duroc × Large White; 72 piglets per treatment) and lasted from weaning (at 25 days of age) until the end of the post-weaning phase (at 95 days). Two dietary protein levels were compared: high (HP; 17.5% crude protein on average, during the experiment) and low (LP; 15.5% on average). Lower (p < 0.01) average daily gain and feed conversion ratio were observed in LP piglets in the first growth phase. However, at the end of the post-weaning period, the growth parameters were not significantly different in the two diets. Diarrhea scores were lower in piglets fed LP diets than in piglets fed HP diets (28.6% of the total vs. 71.4% in the HP piglets). Fibrobacteres, Proteobacteria, and Spirochaetes were more abundant in the feces of the piglets fed LP diets. Feces nitrogen content was lower in piglets fed LP diets. In conclusion, low protein levels in the diet can reduce the incidence of PWD while only marginally affecting growth parameters.

Effect of antibiotics and low-crude protein diets on growth performance, health, immune response, and fecal microbiota of growing pigs

This study aimed to investigate the effects of diets with and without antibiotics supplementation and diets with 18.5% and 13.0% crude protein (CP) on growth performance, carcass characteristics, disease incidence, fecal microbiota, immune response, and antioxidant capacity of growing pigs. One hundred and eighty pigs (59-day-old; 18.5 ± 2.5 kg) were distributed in a randomized complete block design in a 2 × 2 factorial arrangement, nine replicates, and five pigs per pen. The factors were CP (18.5% or 13.0%) and antibiotics (none or 100 mg/kg tiamulin + 506 mg/kg oxytetracycline). Medicated diets were fed from days 59 to 73. After that, all pigs were fed their respective CP diets from 73 to 87 days. Data were analyzed using the Mixed procedure in SAS version 9.4. From days 59 to 73, pigs fed antibiotics diets had higher (P < 0.05) average daily feed intake (ADFI), average daily weight gain (ADG), gain to feed ratio (G:F), compared to the diets without antibiotics. From days 73 to 87 (postmedicated period), any previous supplementation of antibiotics did not affect pig growth performance. Overall (days 59 to 87), pigs-fed antibiotics diets had higher (P < 0.05) G:F compared to pigs-fed diets without antibiotics. In all periods evaluated, pigs fed 18.5% CP diets had higher (P < 0.05) ADG and G:F compared to pigs fed 13.0% CP. Pigs fed the 13.0% CP diets had lower (P < 0.05) fecal score and diarrhea incidence than those fed 18.5% CP. Pigs fed 18.5% CP diets had improved (P < 0.05) loin area compared to pigs-fed diets with 13.0% CP. At 66 days of age, pigs-fed antibiotics diets had lower (P < 0.05) alpha diversity estimated with Shannon and Simpson compared to the pig-fed diets without antibiotics. At family level, pigs fed 18.5% CP diets had higher (P < 0.05) relative abundance of Streptococcaceae, and lower (P < 0.05) relative abundance of Clostridiaceae at days 66 and 87 compared with pigs fed 13.0% CP. Pigs-fed antibiotics diets had lower (P < 0.05) immunoglobulin G and protein carbonyl concentrations at day 66 compared to the pigs-fed diets without antibiotics. The reduction of dietary CP from 18.5% to 13.0% reduced the growth performance and loin muscle area of growing pigs, although it was effective to reduce diarrhea incidence. Antibiotics improved growth performance, lowered diarrhea incidence, improved components of the humoral immune response, and reduced microbiota diversity. However, in the postmedicated period, we found no residual effect on the general health of the animals, and considering the overall period, only G:F was improved by the use of antibiotics.

Dietary supplementation of Bacillus subtilis or antibiotics modified intestinal microbiome of weaned pigs under enterotoxigenic Escherichia coli infection

