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The protozoan parasite Cystoisospora suis causes diarrhea and reduced weight gain in suckling piglets. Infections occur in the first days of life; it is transient but can lead to dysbiosis, exacerbating disease and increasing mortality. Cystoisosporosis is effectively controlled by toltrazuril treatment; however, alterations of the gut microbial composition upon infection and treatment have not been investigated. This study evaluated the development of fecal microbiota of C. suis infected piglets in response to treatment with toltrazuril. Thirty-eight conventional piglets were infected with C. suis on the first day of life (dol 1). Twenty-six of them received either parenteral or oral toltrazuril 2 days later. Fecal samples were collected pre- and post-weaning (dol 1–15 and 31–38) for microbiota analysis using 16S rRNA amplicon sequencing and during dol 5–18 to determine fecal consistency and parasite excretion. All control animals shed parasites at least once and the majority developed diarrhea, while toltrazuril-treated piglets did not excrete parasites and only had low levels of diarrhea. Age-related shifts in the fecal microbiota composition and increase in diversity and species richness were seen until after weaning. Parasite infection disrupted bacterial maturation 2 weeks after infection. Irrespective of the route of administration, fecal communities of piglets in the treated groups clustered separately and were more diverse compared to that of control piglets during the acute phase of infection on dol 11. Control piglet feces showed higher levels of Fusobacteriaceae and Veillonellaceae, while Ruminococcaceae, Lachnospiraceae, S24-7, Clostridiaceae, and Erysipelotrichaceae were more abundant in feces of treated piglets on dol 11. Thereafter, treatment-related effects on the microbial communities were small and mainly detectable on dol 34 (5 days post-weaning), potentially indicating that the oral toltrazuril treatment might have had long-term effects on host physiological responses post-weaning. Irrespective of the administration route, toltrazuril prevented C. suis-related dysbiosis and maintained species richness and diversity on dol 11. In addition to cystoisosporosis prevention, toltrazuril seems to contribute to the stabilization of the gut microbial development during the suckling phase and thus may reduce the need for antibiotics to control infections with secondary bacterial enteropathogens in C. suis-infected suckling piglets.

Besides the major nutrients, phosphorus (P) is an essential mineral for both the host animal and the porcine gut microbiota. Different strategies including phytase supplementation and more recently lactic acid (LA) are used to enhance the P availability from cereals in pig diets; however, their impact on the gut microbiota has been rarely related to fecal shedding of opportunistic pathogens. The present study investigated the effect of phytase supplementation and the treatment of dietary cereals with 2.5% LA on the fecal microbiome composition of metabolic active bacteria and expression of virulence factor genes of enterotoxigenic Escherichia coli and Clostridium perfringens in growing pigs. Phytase supplementation reduced the fecal abundance of the most abundant Lactobacillaceae family, whereas the LA-treatment of cereals had a stronger impact on the bacterial community, reducing amylolytic, pullulanolytic and hemicellulolytic Lactobacillaceae, Lachnospiraceae and Ruminococcaceae as well as the fecal bacterial species richness (Chao1) and diversity (Shannon index). Mainly the family Clostridiaceae benefited from the decline in the aforementioned families, being enriched by both dietary treatments. Multigroup data integration using sparse partial least squares-discriminant analysis showed that among the most discriminative operational taxonomic units (OTU) especially two unclassified Clostridiaceae-OTUs, one Prevotella copri-like OTU and one OTU within the vadinCA11 group were associated with calcium and P levels but were negatively linked with complex carbohydrates in feces. Heat-stable toxin A (Sta) of enterotoxigenic E. coli and Stx2e of Shiga-toxin producing E. coli were expressed in feces but were similar among feeding groups. Without modifying the total bacterial gene copies and virulence factor expression of E. coli, both dietary phytase supplementation and LA-treatment of cereals drastically altered the bacterial community composition in pig feces. Results thereby allowed for the characterization of bacterial nutrient dependencies, indicating a link between fecal P availability, complex carbohydrate composition and alterations in the predominant genera.

