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Colonization of co-evolved, species-specific microbes in early life plays a crucial role in gastrointestinal development and immune function. This study hypothesized that modern pig production practices have resulted in the loss of co-evolved species and critical symbiotic host-microbe interactions. To test this, we reintroduced microbes from wild boars (WB) into conventional piglets to explore their colonization dynamics and effects on gut microbial communities, metabolite profiles, and immune responses. At postnatal day (PND) 21, 48 piglets were assigned to four treatment groups: (i) WB-derived mixed microbial community (MMC), (ii) sow-derived MMC, (iii) a combination of WB and sow MMC (Mix), or (iv) Control (PBS). Post-transplantation analyses at PND 48 revealed distinct microbial communities in WB-inoculated piglets compared with Controls, with trends toward differentiation from Sow but not Mix groups. WB-derived microbes were more successful in colonizing piglets, particularly in the Mix group, where they competed with Sow-derived microbes. WB group cecal digesta enriched with Lactobacillus helveticus , Lactobacillus mucosae , and Lactobacillus pontis . Cecal metabolite analysis showed that WB piglets were enriched in histamine, acetyl-ornithine, ornithine, citrulline, and other metabolites, with higher histamine levels linked to Lactobacillus abundance. WB piglets exhibited lower cecal IL-1β and IL-6 levels compared with Control and Sow groups, whereas the Mix group showed reduced IFN-γ, IL-2, and IL-6 compared with the Sow group. No differences in weight gain, fecal scores, or plasma cytokines were observed, indicating no adverse effects. These findings support that missing WB microbes effectively colonize domestic piglets and may positively impact metabolite production and immune responses.IMPORTANCEThis study addresses the growing concern over losing co-evolved, species-specific microbes in modern agricultural practices, particularly in pig production. The implementation of strict biosecurity measures and widespread antibiotic use in conventional farming systems may disrupt crucial host-microbe interactions that are essential for gastrointestinal development and immune function. Our research demonstrates that by reintroducing wild boar-derived microbes into domestic piglets, these microbes can successfully colonize the gut, influence microbial community composition, and alter metabolite profiles and immune responses without causing adverse effects. These findings also suggest that these native microbes can fill an intestinal niche, positively impacting immune activation. This research lays the groundwork for future strategies to enhance livestock health and performance by restoring natural microbial populations that produce immune-modulating metabolites.

The postweaning period in pigs is a critical window where nutritional interventions are implemented to prevent postweaning diarrhea (PWD) and antibiotic use. One common strategy is feeding low-protein diets immediately following weaning. This intervention may reduce protein fermentation and pathogen proliferation, therefore decreasing the incidence of postweaning diarrhea. These effects may also be mitigated by providing dietary fiber. However, studies examining the role of protein and fiber on gastrointestinal microbiota and metabolism are complicated by the presence of other substrates, including polyphenols and antinutritional factors in complex ingredients. In this study, semipurified diets formulated to meet nutrient requirements were fed to 40 weaned pigs ( n = 10/diet) to examine the effects of high protein (HP), high fiber (HF), or both (HFHP) compared with a control (CON) diet with industry-standard crude protein and fiber content. Critical alterations in host metabolism and cecal transcriptome were identified in response to the CON diet. Diets with lower protein levels (CON and HF) induced alteration in transcripts from the serine synthesis pathways and integrated stress response in cecal tissue alongside systemic increases in metabolic pathways related to lysine degradation. High protein diets did not induce increases in gastrointestinal pathogen abundance. These results challenge the practice of feeding low-protein diets postweaning, by demonstrating a detrimental effect on intestinal cell function and muscle accretion. This suggests that with careful ingredient selection, increased dietary protein postweaning could improve pig health and growth compared with a standard diet. NEW & NOTEWORTHY Although low-protein diets are commonly used for weaned pigs and are thought to decrease diarrhea incidence, this study showed that low-protein diets may induce muscle catabolism and intestinal epithelial stress response. Eventhough high-protein diets increased protein fermentation by gut microbes, no increase in diarrhea was detected. Protein fermentation was mitigated by fiber while still supporting growth and intestinal epithelial cell function, suggesting new strategies for feeding weaned pigs with careful ingredient selection.

Scope: Aging in males can lead to declines in testosterone production, essential for maintaining male reproductive health., Methods and Results: To investigate the effects of dietary supplementation with alpha-linolenic acid (ALA) on testosterone production in aged breeder roosters and understand the underlying molecular mechanisms involved. An in vivo model is established to investigate the effects of dietary ALA supplementation on testosterone production in aged breeder roosters, and the Leydig cell culture is used to identify the potential molecular mechanism. Dietary supplementation with ALA increases in plasma testosterone. Congruently, ALA supplementation enhances the expression of testosterone biosynthesis-related enzymes. ALA supplementation exerts anti-apoptotic effects in testicular mitochondria, as evidenced by a lower expression of pro-apoptotic factors and a higher expression of the anti-apoptotic factor B-cell lymphoma 2 (Bcl-2). Moreover, In Leydig cells, ALA supplementation promotes mitochondrial biogenesis genes. The proposed mechanism is that ALA activates the sirtuin1 (SIRT1) pathway and is supported by higher SIRT1 transcript and protein in Leydig cells. Furthermore, blocking SIRT1 with siRNA reverses ALA's effects on testosterone biosynthesis and mitochondrial function-related genes., Conclusion: These findings indicate that dietary supplementation with ALA can improve testosterone production in aged breeder roosters, possibly by modulation of mitochondrial function via activating the SIRT1 pathway., (© 2024 Wiley‐VCH GmbH.)

The microbiome of wild animals is believed to be co-evolved with host species, which may play an important role in host physiology. It has been hypothesized that the rigorous hygienic practices in combination with antibiotics and diets with simplified formulas used in the modern swine industry may negatively affect the establishment and development of the gut microbiome. In this study, we evaluated the fecal microbiome of 90 domestic pigs sampled from nine farms in Canada and 39 wild pigs sampled from three different locations on two continents (North America and Europe) using 16S rRNA gene amplicon sequencing. Surprisingly, the gut microbiome in domestic pigs exhibited higher alpha-diversity indices than wild pigs ( P < 0.0001). The wild pig microbiome showed a lower Firmicutes-to-Bacteroidetes ratio and a higher presence of bacterial phyla Elusimicrobiota, Verrucomicrobiota, Cyanobacteria, and Fibrobacterota when compared to their domestic counterparts. At the genus level, the wild pig microbiome had enriched genera that were known for fiber degradation and short-chain fatty acid production. Interestingly, the phylum Fusobacteriota was only observed in domestic pigs. We identified 31 ASVs that were commonly found in the pig gut microbiome, regardless of host sources, which could be recognized as members of the core gut microbiome. Interestingly, we found five ASVs missing in domestic pigs that were prevalent in wild ones, whereas domestic pigs harbored 59 ASVs that were completely absent in wild pigs. The present study sheds light on the impact of domestication on the pig gut microbiome, including the gain of new genera, which might provide the basis to identify novel targets to manipulate the pig gut microbiome for improved health., Importance: The microbiome of pigs plays a crucial role in shaping host physiology and health. This study sought to identify if domestication and current rearing practices have resulted in a loss of co-evolved bacterial species by comparing the microbiome of wild boar and conventionally raised pigs. It provides a comparison of domestic and wild pigs with the largest sample sizes and is the first to examine wild boars from multiple sites and continents. We were able to identify core microbiome members that were shared between wild and domestic populations, and on the contrary to expectation, few microbes were identified to be lost from wild boar. Nevertheless, the microbiome of wild boars had a lower abundance of important pathogenic genera and was distinct from domestic pigs. The differences in the microbial composition may identify an opportunity to shift the microbial community of domestic pigs towards that of wild boar with the intent to reduce pathogen load., Competing Interests: The authors declare no conflict of interest.