Our previous research reported that supplementation of Bacillus subtilis DSM 25841 promoted growth and disease resistance of weaned pigs under enterotoxigenic Escherichia coli (ETEC) challenge and its efficacy is comparable to carbadox. This follow-up study aimed to characterize the effects of ETEC infection, supplementing B. subtilis DSM 25841 or carbadox on intestinal microbiota of pigs. Forty-eight weaned pigs (6.17 ± 0.36 kg BW) were randomly allotted to one of four treatments: negative control (NC), positive control (PC), antibiotics (AGP, 50 mg/kg of carbadox), and direct fed microbials (DFM, 2.56 × 10⁹  CFU/kg of B. subtilis). The experiment lasted 28 days with 7 days before and 21 days after first E. coli inoculation (day 0). Pigs in the PC, AGP, and DFM groups were orally inoculated with F18 ETEC for 3 consecutive days with 10¹⁰  CFU per dose per day. Fecal samples were collected on day -7, and day 7 and day 21 post inoculation, digesta samples were collected from jejunum, ileum, and distal colon on day 21 post inoculation to perform 16S rRNA sequencing. Sampling days and locations influenced (p < 0.05) Chao1 index and beta-diversity. Age increased (p  < 0.05) the relative abundance of Firmicutes but decreased (p < 0.05) the relative abundance of Bacteroidetes in feces. ETEC infection increased (p  < 0.05) the relative abundance of Proteobacteria in feces on day 7 post inoculation. AGP reduced (p < 0.05) relative abundance of Firmicutes and Lactobacillaceae in feces compared with PC and DFM. AGP reduced (p < 0.05) relative abundance of Bifidobacteriaceae in jejunum and ileum, while DFM reduced (p < 0.05) relative abundance of Actinomycetaceae in jejunum and Lachnospiraceae in ileum, compared with PC. Pigs fed with DFM had greater (p < 0.05) relative abundance of Ruminococcaceae, Veillonellaceae, Bifidobacteriaceae in jejunum, Lactobacillaceae in ileum and colon, and Bifidobacteriaceae in colon than pigs in AGP. Current results indicate that carbadox or B. subtilis had stronger influences on microbial diversity and composition in ileum than other intestinal segments and feces. Supplementation of B. subtilis could increase or maintain the relative abundance of beneficial bacteria in ileum compared with carbadox.

Characterization of Intestinal Microbiota in Lambs with Different Susceptibility to Escherichia coli F17

Diarrhea is one of the most commonly reported diseases in young farm animals. Escherichia coli (E. coli) F17 is one of the major pathogenic bacteria responsible for diarrhea. However, the pathogenicity of diarrhea in lambs involving E. coli F17 strains and how E. coli F17 infection modifies lambs' intestinal microbiota are largely unknown. To evaluate diarrhea in newborn lambs with an infection of E. coli F17, 50 lambs were selected for challenge experiments and divided into four groups, namely, a high-dose challenge group, low-dose challenge group, positive control group, and negative control group. The E. coli F17 challenge experiments caused diarrhea and increased mortality in the experimental lamb population, with a higher prevalence (90%), mortality (35%), and rapid onset time (4-12 h) being observed in the high-dose challenge group than the results observed in the low-dose challenge group (75%, 10%, 6-24 h, respectively). After the challenge experiment, healthy lambs in the high-dose challenge group and severely diarrheic lamb in the low-dose challenge group were identified as lambs sensitive/resistant to E. coli F17 (E. coli F17 -resistant/-sensitive candidate, AN/SE) according to the histopathological detection. Results of intestinal contents bacteria plate counting revealed that the number of bacteria in the intestinal contents of SE lambs was 10^2~3-fold greater than that of the AN lambs, especially in the jejunum. Then, 16S rRNA sequencing was conducted to profile the intestinal microbiota using the jejunal contents, and the results showed that SE lambs had higher Lactococcus and a lower Bacteroidetes:Firmicutes ratio and intestinal microbiota diversity in the jejunum than AN lambs. Notably, high abundance of Megasphaera elsdenii was revealed in AN lambs, which indicated that Megasphaera elsdenii may serve as a potential probiotic for E. coli F17 infection. Our study provides an alternative challenge model for the identification of E. coli F17-sensitive/-resistant lambs and contributes to the basic understandings of intestinal microbiota in lambs with different susceptibilities to E. coli F17.

Formulating Diets for Improved Health Status of Pigs: Current Knowledge and Perspectives

Our understanding of nutrition has been evolving to support both performance and immune status of pigs, particularly in disease-challenged animals which experience repartitioning of nutrients from growth towards the immune response. In this sense, it is critical to understand how stress may impact nutrient metabolism and the effects of nutritional interventions able to modulate organ (e.g., gastrointestinal tract) functionality and health. This will be pivotal in the development of effective diet formulation strategies in the context of improved animal performance and health. Therefore, this review will address qualitative and quantitative effects of immune system stimulation on voluntary feed intake and growth performance measurements in pigs. Due to the known repartitioning of nutrients, the effects of stimulating the immune system on nutrient requirements, stratified according to different challenge models, will be explored. Finally, different nutritional strategies (i.e., low protein, amino acid-supplemented diets; functional amino acid supplementation; dietary fiber level and source; diet complexity; organic acids; plant secondary metabolites) will be presented and discussed in the context of their possible role in enhancing the immune response and animal performance.