Fecal microbiota transplants (FMT) may be used to improve chicken’s feed efficiency (FE) via modulation of the intestinal microbiota and microbe-host signaling. This study investigated the effect of the administration of FMT from highly feed efficient donors early in life on the jejunal and cecal microbiota, visceral organ size, intestinal morphology, permeability, and expression of genes for nutrient transporters, barrier function and innate immune response in chickens of diverging residual feed intake (RFI; a metric for FE). Chicks (n = 110) were inoculated with the FMT or control transplant (CT) on 1, 6, and 9 days posthatch (dph), from which 56 chickens were selected on 30 dph as the extremes in RFI, resulting in 15 low and 13 high RFI chickens receiving the FMT and 14 low and 14 high RFI chickens receiving the CT. RFI rank and FMT only caused tendencies for alterations in the jejunal microbiota and only one unclassified Lachnospiraceae genus in cecal digesta was indicative of high RFI. By contrast, the FMT caused clear differences in the short-chain fatty acid (SCFA) profile in the crop and cecal microbiota composition compared to the CT, which indicated alterations in amylolytic, pullulanolytic and hemicellulolytic bacteria such as Lactobacillus, Dorea, and Ruminococcus. Moreover, the FMT caused alterations in intestinal development as indicated by the longer duodenum and shallower crypts in the ceca. From the observed RFI-associated variation, energy-saving mechanisms and moderation of the mucosal immune response were indicated by higher jejunal permeability, shorter villi in the ileum, and enhanced cecal expression of the anti-inflammatory cytokine IL10 in low RFI chickens. Relationships obtained from supervised multigroup data integration support that certain bacteria, including Ruminococcocaceae-, Lactobacillus-, and unclassified Clostridiales-phylotypes, and SCFA in jejunal and cecal digesta modulated expression levels of cytokines, tight-junction protein OCLN and nutrient transporters for glucose and SCFA uptake. In conclusion, results suggest that the intestine only played a moderate role for the RFI-associated variation of the present low and high RFI phenotypes, whereas modulating the early microbial colonization resulted in long-lasting changes in bacterial taxonomic and metabolite composition as well as in host intestinal development.

There is a great interest to understand the impact of the gut microbiota on host's nutrient use and FE in chicken production. Both chicken's feed intake and gut bacterial microbiota differ between high and low-feed efficient chickens. To evaluate the impact of the feed intake level on the feed efficiency (FE)-associated variation in the chicken intestinal microbiota, differently feed efficient chickens need to eat the same amount of feed, which can be achieved by feeding chickens restrictively. Therefore, we investigated the effect of restrictive vs. ad libitum feeding on the fecal microbiome at 16 and 29 days posthatch (dph), FE and nutrient retention in chickens of low and high residual feed intake (RFI; metric for FE). Restrictively fed chickens were provided the same amount of feed which corresponded to 85% of the ad libitum fed group from 9 dph. FE was determined for the period between 9 and 30 dph and feces for nutrient retention were collected on 31 to 32 dph. From the 112 chickens (n = 56 fed ad libitum, and n = 56 fed restrictively), 14 low RFI and 15 high RFI ad libitum fed chickens, and 14 low RFI (n = 7 per sex) and 14 high RFI restrictively fed chickens were selected as the extremes in RFI and were retrospectively chosen for data analysis. Bray-Curtis dissimilarity matrices showed significant separation between time points, and feeding level groups at 29 dph for the fecal bacterial communities. Relevance networking indicated positive associations between Acinetobacter and feed intake at 16 dph, whereas at 29 dph Escherichia/Shigella and Turicibacter positively and Lactobacillus negatively correlated to chicken's feed intake. Enterobacteriaceae was indicative for low RFI at 16 dph, whereas Acinetobacter was linked to high RFI across time points. However, restrictive feeding-associated changes in the fecal microbiota were not similar in low and high RFI chickens, which may have been related to the higher nutrient retention and thus lower fecal nutrient availability in restrictively fed high RFI chickens. This may also explain the decreased RFI value in restrictively fed high RFI chickens indicating improved FE, with a stronger effect in females.

Dietary deoxynivalenol (DON) impairs the intestinal functions and performance in broiler chickens, whereas little is known about the effect of DON on the gastrointestinal microbiota. This study evaluated the impact of graded levels of dietary DON contamination on the cecal bacterial microbiota, their predicted metabolic abilities and short-chain fatty acid (SCFA) profiles in chickens. In using a single oral lipopolysaccharide (LPS) challenge we further assessed whether an additional intestinal stressor would potentiate DON-related effects on the cecal microbiota. Eighty 1-day-old chicks were fed diets with increasing DON concentrations (0, 2.5, 5, and 10 mg DON per kg diet) for 5 weeks and were sampled after half of the chickens received an oral LPS challenge (1 mg LPS/kg bodyweight) 1 day before sampling. The bacterial composition was investigated by Illumina MiSeq sequencing of the V3–5 region of the 16S rRNA gene. DON-feeding decreased (p < 0.05) the cecal species richness (Chao1) and evenness (Shannon) compared to the non-contaminated diet. The phyla Firmicutes and Proteobacteria tended to linearly increase and decrease with increasing DON-concentrations, respectively. Within the Firmicutes, DON decreased the relative abundance of Oscillospira, Clostridiaceae genus, Clostridium, and Ruminococcaceae genus 2 (p < 0.05), whereas it increased Clostridiales genus 2 (p < 0.05). Moreover, increasing DON levels linearly decreased a high-abundance Enterobacteriaceae genus and an Escherichia/Shigella-OTU (p < 0.05). Changes in the bacterial composition and their imputed metagenomic capabilities may be explained by DON-related changes in host physiology and cecal nutrient availability. The oral LPS challenge only decreased the abundance of an unassigned Clostridiales genus 2 (p = 0.03). Increasing dietary concentrations of DON quadratically increased the cecal total SCFA and butyrate concentration (p < 0.05), whereas a DON × LPS interaction indicated that LPS mainly increased cecal total SCFA, butyrate, and acetate concentrations in chickens fed the diets that were not contaminated with DON. The present findings showed that even the lowest level of dietary DON contamination had modulatory effects on chicken's cecal bacterial microbiota composition and diversity, whereas the additional oral challenge with LPS did not potentiate DON effects on the cecal bacterial composition.