Egg white protein ovomucin and its hydrolysates were previously reported to exhibit anti-inflammatory and anti-adhesive activities. However, their potential to regulate pathogen colonization and disease severity has not been fully characterized. To investigate the effects of ovomucin (OVM) and its hydrolysates including ovomucin-Protex 26L (OP) and -pepsin/pancreatin (OPP) on host resistance to pathogen infection, a well-documented colitis model in mice for attaching and effacing E. coli pathogens, Citrobacter rodentium , was used in the current study. C57Bl/6J female mice were fed on a basal diet supplemented with OVM or its hydrolysates for 3 weeks prior to the C. rodentium challenge, with the dietary treatments continued for seven days. Body weight was not affected throughout the experimental period. OP supplementation resulted in lower ( P < 0.05) pathogen loads at 7 dpi. Attenuated colitis severity was observed in mice that received OVM and OP, as indicated by reduced colonic pathological scores and pro-inflammatory responses compared with the infected control group. In contrast, OPP consumption resulted in enhanced C. rodentium colonization and disease severity. Notably, reduced microbial diversity indices of the gut microbiota were observed in the OPP-supplemented mice compared with the OVM- and OP-supplemented groups. This study showed the potential of OVM and OP to alleviate the severity of colitis induced by infection while also suggesting the opposite outcome of OPP in mitigating enteric infection.

Importance: This work provides evidence that early-life fungal community composition, or host genetics, influences long-term mycobiome composition. In addition, this work provides the first comparison of the feral pig mycobiome to the mycobiome of intensively raised pigs., Competing Interests: The authors declare no conflict of interest.

Kefir is fermented traditionally with kefir grains, but commercial kefir production often relies on fermentation with planktonic cultures. Kefir has been associated with many health benefits, however, the utilization of kefir grains to facilitate large industrial production of kefir is challenging and makes to difficult to ensure consistent product quality and consistency. Notably, the microbial composition of kefir fermentations has been shown to impact kefir associated health benefits. This study aimed to compare volatile compounds, organic acids, and sugar composition of kefir produced through a traditional grain fermentation and through a reconstituted kefir consortium fermentation. Additionally, the impact of two key microbial communities on metabolite production in kefir was assessed using two modified versions of the consortium, with either yeasts or lactobacilli removed. We hypothesized that the complete kefir consortium would closely resemble traditional kefir, while the consortia without yeasts or lactobacilli would differ significantly from both traditional kefir and the complete consortium fermentation. Kefir fermentations were examined after 12 and 18 h using two-dimensional gas chromatography-time-of-flight mass spectrometry (GC × GC-TOFMS) to identify volatile compounds and high performance liquid chromatography (HPLC) to identify organic acid and sugar composition. The traditional kefir differed significantly from the kefir consortium fermentation with the traditional kefir having 15-20 log 2 (fold change) higher levels of esters and the consortium fermented kefir having between 1 and 3 log 2 (fold change) higher organic acids including lactate and acetate. The use of a version of kefir consortium that lacked lactobacilli resulted in between 2 and 20 log 2 (fold change) lower levels of organic acids, ethanol, and butanoic acid ethyl ester, while the absence of yeast from the consortium resulted in minimal change. In summary, the kefir consortium fermentation is significantly different from traditional grain fermented kefir with respect to the profile of metabolites present, and seems to be driven by lactobacilli, as evidenced by the significant decrease in multiple metabolites when the lactobacilli were removed from the fermentation and minimal differences observed upon the removal of yeast., Competing Interests: Declaration of Competing Interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: BCTB, PDC and BPW hold a patent for the method used to produce the pitched kefir used in the trial. ND, RPD, SLN, APM, AJF, GG, JJH, and MG have no conflicts to declare., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

One of diabetic characteristics is the postprandial hyperglycemia. Inhibiting glucose uptake may be beneficial for controlling postprandial blood glucose levels and regulating the glucose metabolism Peanut skin procyanidins (PSP) have shown a potential for lowering blood glucose; however, the underlying mechanism through which PSP regulate glucose metabolism remains unknown. In the current study, we investigated the effect of PSP on intestinal glucose transporters and serum metabolites using a mouse model of diabetic mice. Results showed that PSP improved glucose tolerance and systemic insulin sensitivity, which coincided with decreased expression of sodium-glucose cotransporter 1 and glucose transporter 2 in the intestinal epithelium induced by an activation of the phospholipase C β2/protein kinase C signaling pathway. Moreover, untargeted metabolomic analysis of serum samples revealed that PSP altered arachidonic acid, sphingolipid, glycerophospholipid, bile acids, and arginine metabolic pathways. The study provides new insight into the anti-diabetic mechanism of PSP and a basis for further research., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

Intensive broiler production practices are structured to prevent the introduction and spread of pathogens; however, they can potentially minimize the exposure of broilers to beneficial commensal bacteria. In this study, we used 16S rRNA amplicon sequencing to characterize the cecal microbiota of 35-day-old broilers from 22 independent commercial farms rearing broilers under intensive (IPS) or extensive production systems (EPS). We aimed to determine which bacteria are normal inhabitants of the broiler ceca and which bacteria might be missing from broilers in IPS. In addition, we generated a collection of 410 bacterial isolates, including 87 different species, to be used as a resource to further explore the effects of selected isolates on bird physiology and to elucidate the role of individual species within the cecal microbial community. Our results indicated significant differences in the microbiota of broilers between systems: the microbiota of broilers from EPS was dominated by Bacteroidetes {55.2% ± 8.9 [mean ± standard deviation (SD)]}, whereas Firmicutes dominated the microbiota of broilers from IPS (61.7% ± 14.4, mean ± SD). Bacterial taxa found to be core in the EPS microbiota, including Olsenella , Alistipes , Bacteroides , Barnesiella , Parabacteroides , Megamonas , and Parasutterella , were shown to be infrequent or absent from the IPS microbiota, and the EPS microbiota presented higher phylogenetic diversity and greater predicted functional potential than that of broilers in IPS. The bacteria shown to be depleted in broilers from IPS should be further investigated for their effects on bird physiology and potential application as next-generation probiotics. IMPORTANCE Production practices in intensive farming systems significantly reduce the introduction and spread of pathogens; however, they may potentially minimize the exposure of animals to beneficial commensal microorganisms. In this study, we identified core bacteria from the cecal microbiota of broilers raised in extensive production systems that are missing or reduced in birds from intensive systems, including Olsenella , Alistipes , Bacteroides , Barnesiella , Parabacteroides , Megamonas , and Parasutterella . Furthermore, the cecal microbiota of broilers from extensive systems showed higher diversity and greater functional potential than that of broilers from intensive systems. In addition, a collection of bacterial isolates containing 87 different species was generated from the current study, and this important resource can be used to further explore the role of selected commensal bacteria on the microbial community and bird physiology.

Kefir has long been associated with health benefits; however, recent evidence suggests that these benefits are dependent on the specific microbial composition of the kefir consumed. This study aimed to compare how consumption of a commercial kefir without traditional kefir organisms and a pitched kefir containing traditional organisms affected plasma lipid levels, glucose homeostasis, and markers of endothelial function and inflammation in males with elevated LDL cholesterol. We utilized a crossover design in n  = 21 participants consisting of two treatments of 4 weeks each in random order separated by a 4-week washout. Participants received either commercial kefir or pitched kefir containing traditional kefir organisms for each treatment period. Participants consumed 2 servings of kefir (350 g) per day. Plasma lipid profile, glucose, insulin, markers of endothelial function, and inflammation were measured in the fasting state before and after each treatment period. Differences within each treatment period and comparison of treatment delta values were performed using paired t tests and Wilcoxon signed-rank test, respectively. When compared to baseline, pitched kefir consumption reduced LDL-C, ICAM-1, and VCAM-1, while commercial kefir consumption increased TNF-α. Pitched kefir consumption resulted in greater reductions in IL-8, CRP, VCAM-1, and TNF-α when compared to commercial kefir consumption. These findings provide strong evidence that microbial composition is an important factor in the metabolic health benefits associated with kefir consumption. They also provide support for larger studies examining these to assess whether traditional kefir organisms are necessary to confer health benefits to individuals at risk of developing cardiovascular disease., Competing Interests: Benjamin C.T. Bourrie, Benjamin P. Willing, and Paul D. Cotter hold a patent for the method used to produce the pitched kefir used in the trial. Caroline Richard, Andrew Forgie, and Alexander Makarowski have no conflicts to declare.