Intestinal and Mucosal Microbiome Response to Oral Challenge of Enterotoxigenic Escherichia coli in Weaned Pigs

Enterotoxigenic Escherichia coli (ETEC) is closely associated with diarrhoea in children in resource-limited countries. This study aims to investigate the change of the mucosal microbiome and protein expression in the ileum induced by E. coli K88 (ETEC) using pigs as a model. Seven weaned male pigs were orally given ETEC (1 × 10⁹ CFU, n = 7), and the other seven received saline (CON, n = 7). Ileal tissues were obtained 48 hours after the ETEC challenge for both proteomic and mucosal microbiome analyses. Nine proteins were found with altered abundance between the two groups, including a decrease in FABP1 and FABP6, involved in bile acid circulation. The TLR-9 mediated pathway was also affected showing increased transcription of genes SIGIRR and MyD88. Correlations between the ileal proteins and mucosal bacterial taxa found included a positive correlation between Lactobacilllus and PPP3CA (r = 0.9, p < 0.001) and a negative correlation between Prevotella with CTNND1 (r = −0.7, p < 0.01). In conclusion, ETEC infection caused inflammation and impaired the circulation of bile acids and the mucosal microbiome may affect the expression of intestinal proteins. Further studies are needed to explain the exact roles of these affected processes in the pathogenesis of ETEC-triggered diarrhoea.

Effects of a blend of essential oils, medium-chain fatty acids and a toxin-adsorbing mineral on diarrhea and gut microbiome of weanling pigs experimentally infected with a pathogenic E. coli

A proprietary antimicrobial feed additive comprised of essential oils, medium-chain fatty acids, and a toxin-adsorbing mineral showed promising bacteriostatic and bactericidal effects in vitro. This study investigated the impacts of supplementing this blend on growth, gut microbiome, and enteric disease resilience in weaned pigs experimentally challenged with an enterotoxigenic Escherichia coli (ETEC). Thirty-six weanling pigs (6.88 ± 0.30 kg body weight (BW)) blocked by weight and gender were assigned to one of three dietary treatments: control or dietary supplementation with 0.25% or 0.50% of the antimicrobial blend. This study lasted 28 d with 7 d before and 21 d after the first ETEC inoculation (d 0). All pigs were orally inoculated with 10 10 cfu F18+ ETEC/3-mL dose for 3 consecutive days. Growth performance data and diarrhea scores were recorded throughout the experiment. Fecal samples collected on d -7, 0, 7 and 21 post first inoculation (PI), and ileal digesta and mucosal tissue collected on d 21 PI were further analyzed for gut microbiome using 16S rRNA sequencing. All data, except for frequency of diarrhea and gut microbiome, were analyzed by ANOVA using the PROC MIXED of SAS. The Chi-square test was used for analyzing frequency of diarrhea. Gut microbiome data were analyzed using QIIME2 and visualized using the R program. Dietary supplementation of 0.25% or 0.5% of the antimicrobial blend increased (P < 0.05) feed efficiency on d 14 to 21 PI of ETEC and reduced (P < 0.05) frequency of diarrhea during the study. Compared to the control group, adding 0.5% dietary antimicrobial blend increased (P < 0.05) relative abundance of Firmicutes but reduced (P < 0.05) Bacteroidetes and Proteobacteria in feces on d 7 PI. Pigs that received the antimicrobial blend also had higher (P < 0.05) relative abundance of Lactobacillaceae, but lower (P < 0.05) relative abundance of Enterobacteriaceae in feces on d 7 PI than pigs in control. In conclusion, supplementation of this antimicrobial blend at 0.5% reduced incidence of severe diarrhea in weaned pigs challenged with F18 ETEC and enhanced feed efficiency of weaned pigs at the last week of the experiment. Supplementation of this antimicrobial blend also modified the microbiota diversity in feces and ileal mucosa of weaned pigs.