Dietary inclusion of resistant starches can promote host health through modulation of the gastrointestinal microbiota, short-chain fatty acid (SCFA) profiles, and lipid metabolism. This study investigated the impact of a transglycosylated cornstarch (TGS) on gastric, ileal, cecal, proximal-colonic, and mid-colonic bacterial community profiles and fermentation metabolites using a growing pig model. It additionally evaluated the effect of TGS on the expression of host genes related to glucose and SCFA absorption, incretins, and satiety in the gut as well as host genes related to lipid metabolism in hepatic and adipose tissue. Sixteen growing pigs (4 months of age) were fed either a TGS or control (CON) diet for 11 days. Bacterial profiles were determined via Illumina MiSeq sequencing of the V3–5 region of the 16S rRNA gene, whereas SCFA and gene expression were measured using gas chromatography and reverse transcription-quantitative PCR. Megasphaera, which was increased at all gut sites, began to benefit from TGS feeding in gastric digesta, likely through cross-feeding with other microbes, such as Lactobacillus. Shifts in the bacterial profiles from dietary TGS consumption in the cecum, proximal colon, and mid colon were similar. Relative abundances of Ruminococcus and unclassified Ruminococcaceae genus were lower, whereas that of unclassified Veillonellaceae genus was higher in TGS- compared to CON-fed pigs (p < 0.05). TGS consumption also increased (p < 0.05) concentrations of SCFA, especially propionate, and lactate in the distal hindgut compared to the CON diet which might have up-regulated GLP1 expression in the cecum (p < 0.05) and mid colon compared to the control diet (p < 0.10). TGS-fed pigs showed increased hepatic and decreased adipocyte expression of genes for lipid synthesis (FASN, SREBP1, and ACACA) compared to CON-fed pigs, which may be related to postprandial portal nutrient flow and reduced systemic insulin signaling. Overall, our data show that TGS consumption may affect gastrointestinal bacterial signaling, caused by changes in gut bacterial profiles and the action of propionate, and host lipid metabolism.

The exploration of microbiomes in lymphatic organs is relevant for basic and applied research into explaining microbial translocation processes and understanding cross-contamination during slaughter. This study aimed to investigate whether metabolically active bacteria (MAB) could be detected within tonsils and mandibular lymph nodes (MLNs) of pigs. The hypervariable V1-V2 region of the bacterial 16S rRNA genes was amplified from cDNA from tonsils and MLNs of eight clinically healthy slaughter pigs. Pyrosequencing yielded 82,857 quality-controlled sequences, clustering into 576 operational taxonomic units (OTUs), which were assigned to 230 genera and 16 phyla. The actual number of detected OTUs per sample varied highly (23-171 OTUs). Prevotella zoogleoformans and Serratia proteamaculans (best type strain hits) were most abundant (10.6% and 41.8% respectively) in tonsils and MLNs, respectively. To explore bacterial correlation patterns between samples of each tissue, pairwise Spearman correlations (rs) were calculated. In total, 194 strong positive and negative correlations |rs| ≥ 0.6 were found. We conclude that (i) lymphatic organs harbor a high diversity of metabolically active bacteria, (ii) the occurrence of viable bacteria in lymph nodes is not restricted to pathological processes and (iii) lymphatic tissues may serve as a contamination source in pig slaughterhouses. This study confirms the necessity of the EFSA regulation with regard to a meat inspection based on visual examinations to foster a minimization of microbial contamination.

The impact of a long-term subacute rumen acidosis (SARA) on the bovine epimural bacterial microbiome (BEBM) and its consequences for rumen health is poorly understood. This study aimed to investigate shifts in the BEBM during a long-term transient SARA model consisting of two concentrate-diet-induced SARA challenges separated by a one-week challenge break. Eight cows were fed forage and varying concentrate amounts throughout the experiment. In total, 32 rumen papilla biopsies were taken for DNA isolation (4 sampling time points per cow: at the baseline before concentrate was fed, after the first SARA challenge, after the challenge break, and after the second SARA challenge). Ruminal pH was continuously monitored. The microbiome was determined using Illumina MiSeq sequencing of the 16S rRNA gene (V345 region). In total 1,215,618 sequences were obtained and clustered into 6,833 operational taxonomic units (OTUs). Campylobacter and Kingella were the most abundant OTUs (16.5% and 7.1%). According to ruminal pH dynamics, the second challenge was more severe than the first challenge. Species diversity estimates and evenness increased during the challenge break compared to all other sampling time points (P