Inclusion of additive blends is a common dietary strategy to manage post-weaning diarrhea and performance in piglets. However, there is limited mechanistic data on how these additives improve outcomes during this period. To evaluate the effects of Presan FX (MCOA) on the intestinal microbiota and metabolome, diets with or without 0.2% MCOA were compared. Pigs fed MCOA showed improved whole-body metabolism 7 days post-weaning, with decreased (P < 0.05) creatine, creatinine and β-hydroxybutyrate. Alterations in bile-associated metabolites and cholic acid were also observed at the same time-point (P < 0.05), suggesting MCOA increased bile acid production and secretion. Increased cholic acid was accompanied by increased tryptophan metabolites including indole-3-propionic acid (IPA) in systemic circulation (P = 0.004). An accompanying tendency toward increased Lactobacillus sp. in the small intestine was observed (P = 0.05). Many lactobacilli have bile acid tolerance mechanisms and contribute to production of IPA, suggesting increased bile acid production resulted in increased abundance of lactobacilli capable of tryptophan fermentation. Tryptophan metabolism is associated with the mature pig microbiota and many tryptophan metabolites such as IPA are considered beneficial to gut barrier function. In conclusion, MCOA may help maintain tissue metabolism and aid in microbiota re-assembly through bile acid production and secretion., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Diether et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Background: Preclinical and observational studies suggest that the gut microbiome plays a role in the pathogenesis of heart failure (HF); the gut microbiome may be modified by fermentable dietary fibre (FDF). The Need for F ib e r A ddition in S ymp t omatic H eart F ailure (FEAST-HF) trial evaluated feasibility of recruitment and supplementation with FDF in HF and whether FDF (acacia), compared to control, reduced the level of N-terminal pro-b-type natriuretic peptide (NT-proBNP) and growth stimulation expressed gene 2 (ST2), and produced changes in the gut microbiome., Methods: Participants were randomly allocated 1:1:1 to either of the intervention arms (5 g/d or 10 g/d acacia) or to the control arm (10 g/d microcrystalline cellulose (MCC; nonfermentable active control). Adherence and tolerance were assessed, and clinical events were monitored for safety. All outcomes (NT-proBNP, ST2, New York Heart Association class, Kansas City Cardiomyopathy Questionnaire scores, 6-minute walk test score, gut microbiome) were measured at baseline, and at 6 and 12 weeks., Results: Between September 13, 2018 and December 16, 2021, 51 patients were randomly allocated to either MCC (n = 18), acacia 5 g daily (n = 13), or acacia 10 g daily (n = 18). No differences occurred between either dose of acacia and MCC in NT-proBNP level, ST2, New York Heart Association class, or questionnaire scores over 12 weeks. Dietary treatment arms had a negligible impact on microbial communities. No safety, tolerability, or adherence issues were observed., Conclusions: Dietary supplementation with acacia gum was both safe and well tolerated in ambulatory patients with HF; however, it did not change NT-proBNP level, ST2, or the composition of the gut microbiome.ClinicalTrials.gov: NCT03409926., (© 2023 The Authors.)

The gut microbiome has a profound influence on host physiology, including energy metabolism, which is the process by which energy from nutrients is transformed into other forms of energy to be used by the body. However, mechanistic evidence for how the microbiome influences energy metabolism is derived from animal models. In this narrative review, we included human studies investigating the relationship between gut microbiome and energy metabolism -i.e., energy expenditure in humans and energy harvest by the gut microbiome. Studies have found no consistent gut microbiome patterns associated with energy metabolism, and most interventions were not effective in modulating the gut microbiome to influence energy metabolism. To date, cause-and-effect relationships and mechanistic evidence on the impact of the gut microbiome on energy expenditure have not been established in humans. Future longitudinal observational studies and randomized controlled trials utilizing robust methodologies and advanced statistical analysis are needed. Such knowledge would potentially inform the design of therapeutic avenues and specific dietary recommendations to improve energy metabolism through gut microbiome modulation., (Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved.)

Fecal microbiota transplantation (FMT) is an emerging technique for modulating the pig microbiota, however, donor variability is one of the major reasons for inconsistent outcomes across studies. Cultured microbial communities may address some limitations of FMT; however, no study has tested cultured microbial communities as inocula in pigs. This pilot study compared the effects of microbiota transplants derived from sow feces to cultured mixed microbial community (MMC) following weaning. Control, FMT4X, and MMC4X were applied four times, while treatment FMT1X was administered once (n = 12/group). On postnatal day 48, microbial composition was modestly altered in pigs receiving FMT in comparison with Control (Adonis, P = .003), mainly attributed to reduced inter-animal variations in pigs receiving FMT4X (Betadispersion, P = .018). Pigs receiving FMT or MMC had consistently enriched ASVs assigned to genera Dialister and Alloprevotella. Microbial transplantation increased propionate production in the cecum. MMC4X piglets showed a trend of higher acetate and isoleucine compared to Control. A consistent enrichment of metabolites from amino acid metabolism in pigs that received microbial transplantation coincided with enhanced aminoacyl-tRNA biosynthesis pathway. No differences were observed among treatment groups for body weight or cytokine/chemokine profiles. Overall, FMT and MMC exerted similar effects on gut microbiota composition and metabolite production., (© The Author(s) 2023. Published by Oxford University Press on behalf of FEMS.)

Broilers in intensive systems may lack commensal microbes that have coevolved with chickens in nature. This study evaluated the effects of microbial inocula and delivery methods applied to day-old chicks on the development of the cecal microbiota. Specifically, chicks were inoculated with cecal contents or microbial cultures, and the efficacies of three delivery methods (oral gavage, spraying inoculum into the bedding, and cohousing) were evaluated. Also, a competitive study evaluated the colonization ability of bacteria sourced from extensive or intensive poultry production systems. The microbiota of inoculated birds presented higher phylogenetic diversity values (PD) and higher relative abundance values of Bacteroidetes, compared with a control. Additionally, a reduction in the ileal villus height/crypt depth ratio and increased cecal IL-6, IL-10, propionate, and valerate concentrations were observed in birds that were inoculated with cecal contents. Across the experiments, the chicks in the control groups presented higher relative abundance values of Escherichia /Shigella than did the inoculated birds. Specific microbes from intensively or extensively raised chickens were able to colonize the ceca, and inocula from intensive production systems promoted higher relative abundance values of Escherichia /Shigella . We concluded that Alistipes , Bacteroides , Barnesiella , Mediterranea , Parabacteroides, Megamonas , and Phascolarctobacterium are effective colonizers of the broiler ceca. In addition, oral gavage, spray, and cohousing can be used as delivery methods for microbial transplantation, as indicated by their effects on the cecal microbiota, intestinal morphology, short-chain fatty acids concentration, and cytokine/chemokine levels. These findings will guide future research on the development of next-generation probiotics that are able to colonize and persist in the chicken intestinal tract after a single exposure. IMPORTANCE The strict biosecurity procedures employed in the poultry industry may inadvertently hinder the transmission of beneficial commensal bacteria that chickens would encounter in natural environments. This research aims at identifying bacteria that can colonize and persist in the chicken gut after a single exposure. We evaluated different microbial inocula that were obtained from healthy adult chicken donors as well as three delivery methods for their effects on microbiota composition and bird physiology. In addition, we conducted a competitive assay to test the colonization abilities of bacteria sourced from intensively versus extensively raised chickens. Our results indicated that some bacteria are consistently increased in birds that are exposed to microbial inoculations. These bacteria can be isolated and employed in future research on the development of next-generation probiotics that contain species that are highly adapted to the chicken gut., Competing Interests: The authors declare no conflict of interest.