Milk microbiome in dairy cattle and the challenges of low microbial biomass and exogenous contamination

Background

The blanket usage of antimicrobials at the end of lactation (or “drying off”) in dairy cattle is under increasing scrutiny due to concerns about antimicrobial resistance. To lower antimicrobial usage in dairy farming, farmers are now encouraged to use “selective dry cow therapy” whereby only cows viewed as at high risk of mastitis are administered antimicrobial agents. It is important to gain a better understanding of how this practice affects the udder-associated microbiota and the potential knock-on effects on antimicrobial-resistant bacterial populations circulating on the farm. However, there are challenges associated with studying low biomass environments such as milk, due to known contamination effects on microbiome datasets. Here, we obtained milk samples from cattle at drying off and at calving to measure potential shifts in bacterial load and microbiota composition, with a critical assessment of contamination effects.

Results

Several samples had no detectable 16S rRNA gene copies and crucially, exogenous contamination was detected in the initial microbiome dataset. The affected samples were removed from the final microbiome analysis, which compromised the experimental design and statistical analysis. There was no significant difference in bacterial load between treatments (P > 0.05), but load was lower at calving than at drying off (P = 0.039). Escherichia coli counts by both sequence and culture data increased significantly in the presence of reduced bacterial load and a decreasing trend of microbiome richness and diversity. The milk samples revealed diverse microbiomes not reflecting a typical infection profile and were largely comprised of gut- and skin-associated taxa, with the former decreasing somewhat after prolonged sealing of the teats.

Conclusions

The drying off period had a key influence on microbiota composition and bacterial load, which appeared to be independent of antimicrobial usage. The interactions between drying off treatment protocol and milk microbiome dynamics are clearly complex, and our evaluations of these interactions were restricted by low biomass samples and contamination effects. Therefore, our analysis will inform the design of future studies to establish whether different selection protocols could be implemented to further minimise antimicrobial usage.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-021-00144-x.

Temporal and nutritional effects on the weaner pig ileal microbiota

BACKGROUND

The porcine gastrointestinal microbiota has been linked to both host health and performance. Most pig gut microbiota studies target faecal material, which is not representative of microbiota dynamics in other discrete gut sections. The weaning transition period in pigs is a key development stage, with gastrointestinal problems being prominent after often sudden introduction to a solid diet. A better understanding of both temporal and nutritional effects on the small intestinal microbiota is required. Here, the development of the porcine ileal microbiota under differing levels of dietary protein was observed over the immediate post-weaning period.

RESULTS

Ileal digesta samples were obtained at post-mortem prior to weaning day (day - 1) for baseline measurements. The remaining pigs were introduced to either an 18% (low) or 23% (high) protein diet on weaning day (day 0) and further ileal digesta sampling was carried out at days 5, 9 and 13 post-weaning. We identified significant changes in microbiome structure (P = 0.01), a reduction in microbiome richness (P = 0.02) and changes in the abundance of specific bacterial taxa from baseline until 13 days post-weaning. The ileal microbiota became less stable after the introduction to a solid diet at weaning (P = 0.036), was highly variable between pigs and no relationship was observed between average daily weight gain and microbiota composition. The ileal microbiota was less stable in pigs fed the high protein diet (P = 0.05), with several pathogenic bacterial genera being significantly higher in abundance in this group. Samples from the low protein and high protein groups did not cluster separately by their CAZyme (carbohydrate-active enzyme) composition, but GH33 exosialidases were found to be significantly more abundant in the HP group (P = 0.006).

CONCLUSIONS

The weaner pig ileal microbiota changed rapidly and was initially destabilised by the sudden introduction to feed. Nutritional composition influenced ileal microbiota development, with the high protein diet being associated with an increased abundance of significant porcine pathogens and the upregulation of GH33 exosialidases-which can influence host-microbe interactions and pathogenicity. These findings contribute to our understanding of a lesser studied gut compartment that is not only a key site of digestion, but also a target for the development of nutritional interventions to improve gut health and host growth performance during the critical weaning transition period.