Changes in the gut microbiota have been linked to metabolic endotoxemia as a contributing mechanism in the development of obesity and type 2 diabetes. Although identifying specific microbial taxa associated with obesity and type 2 diabetes remains difficult, certain bacteria may play an important role in initiating metabolic inflammation during disease development. The enrichment of the family Enterobacteriaceae , largely represented by Escherichia coli, induced by a high-fat diet (HFD) has been correlated with impaired glucose homeostasis; however, whether the enrichment of Enterobacteriaceae in a complex gut microbial community in response to an HFD contributes to metabolic disease has not been established. To investigate whether the expansion of Enterobacteriaceae amplifies HFD-induced metabolic disease, a tractable mouse model with the presence or absence of a commensal E. coli strain was established. With an HFD treatment, but not a standard-chow diet, the presence of E. coli significantly increased body weight and adiposity and induced impaired glucose tolerance. In addition, E. coli colonization led to increased inflammation in liver and adipose and intestinal tissue under an HFD regimen. With a modest effect on gut microbial composition, E. coli colonization resulted in significant changes in the predicted functional potential of microbial communities. The results demonstrated the role of commensal E. coli in glucose homeostasis and energy metabolism in response to an HFD, indicating contributions of commensal bacteria to the pathogenesis of obesity and type 2 diabetes. The findings of this research identified a targetable subset of the microbiota in the treatment of people with metabolic inflammation. IMPORTANCE Although identifying specific microbial taxa associated with obesity and type 2 diabetes remains difficult, certain bacteria may play an important role in initiating metabolic inflammation during disease development. Here, we used a mouse model distinguishable by the presence or absence of a commensal Escherichia coli strain in combination with a high-fat diet challenge to investigate the impact of E. coli on host metabolic outcomes. This is the first study to show that the addition of a single bacterial species to an animal already colonized with a complex microbial community can increase severity of metabolic outcomes. This study is of interest to a wide group of researchers because it provides compelling evidence to target the gut microbiota for therapeutic purposes by which personalized medicines can be made for treating metabolic inflammation. The study also provides an explanation for variability in studies investigating host metabolic outcomes and immune response to diet interventions.

Purpose: To understand the effects of consuming high-fat and low-fat dairy products on postprandial cardiometabolic risk factors and intestinal immune function, we used an established low birthweight (LBW) swine model of diet-induced insulin resistance., Methods: LBW piglets were randomized to consume one of the 3 experimental high fat diets and were fed for a total of 7 weeks: (1) Control high fat (LBW-CHF), (2) CHF diet supplemented with 3 servings of high-fat dairy (LBW-HFDairy) and (3) CHF diet supplemented with 3 servings of low-fat dairy (LBW-LFDairy). As comparison groups, normal birthweight (NBW) piglets were fed a CHF (NBW-CHF) or standard pig grower diet (NBW-Chow). At 11 weeks of age, all piglets underwent an established modified oral glucose and fat tolerance test. At 12 weeks of age, piglets were euthanized and ex vivo cytokine production by cells isolated from mesenteric lymph node (MLN) stimulated with mitogens was assessed., Results: Dairy consumption did not modulate postprandial plasma lipid, inflammatory markers and glucose concentrations. A lower production of IL-2 and TNF-α after pokeweed mitogen (PWM) stimulation was observed in LBW-CHF vs NBW-Chow (P < 0.05), suggesting impaired MLN T cell function. While feeding high-fat dairy had minimal effects, feeding low-fat dairy significantly improved the production of IL-2 and TNF-α after PWM stimulation (P < 0.05)., Conclusions: Irrespective of fat content, dairy had a neutral effect on postprandial cardiometabolic risk factors. Low-fat dairy products improved intestinal T cell function to a greater extent than high-fat dairy in this swine model of obesity and insulin resistance., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany.)

Background: Vitamin B12 supplements typically contain doses that far exceed the recommended daily amount, and high exposures are generally considered safe. Competitive and syntrophic interactions for B12 exist between microbes in the gut. Yet, to what extent excessive levels contribute to the activities of the gut microbiota remains unclear. The objective of this study was to evaluate the effect of B12 on microbial ecology using a B12 supplemented mouse model with Citrobacter rodentium, a mouse-specific pathogen. Mice were fed a standard chow diet and received either water or water supplemented with B12 (cyanocobalamin: ~120 μg/day), which equates to approximately 25 mg in humans. Infection severity was determined by body weight, pathogen load, and histopathologic scoring. Host biomarkers of inflammation were assessed in the colon before and after the pathogen challenge., Results: Cyanocobalamin supplementation enhanced pathogen colonization at day 1 (P < 0.05) and day 3 (P < 0.01) postinfection. The impact of B12 on gut microbial communities, although minor, was distinct and attributed to the changes in the Lachnospiraceae populations and reduced alpha diversity. Cyanocobalamin treatment disrupted the activity of the low-abundance community members of the gut microbiota. It enhanced the amount of interleukin-12 p40 subunit protein (IL12/23p40; P < 0.001) and interleukin-17a (IL-17A; P < 0.05) in the colon of naïve mice. This immune phenotype was microbe dependent, and the response varied based on the baseline microbiota. The cecal metatranscriptome revealed that excessive cyanocobalamin decreased the expression of glucose utilizing genes by C. rodentium, a metabolic attribute previously associated with pathogen virulence., Conclusions: Oral vitamin B12 supplementation promoted C. rodentium colonization in mice by altering the activities of the Lachnospiraceae populations in the gut. A lower abundance of select Lachnospiraceae species correlated to higher p40 subunit levels, while the detection of Parasutterella exacerbated inflammatory markers in the colon of naïve mice. The B12-induced change in gut ecology enhanced the ability of C. rodentium colonization by impacting key microbe-host interactions that help with pathogen exclusion. This research provides insight into how B12 impacts the gut microbiota and highlights potential consequences of disrupting microbial B12 competition/sharing through over-supplementation. Video Abstract., (© 2023. The Author(s).)

Spontaneous fermentations that do not rely on backslopping or industrial starter cultures were especially important to the early development of society and are still practiced around the world today. While current literature on spontaneous fermentations is observational and descriptive, it is important to understand the underlying mechanism of microbial community assembly and how this correlates with changes observed in microbial succession, composition, interaction, and metabolite production. Spontaneous food and beverage fermentations are home to autochthonous bacteria and fungi that are naturally inoculated from raw materials, environment, and equipment. This review discusses the factors that play an important role in microbial community assembly, particularly focusing on commonly reported yeasts and bacteria isolated from spontaneously fermenting food and beverages, and how this affects the fermentation dynamics. A wide range of studies have been conducted in spontaneously fermented foods that highlight some of the mechanisms that are involved in microbial interactions, niche adaptation, and lifestyle of these microorganisms. Moreover, we will also highlight how controlled culture experiments provide greater insight into understanding microbial interactions, a modest attempt in decoding the complexity of spontaneous fermentations. Further research using specific in vitro microbial models to understand the role of core microbiota are needed to fill the knowledge gap that currently exists in understanding how the phenotypic and genotypic expression of these microorganisms aid in their successful adaptation and shape fermentation outcomes. Furthermore, there is still a vast opportunity to understand strain level implications on community assembly. Translating these findings will also help in improving other fermentation systems to help gain more control over the fermentation process and maintain consistent and superior product quality.

As important commensals in the chicken intestine, Bacteroides are essential complex carbohydrate degraders, and short-chain fatty acid (SCFA) producers that are highly adapted to the distal gut. Previous studies have shown large variation in Bacteroides abundance in young chickens. However, limited information is available regarding how this variation affects the gut microbiome and host immunity. To investigate how elevated or depleted Bacteroides levels affect gut microbial functional capacity and impact host response, we sampled 7-day-old broiler chickens from 14 commercial production flocks. Week-old broiler chickens were screened and birds with low Bacteroides (LB) and high Bacteroides (HB) abundance were identified via 16S rRNA gene amplicon sequencing and quantitative PCR (qPCR) assays. Cecal microbial functionality and SCFA concentration of chickens with distinct cecal Bacteroides abundance were profiled by shotgun metagenomic sequencing and gas chromatography, respectively. The intestinal immune responses of LB and HB chickens were assessed via reverse transcription qPCR. Results showed that the gut microbiota of the LB group had increased abundance of lactic acid bacteria pyruvate fermentation pathway, whereas complex polysaccharide degradation and SCFA production pathways were enriched in the HB group ( P <  0.05), which was supported by increased SCFA concentrations in the ceca of HB chickens ( P <  0.05). HB chickens also showed decreased expression of interleukin-1β and increased expression of interleukin-10 and tight-junction protein claudin-1 ( P <  0.05). Overall, the results indicated that elevated Bacteroides may benefit the 7-day broiler gut and that further work should be done to confirm the causal role of Bacteroides in the observed positive outcomes. IMPORTANCE To date, limited information is available comparing distinct Bacteroides compositions in the chicken gut microbial communities, particularly in the context of microbial functional capacities and host responses. This study showed that possessing a microbiome with elevated Bacteroides in early life may confer beneficial effects to the chicken host, particularly in improving SCFA production and gut health. This study is among the first metagenomic studies focusing on the early life chicken gut microbiota structure, microbial functionality, and host immune responses. We believe that it will offer insights to future studies on broiler gut microbial population and their effects on host health.

Early-life antibiotic exposure is associated with diverse long-term adverse health outcomes. Despite the immunomodulatory effects of gastrointestinal fungi, the impact of antibiotics on the fungal community (mycobiome) has received little attention. The objectives of this study were to determine the impact of commonly prescribed infant antibiotic treatments on the microbial loads and structures of bacterial and fungal communities in the gastrointestinal tract. Thirty-two piglets were divided into four treatment groups: amoxicillin (A), amoxicillin-clavulanic acid (AC), gentamicin-ampicillin (GA), and flavored placebo (P). Antibiotics were administered orally starting on postnatal day (PND) 1 until PND 8, except for GA, which was given on PNDs 5 and 6 intramuscularly. Fecal swabs were collected from piglets on PNDs 3 and 8, and sow feces were collected 1 day after farrowing. The impacts of antibiotics on bacterial and fungal communities were assessed by sequencing the 16S rRNA and the internal transcribed spacer 2 (ITS2) rRNA genes, respectively, and quantitative PCR was performed to determine total bacterial and fungal loads. Antibiotics did not alter the α-diversity ( P  = 0.834) or β-diversity ( P  = 0.565) of fungal communities on PND 8. AC increased the ratio of total fungal/total bacterial loads on PND 8 ( P  = 0.027). There was strong clustering of piglets by litter on PND 8 ( P  < 0.001), which corresponded to significant differences in the sow mycobiome, especially the presence of Kazachstania slooffiae. In summary, we observed a strong litter effect and showed that the maternal mycobiome is essential for shaping the piglet mycobiome in early life. IMPORTANCE This work provides evidence that although the fungal community composition is not altered by antibiotics, the overall fungal load increases with the administration of amoxicillin-clavulanic acid. Additionally, we show that the maternal fungal community is important in establishing the fungal community in piglets.

Brachyspira hyodysenteriae, an etiologic agent of swine dysentery (SD), is known for causing colitis. Although some aspects of colonic defenses during infection have been described previously, a more comprehensive picture of the host and microbiota interaction in clinically affected animals is required. This study aimed to characterize multiple aspects of colonic innate defenses and microbiome factors in B. hyodysenteriae-infected pigs that accompany clinical presentation of hemorrhagic diarrhea. We examined colonic mucus barrier modifications, leukocyte infiltration, cathelicidin expression, as well as microbiome composition. We showed that B. hyodysenteriae infection caused microscopic hemorrhagic colitis with abundant neutrophil infiltration in the colonic lamina propria and lumen, with minor macrophage infiltration. Mucus hypersecretion with abundant sialylated mucus in the colon, as well as mucosal colonization by [Acetivibrio] ethanolgignens, Lachnospiraceae, and Campylobacter were pathognomonic of B. hyodysenteriae infection. These findings demonstrate that B. hyodysenteriae produces clinical disease through multiple effects on host defenses, involving alterations of mucosal innate immunity and microbiota. Given that B. hyodysenteriae is increasingly resistant to antimicrobials, this understanding of SD pathogenesis may lead to future development of non-antibiotic and anti-inflammatory alternative therapeutics., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Eduardo R Cobo reports financial support was provided by University of Calgary., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

Introduction: Kefir consumption can have many metabolic health benefits, including, in the case of specific kefirs, improvements in plasma and liver lipid profiles. Our group has previously shown that these health benefits are dependent on the microbial composition of the kefir fermentation, and that a pitched kefir (PK1) containing specific traditional microbes can recapitulate the health benefits of a traditional kefir. In this study we investigated how different preparations of kefir impact cholesterol and lipid metabolism and circulating markers of cardiovascular disease risk and determine if freeze-drying impacts health benefits relative to past studies., Materials and Methods: Eight-week-old male and female C57Bl/6 mice were fed a high fat diet (40% kcal from fat) supplemented with one of 3 freeze-dried kefir preparations (whole kefir, cell-free kefir, or heat-treated kefir) for 8 weeks prior to analysis of plasma and liver lipid profiles, circulating cardiovascular disease (CVD) biomarkers, cecal microbiome composition, and cecal short-chain fatty acid levels. These groups of mice were compared to others that were fed a control low-fat diet, control high fat diet or high fat diet supplemented with milk, respectively., Results: All kefir preparations lowered plasma cholesterol in both male and female mice, while only whole kefir lowered liver cholesterol and triglycerides. Plasma vascular cell adhesion molecule 1 (VCAM-1) was lowered by both whole kefir and heat-treated kefir in male mice but not females, while c-reactive protein (CRP) was unchanged across all high fat diet fed groups in males and females., Conclusion: These results indicate that some of the metabolic benefits of consumption of this kefir do not require whole kefir while also indicating that there are multiple compounds or components responsible for the different benefits observed., Competing Interests: BCTB, BPW, and PDC hold a patent for the method used to produce the pitched kefir used in the trial. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Bourrie, Forgie, Ju, Richard, Cotter and Willing.)