Low Crude Protein Diet Affects the Intestinal Microbiome and Metabolome Differently in Barrows and Gilts

Low protein diets are commonly used in the growing-finishing pig stage of swine production; however, the effects of low dietary protein on the intestinal microbiota and their metabolites, and their association with pig sex, remain unclear. The present study aimed to assess the impact of a low crude protein (CP) diet on the gut microbiome and metabolome, and to reveal any relationship with sex. Barrows and gilts (both n = 24; initial body = 68.33 ± 0.881 kg) were allocated into two treatments according to sex. The four groups comprised two pairs of gilts and barrows fed with a high protein diet (CP 17% at stage I; CP 13% at stage II) and a low protein diet (CP 15% at stage I; CP 11% at stage II), respectively, for 51 d. Eight pigs in each group were slaughtered and their colon contents were collected. Intestinal microbiota and their metabolites were assessed using 16S rRNA sequencing and tandem mass spectrometry, respectively. The low protein diet increased intestinal microbiota species and richness indices (P < 0.05) in both sexes compared with the high protein diet. The sample Shannon index was different (P < 0.01) between barrows and gilts. At the genus level, unidentified Clostridiales (P < 0.05), Neisseria (P < 0.05), unidentified Prevotellaceae (P < 0.01) and Gracilibacteria (P < 0.05) were affected by dietary protein levels. The relative abundance of unidentified Prevotellaceae was different (P < 0.01) between barrows and gilts. The influence of dietary protein levels on Neisseria (P < 0.05), unidentified Prevotellaceae (P < 0.01) and Gracilibacteria (P < 0.05) were associated with sex. Metabolomic profiling indicated that dietary protein levels mainly affected intestinal metabolites in gilts rather than barrows. A total of 434 differentially abundant metabolites were identified in gilts fed the two protein diets. Correlation analysis identified that six differentially abundant microbiota communities were closely associated with twelve metabolites that were enriched for amino acids, inflammation, immune, and disease-related metabolic pathways. These results suggested that decreasing dietary protein contents changed the intestinal microbiota in growing-finishing pigs, which selectively affected the intestinal metabolite profiles in gilts.

Infection Heterogeneity and Microbiota Differences in Chicks Infected by Salmonella enteritidis

This study was conducted to compare the infection heterogeneity and cecal microbiota in chicks infected by S. enteritidis. Forty-eight 8-d-old female Arbor Acres chicks were challenged with S. enteritidis and euthanized 24 h later. The eight chicks with the highest Salmonella tissue loads were assigned to group S (S. enteritidis-susceptible), and the eight chicks with the lowest Salmonella tissue loads were assigned to group R (S. enteritidis-resistant). Chicks in group S showed a higher liver index (p < 0.05), obvious liver lesions, and an decreasing trend for the villus height-to-crypt depth ratio (p < 0.10), compared with those in group R. Gene expression of occludin, MUC2, and IL10 was higher, whereas that of iNOS and IL6 was lower (p < 0.05), in chicks of group R relative to those in group S. Separation of the cecal microbial community structure has been found between the two groups. The S. enteritidis-susceptible chicks showed higher abundance of pathogenic bacteria (Fusobacterium and Helicobacter) in their cecal, while Desulfovibrio_piger was enriched in the cecal of S. enteritidis-resistant chicks. In summary, chicks showed heterogeneous responses to S. enteritidis infection. Enhanced intestinal barrier function and cecal microbiota structure, especially a higher abundance of Desulfovibrio_piger, may help chicks resist S. enteritidis invasion.

Evolution of Pig Fecal Microbiota Composition and Diversity in Response to Enterotoxigenic Escherichia coli Infection and Colistin Treatment in Weaned Piglets

The intestinal microbiota plays several important roles in pig health and growth. The aim of the current study was to characterize the changes in the fecal microbiota diversity and composition of weaned piglets following an oral challenge with an ETEC: F4 strain and/or a treatment with colistin sulfate (CS). Twenty-eight piglets were used in this experiment and were divided into four groups: challenged untreated, challenged treated, unchallenged treated, and unchallenged untreated. Rectal swab samples were collected at five sampling times throughout the study. Total genomic DNA was used to assess the fecal microbiota diversity and composition using the V4 region of the 16S rRNA gene. The relative abundance, the composition, and the community structure of piglet fecal microbiota was highly affected by the ETEC: F4 challenge throughout the experiment, while the oral treatment with CS, a narrow spectrum antibiotic, resulted in a significant decrease of E. coli/Shigella populations during the treatment period only. This study was the first to identify some gut microbiota subgroups (e.g., Streptococcus, Lachnospiraceae) that are associated with healthy piglets as compared to ETEC: F4 challenged animals. These key findings might contribute to the development of alternative strategies to reduce the use of antimicrobials in the control of post-weaning diarrhea in pigs.

Interaction of CP levels in maternal and nursery diets, and its effect on performance, protein digestibility, and serum urea levels in piglets

Reduced protein levels in nursery diets have been associated with a lower risk of postweaning diarrhea, but the interaction with CP levels in maternal diet on the performance of the offspring remains unclear. The objective of this study was to determine the effect of protein content in sow gestation and piglet nursery diets on the performance of the piglets until slaughter. This was studied in a 2 × 2 factorial trial (35 sows, 209 piglets), with higher or lower (H or L) dietary CP in sow diets (168 vs 122 g CP/kg) during late gestation. A standard lactation feed was provided for all sows (160 g CP/kg). For both sow treatments, half of the litters received a higher or lower CP in the piglet nursery diet (210 vs 166 g CP/kg). This resulted in four possible treatment combinations: HH, HL, LH and LL, with sow treatment as first and piglet treatment as second letter. For each phase, all diets were iso-energetic and had a similar level of essential amino acids. P_s*p is the p-value for the interaction effect between sow and piglet treatment. In the nursery phase (3.5-9 weeks of age), a tendency toward interaction between piglet and sow treatments with feed efficiency (P_s*p = 0.08) was observed with HH having the highest gain:feed ratio (G:F) (0.74 ± 0.01), LH the lowest (0.70 ± 0.01) and the other two groups intermediate. In the growing-finishing phase, an interaction was observed between the piglet and sow diets with decreased G:F for LH (P_s*p = 0.04) and a tendency toward interaction with increased daily feed intake for LH (P_s*p = 0.07). The sow diet showed a tendency toward a long-lasting effect on the dressing percentage and meat thickness of the offspring, which was higher for the progeny of H sows (P_s < 0.01 and P_s = 0.02, respectively). At 23 weeks, serum urea concentrations tended to be lower for the HH and LL groups (P_s*p = 0.07). Fecal consistency scores were higher at day 10-day 14 after weaning for piglets from L sows (P_s = 0.03 and P_s < 0.01, respectively). At day 7 after weaning, fecal consistency score was higher for piglets fed the higher protein diet (P_p < 0.01). At 8 weeks of age, the apparent total tract digestibility of CP (ATTD_CP) interacted between piglet and sow diet (P_s*p = 0.02), with HH showing the highest digestibility values. In conclusion, the protein levels in sow late-gestation and piglet nursery diets interacted with feed efficiency, ATTD_CP and serum urea concentrations in the nursery phase.

Comparison of Strategies for Isolating Anaerobic Bacteria from the Porcine Intestine

The isolation of bacteria that represent the diversity of autochthonous taxa in the gastrointestinal tract is necessary to fully ascertain their function, but the majority of bacterial species inhabiting the intestines of mammals are fastidious and thus challenging to isolate. The goal of the current study was to isolate a diverse assemblage of anaerobic bacteria from the intestine of pigs as a model animal and to comparatively examine various novel and traditional isolation strategies. Methods used included long-term enrichments, direct plating, a modified ichip method, as well as ethanol and tyndallization treatments of samples to select for endospore-forming taxa. A total of 234 taxa (91 previously uncultured) comprising 80 genera and 7 phyla were isolated from mucosal and luminal samples from the ileum, cecum, ascending colon, and spiral colon removed from animals under anesthesia. The diversity of bacteria isolated from the large intestine was less than that detected by next-generation sequence analysis. Long-term enrichments yielded the greatest diversity of recovered bacteria (Shannon's index [SI] = 4.7). Methods designed to isolate endospore-forming bacteria produced the lowest diversity (SI ≤ 2.7), with tyndallization yielding lower diversity than the ethanol method. However, the isolation frequency of previously uncultured bacteria was highest for ethanol-treated samples (41.9%) and the ichip method (32.5%). The goal of recovering a diverse collection of enteric bacteria was achieved. Importantly, the study findings demonstrate that it is necessary to use a combination of methods in concert to isolate bacteria that are representative of the diversity within the intestines of mammals.IMPORTANCE This work determined that using a combination of anaerobic isolation methods is necessary to increase the diversity of bacteria recovered from the intestines of monogastric mammals. Direct plating methods have traditionally been used to isolate enteric bacteria, and recent methods (e.g., diffusion methods [i.e., ichip] or differential isolation of endospore-forming bacteria) have been suggested to be superior at increasing diversity, including the recovery of previously uncultured taxa. We showed that long-term enrichment of samples using a variety of media isolated the most diverse and novel bacteria. Application of the ichip method delivered a diversity of bacteria similar to those of enrichment and direct plating methods. Methods that selected for endospore-forming bacteria generated collections that differed in composition from those of other methods with reduced diversity. However, the ethanol treatment frequently isolated novel bacteria. By using a combination of methods in concert, a diverse collection of enteric bacteria was generated for ancillary experimentation.