Inclusion of enzymes and organic acids in pig diets is an important strategy supporting decreased antibiotic usage in pork production. However, limited knowledge exists about how these additives impact intestinal microbes and their metabolites. To examine the effects of benzoic acid and enzymes on gut microbiota and metabolome, 160 pigs were assigned to one of four diets 7 days after weaning: a control diet or the addition of 0.5% benzoic acid, 0.045% dietary enzymes (phytase, β-glucanase, xylanase, and α-amylase), or both and fed ad libitum for 21 to 22 d. Individual growth performance and group diarrhea incidence data were collected throughout the experimental period. A decrease of 20% in pen-level diarrhea incidence from days 8 to 14 in pigs-fed both benzoic acid and enzymes compared to the control diet (P = 0.047). Cecal digesta samples were collected at the end of the experimental period from 40 piglets (n = 10 per group) and evaluated for differences using 16S rRNA sequencing and two-dimensional gas chromatography and time-of-flight mass spectrometry (GCxGC-TOFMS). Analysis of cecal microbiota diversity revealed that benzoic acid altered microbiota composition (Unweighted Unifrac, P = 0.047, r2 = 0.07) and decreased α-diversity (Shannon, P = 0.041; Faith's Phylogenetic Diversity, P = 0.041). Dietary enzymes increased fiber-fermenting bacterial taxa such as Prevotellaceae. Two-step feature selection identified 17 cecal metabolites that differed among diets, including increased microbial cross-feeding product 1,2-propanediol in pigs-fed benzoic acid-containing diets. In conclusion, dietary benzoic acid and enzymes affected the gut microbiota and metabolome of weaned pigs and may support the health and resolution of postweaning diarrhea., (© The Author(s) 2022. Published by Oxford University Press on behalf of the American Society of Animal Science. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Although dairy intake has been shown to have a neutral or some beneficial effect on major cardiometabolic risk factors, the impact of dairy, and especially dairy fat, on immune function remains to be investigated. To understand the effect of consuming dairy fat on cardiometabolic risk factors and immune function, we used an established low birthweight (LBW) swine model of diet-induced insulin resistance to compare high-fat and low-fat dairy products to a control high-fat diet (CHF). LBW piglets were randomized to consume one of the 3 experimental HF diets: (1) CHF, (2) CHF diet supplemented with 3 servings/day of high-fat dairy (HFDairy) and (3) CHF diet supplemented with 3 servings/day of low-fat dairy (LFDairy). As comparison groups, normal birthweight (NBW) piglets were fed a CHF (NBW-CHF) or standard pig grower diet (NBW-Chow). A total of 35 pigs completed the study and were fed for a total of 7 weeks, including 1 week of CHF transition diet. At 12 weeks of age, piglets were euthanized. Fasting blood and tissue samples were collected. Ex vivo cytokine production by peripheral blood mononuclear cells (PBMCs) stimulated with pokeweed (PWM), phytohemagglutinin (PHA) and phorbol myristate acetate-ionomycin (PMA-I) were assessed. As expected, LBW-CHF piglets showed early signs of insulin resistance (HOMA-IR, P model = 0.08). Feeding high-fat dairy products improved fasting plasma glucose concentrations more than low-fat dairy compared to LBW-CHF ( P < 0.05). Irrespective of fat content, dairy consumption had neutral effect on fasting lipid profile. We have also observed lower production of IL-2 after PWM and PHA stimulation as well as lower production of TNF-α and IFN-γ after PWM stimulation in LBW-CHF than in NBW-Chow (all, P < 0.05), suggesting impaired T cell and antigen presenting cell function. While feeding high-fat dairy had minimal effect on immune function, feeding low-fat dairy significantly improved the production of IL-2, TNF-α and IFN-γ after PWM stimulation, IL-2 and IFN-γ after PHA stimulation as well as TNF-α after PMA-I stimulation compared to LBW-CHF (all, P < 0.05). These data provide novel insights into the role of dairy consumption in counteracting some obesity-related cardiometabolic and immune perturbations., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 She, Wang, Makarowski, Mangat, Tsai, Willing, Proctor and Richard.)

To maintain food safety and flock health in broiler chicken production, biosecurity approaches to keep chicken barns free of pathogens are important. Canadian broiler chicken producers must deep clean their barns with chemical disinfectants at least once annually (full disinfection [FD]) and may wash with water (water wash [WW]) throughout the year. However, many producers use FD after each flock, assuming a greater efficacy of more stringent cleaning protocols, although little information is known regarding how these two cleaning practices affect pathogen population and gut microbiota. In the present study, a crossover experiment over four production cycles was conducted in seven commercial chicken barns to compare WW and FD. We evaluated the effects of barn cleaning methods on commercial broiler performance, cecal microbiota composition, Campylobacter and Salmonella occurrence, and Campylobacter jejuni and Clostridium perfringens abundance, as well as on short-chain fatty acid (SCFA) concentrations in the month-old broiler gut. The 30-day body weight and mortality rate were not affected by the barn cleaning methods. The WW resulted in a modest but significant effect on the structure of broiler cecal microbiota (weighted-UniFrac; adonis P =  0.05, and unweighted-UniFrac; adonis P =  0.01), with notable reductions in C. jejuni occurrence and abundance. In addition, the WW group had increased cecal acetate, butyrate, and total SCFA concentrations, which were negatively correlated with C. jejuni abundance. Our results suggest that WW may result in enhanced activity of the gut microbiota and reduced zoonotic transmission of C. jejuni in broiler production relative to FD in the absence of a disease challenge. IMPORTANCE We compared the effects of barn FD and WW methods on gut microbial community structures and pathogen prevalence of broiler chickens in a nonchallenging commercial production setting. The results revealed that barn cleaning methods had little impact on the 30-day body weight and mortality rate of broiler chickens. In addition, the FD treatment had a subtle but significant effect on the broiler cecal microbiota with increased abundances of Campylobacter and decreased SCFA concentrations, which would support the adoption of WW as a standard practice. Thus, compared to FD, WW can be beneficial to broiler chicken production by inhibiting zoonotic pathogen colonization in the chicken gut with reduced cost and labor of cleaning.

In this study, we describe the isolation and characterization of novel bacteriophage vB&#95;EcoP&#95;Kapi1 (Kapi1) isolated from a strain of commensal Escherichia coli inhabiting the gastrointestinal tract of healthy mice. We show that Kapi1 is a temperate phage integrated into tRNA argW of strain MP1 and describe its genome annotation and structure. Kapi1 shows limited homology to other characterized prophages but is most similar to the seroconverting phages of Shigella flexneri and clusters taxonomically with P22-like phages. The receptor for Kapi1 is the lipopolysaccharide O-antigen, and we further show that Kapi1 alters the structure of its host's O-antigen in multiple ways. Kapi1 displays unstable lysogeny, and we find that the lysogenic state is more stable during growth in simulated intestinal fluid. Furthermore, Kapi1 lysogens have a competitive advantage over their nonlysogenic counterparts both in vitro and in vivo , suggesting a role for Kapi1 during colonization. We thus report the use of MP1 and Kapi1 as a model system to explore the molecular mechanisms of mammalian colonization by E. coli to ask what the role(s) of prophages in this context might be. IMPORTANCE Although research exploring the microbiome has exploded in recent years, our understanding of the viral component of the microbiome is lagging far behind our understanding of the bacterial component. The vast majority of intestinal bacteria carry prophages integrated into their chromosomes, but most of these bacteriophages remain uncharacterized and unexplored. Here, we isolate and characterize a novel temperate bacteriophage infecting a commensal strain of Escherichia coli. We aim to explore the interactions between bacteriophages and their hosts in the context of the gastrointestinal tract, asking what role(s) temperate bacteriophages may play in growth and survival of bacteria in the gut. Understanding the fundamental biology of gut commensal bacteria can inform the development of novel antimicrobial or probiotic strategies for intestinal infections.