Functional amino acid supplementation, regardless of dietary protein content, improves growth performance and immune status of weaned pigs challenged with Salmonella Typhimurium

High dietary protein may increase susceptibility of weaned pigs to enteric pathogens. Dietary supplementation with functional amino acids (FAA) may improve growth performance of pigs during disease challenge. The objective of this study was to evaluate the interactive effects of dietary protein content and FAA supplementation above requirements for growth on performance and immune response of weaned pigs challenged with Salmonella. Sixty-four mixed-sex weanling pigs (13.9 ± 0.82 kg) were randomly assigned to dietary treatments in a 2 × 2 factorial arrangement with low (LP) or high protein (HP) content and basal (AA-) or FAA profile (AA+; Thr, Met, and Trp at 120% of requirements) as factors. After a 7-d adaptation period, pigs were inoculated with either a sterile saline solution (CT) or saline solution containing Salmonella Typhimurium (ST; 3.3 × 109 CFU/mL). Growth performance, body temperature, fecal score, acute-phase proteins, oxidant/antioxidant balance, ST shedding score in feces and intestinal colonization, fecal and digesta myeloperoxidase (MPO), and plasma urea nitrogen (PUN) were measured pre- and postinoculation. There were no dietary effects on any measures pre-inoculation or post-CT inoculation (P > 0.05). Inoculation with ST increased body temperature and fecal score (P < 0.05), serum haptoglobin, plasma superoxide dismutase (SOD), malondialdehyde (MDA), PUN, and fecal MPO, and decreased serum albumin and plasma reduced glutathione (GSH):oxidized glutathione (GSSG) compared with CT pigs (P < 0.05). ST-inoculation reduced average daily gain (ADG) and feed intake (ADFI) vs. CT pigs (P < 0.05) but was increased by AA+ vs. AA- in ST pigs (P < 0.05). Serum albumin and GSH:GSSG were increased while haptoglobin and SOD were decreased in ST-inoculated pigs fed AA+ vs. AA- (P < 0.05). PUN was higher in HP vs. LP-fed pigs postinoculation (P < 0.05). Fecal ST score was increased in ST-inoculated pigs on days 1 and 2 postinoculation and declined by day 6 (P < 0.05) in all pigs while the overall score was reduced in AA+ vs. AA- pigs (P < 0.05). Cecal digesta ST score was higher in HP vs. LP-fed pigs and were lower in AA+ compared with AA- fed pigs in the colon (P < 0.05). Fecal and digesta MPO were reduced in ST pigs fed AA+ vs. AA- (P < 0.05). These results demonstrate a positive effect of FAA supplementation, with minimal effects of dietary protein, on performance and immune status in weaned pigs challenged with Salmonella.

Metabolomic Profile of Weaned Pigs Challenged with E. coli and Supplemented with Carbadox or Bacillus subtilis

This study explored the metabolomic profiles in ileal mucosa and colon digesta in response to enterotoxigenic Escherichia coli F18 (ETEC) infection and dietary use of probiotics and low-dose antibiotics. Weaned pigs (n = 48, 6.17 ± 0.36 kg body weight) were randomly allotted to one of four treatments. Pigs in the negative control (NC) were fed a basal diet without ETEC challenge, whereas pigs in the positive control (PC), antibiotic, and probiotic groups were fed the basal diet, basal diet supplemented with 50 mg/kg of carbadox, or 500 mg/kg of Bacillus subtilis, respectively, and orally challenged with ETEC F18. All pigs were euthanized at day 21 post-inoculation to collect ileal mucosa and colon digesta for untargeted metabolomic profiling using gas chromatography coupled with time-of-flight mass spectrometry. Multivariate analysis highlighted a more distinct metabolomic profile of ileal mucosa metabolites in NC compared to the ETEC-challenged groups. The relative abundance of 19 metabolites from the ileal mucosa including polyamine, nucleotide, monosaccharides, fatty acids, and organic acids was significantly different between the NC and PC groups (q < 0.1). In colon digesta, differential metabolites including 2-monoolein, lactic acid, and maltose were reduced in the carbadox group compared with the probiotics group. In conclusion, several differential metabolites and metabolic pathways were identified in ileal mucosa, which may suggest an ongoing intestinal mucosal repair in the ileum of ETEC-challenged pigs on day 21 post-inoculation.

Relationships among Fecal, Air, Oral, and Tracheal Microbial Communities in Pigs in a Respiratory Infection Disease Model

The association of the lower respiratory tract microbiome in pigs with that of other tissues and environment is still unclear. This study aimed to describe the microbiome of tracheal and oral fluids, air, and feces in the late stage of Mycoplasma hyopneumoniae infection in pigs, and assess the association between the tracheal microbiome and those from air, feces, and oral fluids. Tracheal fluids (n = 73), feces (n = 71), oropharyngeal fluids (n = 8), and air (n = 12) were collected in seeder pigs (inoculated with M. hyopneumoniae) and contact pigs (113 days post exposure to seeder pigs). After DNA extraction, the V4 region from 16S rRNA gene was sequenced and reads were processed using Divisive Amplicon Denoising Algorithm (DADA2). Clostridium and Streptococcus were among the top five genera identified in all sample types. Mycoplasma hyopneumoniae in tracheal fluids was associated with a reduction of diversity and increment of M. hyorhinis, Glaesserella parasuis, and Pasteurella multocida in tracheal fluids, as well as a reduction of Ruminiclostridium, Barnesiella, and Lactobacillus in feces. Air contributed in a greater proportion to bacteria in the trachea compared with feces and oral fluids. In conclusion, evidence suggests the existence of complex interactions between bacterial communities from distant and distinct niches.

Impact of dietary components on enteric infectious disease

Diets impact host health in multiple ways and an unbalanced diet could contribute to the initiation or progression of a variety of diseases. Although a wealth of information exists on the connections between diet and chronic metabolic diseases such as cardiovascular disease, diabetes mellitus, etc., how diet influences enteric infectious disease still remain underexplored. The review summarizes the current findings on the link between various dietary components and diverse enteric infectious diseases. Dietary ingredients discussed include macronutrients (carbohydrates, lipids, proteins), micronutrients (vitamins, minerals), and other dietary ingredients (phytonutrients and probiotic supplements). We first describe the importance of enteric infectious diseases and the direct and indirect relationship between diet and enteric infectious diseases. Then we discuss the effects of different dietary components on the susceptibility to or progression of enteric infectious disease. Finally, we delineate current knowledge gap and highlighted future research directions. The literature review revealed that different dietary components affect host resistance to enteric infections through a variety of mechanisms. Dietary components may directly inhibit or bind to enteric pathogens, or indirectly influence enteric infections through modulating immune function and gut microbiota. Elucidating the unique repercussions of different diets on enteric infections in this review may help provide dietary guidelines or design dietary interventions to prevent or alleviate enteric infectious diseases.

Alternatives to antibiotics in a One Health context and the role genomics can play in reducing antimicrobial use

BACKGROUND

This review follows on from the International Conference on One Health Antimicrobial Resistance (ICOHAR 2019), where strategies to improve the fundamental understanding and management of antimicrobial resistance at the interface between humans, animals and the environment were discussed.

OBJECTIVE

This review identifies alternatives to antimicrobials in a One Health context, noting how advances in genomic technologies are assisting their development and enabling more targeted use of antimicrobials.

SOURCES

Key articles on the use of microbiota modulation, livestock breeding and gene editing, vaccination, antivirulence strategies and bacteriophage therapy are discussed.

CONTENT

Antimicrobials are central for disease control, but reducing their use is paramount as a result of the rise of transmissible antimicrobial resistance. This review discusses antimicrobial alternatives in the context of improved understanding of fundamental host-pathogen and microbiota interactions using genomic tools.

IMPLICATIONS

Host and microbial genomics and other novel technologies play an important role in devising disease control strategies for healthier animals and humans that in turn reduce our reliance on antimicrobials.