High-fat diets (HFD) have been shown to induce substantial shifts in intestinal microbial community composition and activity which are associated with adverse metabolic outcomes. Furthermore, changes in microbial composition are affected by fatty acid composition; saturated, monounsaturated (MUFA), and industrial trans fats (iTFA) adversely affect microbial diversity while polyunsaturated fats (PUFA) have been shown to have neutral effects. The effects of naturally occurring trans fats on gut microbial composition are unknown. Vaccenic acid (VA) is the most abundant naturally occurring trans fat (abundant in meat and dairy), can be elevated by altering a cow's diet, and has been shown to have hypolipidemic effects. The aim of this study was to determine how variations of VA content in beef fat affect gut microbial composition, insulin resistance, and lipid metabolism in pigs. Low birth weight (LBW) and control pigs were fed a control or high-fat, high-carbohydrate (HFHC) diet supplemented with beef fat containing either high or low VA levels for 7 weeks. An adapted modified oral glucose tolerance test and fat challenge test were performed at 9 weeks of age following implantation of jugular catheters. Impacts on microbial composition were assessed using 16S rRNA gene amplicon sequencing. The HFHC diet containing beef fat rich in VA had a mild insulin sensitizing effect ( p < 0.05, slope of curve), increased plasma HDL cholesterol ( p < 0.05, +28%), reduced postprandial plasma TG ( p < 0.05), and showed protection from HFHC-induced changes to gut microbial composition in LBW pigs as compared to HFHC diet containing standard beef fat. This is the first study to show effects of natural trans fats on gut dysbiosis; further studies are needed to elucidate mechanisms.

The consumption of a high-fat diet can cause metabolic syndrome and induces host gut microbial dysbiosis and non-alcoholic fatty liver disease (NAFLD). We evaluated the effect of polyphenol-rich jaboticaba peel and seed powder (JPSP) on the gut microbial community composition and liver health in a mouse model of NAFLD. Three-month-old C57BL/6 J male mice, received either a control (C, 10% of lipids as energy, n = 16) or high-fat (HF, 50% of lipids as energy, n = 64) diet for nine weeks. The HF mice were randomly subdivided into four groups (n = 16 in each group), three of which (HF-J5, HF-J10, and HF-J15) were supplemented with dietary JPSP for four weeks (5%, 10%, and 15%, respectively). In addition to attenuating weight gain, JPSP consumption improved dyslipidemia and insulin resistance. In a dose-dependent manner, JPSP consumption ameliorated the expression of hepatic lipogenesis genes (AMPK, SREBP-1, HGMCoA, and ABCG8). The effects on the microbial community structure were determined in all JPSP-supplemented groups; however, the HF-J10 and HF-J15 diets led to a drastic depletion in the species of numerous bacterial families (Bifidobacteriaceae, Mogibacteriaceae, Christensenellaceae, Clostridiaceae, Dehalobacteriaceae, Peptococcaceae, Peptostreptococcaceae, and Ruminococcaceae) compared to the HF diet, some of which represented a reversal of increases associated with HF. The Lachnospiraceae and Enterobacteriaceae families and the Parabacteroides, Sutterella, Allobaculum, and Akkermansia genera were enriched more in the HF-J10 and HF-J15 groups than in the HF group. In conclusion, JPSP consumption improved obesity-related metabolic profiles and had a strong impact on the microbial community structure, thereby reversing NAFLD and decreasing its severity., (Copyright © 2021 The Authors. Published by Elsevier Masson SAS.. All rights reserved.)

The objectives of this pilot study were to examine fecal microbiota composition of pediatric patients with celiac disease (CD) before and after a 1-year gluten-free diet (GFD) and to determine the association with symptoms and anti-tissue transglutaminase (aTTG) antibody., Methods: Stool samples were obtained from pediatric patients with CD and from healthy controls. Patients were classified by the presence (diarrhea, abdominal pain, weight loss) or absence (asymptomatic, headache, fatigue, etc.) of typical CD gastrointestinal symptoms and by aTTG normalization post-GFD intervention (< 7 U/mL). Fecal microbial composition was measured using 16S ribosomal RNA gene amplicon sequencing of the V3-V4 region., Results: At diagnosis, 13 of 22 patients with CD had typical gastrointestinal symptoms, the remaining patients having atypical or asymptomatic presentations. After a 1-year GFD, all symptomatic patients improved and 9 of 19 had normalized aTTG. Prior to GFD, no distinct microbial signature was observed between patients and controls ( P = 0.39). Post-GFD, patients with CD had a unique microbial signature with reductions in known fiber-degrading bacteria, including Blautia , Dorea , Lactobacillus , and Prevotella compared with controls. Within the patients with CD, microbial composition was not associated with reported symptom presentation or aTTG normalization., Conclusions: Pediatric patients with CD only had a unique microbial signature compared with healthy controls when placed on the GFD. These results suggest that pediatric patients with CD may not have a unique fecal microbial signature indicative of inherent dysbiosis, in contrast to that suggested for older patients. In children with CD, diet may play a role in shaping microbial composition more so than disease status., Competing Interests: D. Sample received funding from Women and Children’s Health Research Institute; Maternal Newborn Child Youth Strategic Clinical Network. Dr Fouhse received funding from Natural Sciences and Engineering Research Council Post Doctoral Fellowship. Drs Huynh and Dieleman received funding from Broad Foundation—Medical Research Program Grant Number MOP 0243. Dr Willing received funding from Canada Research Chairs program. The remaining authors report no conflicts of interest., (Copyright © 2021 The Author(s). Published by Wolters Kluwer on behalf of European Society for Pediatric Gastroenterology, Hepatology, and Nutrition and North American Society for Pediatric Gastroenterology, Hepatology, and Nutrition.)

Neonatal antibiotics administered to human infants initiate gut microbiota dysbiosis that may have long-term effects on body weight and metabolism. We examined antibiotic-induced adaptations in pancreatic islets of the piglet, a well-accepted model of human infant microbiota and pancreas development. Neonatal piglets randomized to amoxicillin [30 mg/kg body wt/day; n = 7, antibiotic (ANTI)] or placebo [vehicle control; n = 7, control (CON)] from postnatal day ( PND ) 0 - 13 were euthanized at PND7 , 14 , and 49 . The metabolic phenotype along with functional, immunohistological, and transcriptional phenotypes of the pancreatic islets were studied. The gut microbiome was characterized by 16S rRNA gene sequencing, and microbial metabolites and microbiome-sensitive host molecules were measured. Compared with CON, ANTI PND7 piglets had elevated transcripts of genes involved in glucagon-like peptide 1 ((GLP-1) synthesis or signaling in islets ( P < 0.05) coinciding with higher plasma GLP-1 ( P = 0.11), along with increased tumor necrosis factor α ( Tnf ) ( P < 0.05) and protegrin 1 ( Npg1 ) ( P < 0.05). Antibiotic-induced relative increases in Escherichia , Coprococcus , Ruminococcus , Dehalobacterium , and Oscillospira of the ileal microbiome at PND7 normalized after antibiotic withdrawal. In ANTI islets at PND14 , the expression of key regulators pancreatic and duodenal homeobox 1 ( Pdx1 ), insulin-like growth factor-2 ( Igf2 ), and transcription factor 7-like 2 ( Tcf7l2 ) was downregulated, preceding a 40% reduction of β-cell area ( P < 0.01) and islet insulin content at PND49 ( P < 0.05). At PND49 , a twofold elevated plasma insulin concentration ( P = 0.07) was observed in ANTI compared with CON. We conclude that antibiotic treatment of neonatal piglets elicited gut microbial changes accompanied by phasic alterations in key regulatory genes in pancreatic islets at PND7 and 14 . By PND49 , reduced β-cell area and islet insulin content were accompanied by elevated nonfasted insulin despite normoglycemia, indicative of islet stress.

Kefir consumption has been demonstrated to improve lipid and cholesterol metabolism; however, our previous study identified that benefits vary between different commercial and traditional kefir. Here, we investigate the ability of pitched culture kefir, that is, kefir produced by a small number of specific strains, to recapitulate health benefits of a traditional kefir, in a diet-induced obesity mouse model, and examine how microbial composition of kefir impacts these benefits. Eight-week-old female C57BL/6 mice were fed a high-fat diet (40 % energy from fat) supplemented with one of five kefir varieties (traditional, pitched, pitched with no Lactobacillus, pitched with no yeast and commercial control) at 2 ml in 20 g of food for 8 weeks prior to analysis of plasma and liver lipid profiles, and liver gene expression profiles related to lipid metabolism. Both traditional and pitched kefir lowered plasma cholesterol by about 35 % (P = 0·0005) and liver TAG by about 55 % (P = 0·0001) when compared with commercial kefir despite no difference in body weight. Furthermore, pitched kefir produced without either yeast or Lactobacillus did not lower cholesterol. The traditional and pitched kefir with the full complement of microbes were able to impart corresponding decreases in the expression of the cholesterol and lipid metabolism genes encoding 3-hydroxy-3-methylglutaryl-coenzyme A reductase, PPARγ and CD36 in the liver. These results demonstrate that traditional kefir organisms can successfully be utilised in a commercial process, while highlighting the importance of microbial interactions during fermentation in the ability of fermented foods to benefit host health.

Dietary choline, which is converted to phosphatidylcholine (PC) in intestinal enterocytes, may benefit inflammatory bowel disease patients who typically have reduced intestinal choline and PC. The present study investigated the effect of dietary choline supplementation on colitis severity and intestinal mucosal homoeostasis using a Citrobacter rodentium-induced colitis model. C57BL/6J mice were fed three isoenergetic diets differing in choline level: choline-deficient (CD), choline-sufficient (CS) and choline-excess (CE) for 3 weeks prior to infection with C. rodentium. The effect of dietary choline levels on the gut microbiota was also characterised in the absence of infection using 16S rRNA gene amplicon sequencing. At 7 d following infection, the levels of C. rodentium in CD mice were significantly greater than that in CS or CE groups (P < 0·05). CD mice exhibited greater damage to the surface epithelium and goblet cell loss than the CS or CE mice, which was consistent with elevated pro-inflammatory cytokine and chemokine levels in the colon. In addition, CD group exhibited decreased concentrations of PC in the colon after C. rodentium infection, although the decrease was not observed in the absence of challenge. Select genera, including Allobaculum and Turicibacter, were enriched in response to dietary choline deficiency; however, there was minimal impact on the total bacterial abundance or the overall structure of the gut microbiota. Our results suggest that insufficient dietary choline intake aggravates the severity of colitis and demonstrates an essential role of choline in maintaining intestinal homoeostasis.

Background & Aims: Patients with ulcerative colitis have low concentrations of the major membrane lipid phosphatidylcholine (PC) in gastrointestinal mucus, suggesting that defects in colonic PC metabolism might be involved in the development of colitis. To determine the precise role that PC plays in colonic barrier function, we examined mice with intestinal epithelial cell (IEC)-specific deletion of the rate-limiting enzyme in the major pathway for PC synthesis: cytidine triphosphate:phosphocholine cytidylyltransferase-α (CTα IKO mice)., Methods: Colonic tissue of CTα IKO mice and control mice was analyzed by histology, immunofluorescence, electron microscopy, quantitative polymerase chain reaction, Western blot, and thin-layer chromatography. Histopathologic colitis scores were assigned by a pathologist blinded to the experimental groupings. Intestinal permeability was assessed by fluorescein isothiocyanate-dextran gavage and fecal microbial composition was analyzed by sequencing 16s ribosomal RNA amplicons. Subsets of CTα IKO mice and control mice were treated with dietary PC supplementation, antibiotics, or 4-phenylbutyrate., Results: Inducible loss of CTα in the intestinal epithelium reduced colonic PC concentrations and resulted in rapid and spontaneous colitis with 100% penetrance in adult mice. Colitis development in CTα IKO mice was traced to a severe and unresolving endoplasmic reticulum stress response in IECs with altered membrane phospholipid composition. This endoplasmic reticulum stress response was linked to the necroptotic death of IECs, leading to excessive loss of goblet cells, formation of a thin mucus barrier, increased intestinal permeability, and infiltration of the epithelium by microbes., Conclusions: Maintaining the PC content of IEC membranes protects against colitis development in mice, showing a crucial role for IEC phospholipid equilibrium in colonic homeostasis. SRA accession number: PRJNA562603., (Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.)

A diverse and dynamic microbial community (known as microbiota) resides within the pig gastrointestinal tract (GIT). The microbiota contributes to host health and performance by mediating nutrient metabolism, stimulating the immune system, and providing colonization resistance against pathogens. Manipulation of gut microbiota to enhance growth performance and disease resilience in pigs has recently become an active area of research in an era defined by increasing scrutiny of antimicrobial use in swine production. In order to develop microbiota-targeted strategies, or to identify potential next-generation probiotic strains originating from the endogenous members of GIT microbiota in pigs, it is necessary to understand the role of key commensal members in host health. Many, though not all, correlative studies have associated members of the genus Prevotella with positive outcomes in pig production, including growth performance and immune response; therefore, a comprehensive review of the genus in the context of pig production is needed. In the present review, we summarize the current state of knowledge about the genus Prevotella in the intestinal microbial community of pigs, including relevant information from other animal species that provide mechanistic insights, and identify gaps in knowledge that must be addressed before development of Prevotella species as next-generation probiotics can be supported.

For decades, traditional drug discovery has used natural product and synthetic chemistry approaches to generate libraries of compounds, with some ending as promising drug candidates. A complementary approach has been to adopt the concept of biomimicry of natural products and metabolites so as to improve multiple drug-like features of the parent molecule. In this effort, promiscuous and weak interactions between ligands and receptors are often ignored in a drug discovery process. In this Emerging Concepts article, we highlight microbial metabolite mimicry, whereby parent metabolites have weak interactions with their receptors that then have led to discrete examples of more potent and effective drug-like molecules. We show specific examples of parent-metabolite mimics with potent effects in vitro and in vivo. Furthermore, we show examples of emerging microbial ligand-receptor interactions and provide a context in which these ligands could be improved as potential drugs. A balanced conceptual advance is provided in which we also acknowledge potential pitfalls-hyperstimulation of finely balanced receptor-ligand interactions could also be detrimental. However, with balance, we provide examples of where this emerging concept needs to be tested. SIGNIFICANCE STATEMENT: Microbial metabolite mimicry is a novel way to expand on the chemical repertoire of future drugs. The emerging concept is now explained using specific examples of the discovery of therapeutic leads from microbial metabolites., Competing Interests: We (S.M., Z.D.) have filed a patent application US 2019/0367475 A1: PXR agonists and uses thereof for gut barrier dysfunction and treatment prevention., (Copyright © 2020 by The American Society for Pharmacology and Experimental Therapeutics.)

Purpose of Review: This review summarizes recent animal and human trials examining the potential for kefir to improve obesity, type 2 diabetes, dyslipidemia, and non-alcoholic fatty liver disease (NAFLD). Evidence for pathways affected and suggestions of possible mechanisms of action are also considered., Recent Findings: Human trials examining the ability of kefir to recapitulate metabolic health benefits previously observed in rodent models have found mixed results. Kefir has long been associated with improvements in health including obesity, diabetes, NAFLD, and dyslipidemia in preventative animal trials. While recent evidence from human trials supports a positive role of kefir in modulating diabetes-related markers, the impact of kefir consumption on markers of dyslipidemia, NAFLD, and body composition has been for the most part contradictory to animal findings. Variability in organisms for kefir fermentation poses a significant challenge in making meaningful comparisons. Recommendations for future well-controlled animal and human research are provided.

The gut microbiota comprises a large and diverse community of bacteria that play a significant role in swine health. Indeed, there is a tight association between the enteric immune system and the overall composition and richness of the microbiota, which is key in the induction, training and function of the host immunity, and may therefore, influence the immune response to vaccination. Using vaccination against Mycoplasma hyopneumoniae ( M. hyo ) as a model, we investigated the potential of early-life gut microbiota in predicting vaccine response and explored the post-vaccination dynamics of fecal microbiota at later time points. At 28 days of age (0 days post-vaccination; dpv), healthy piglets were vaccinated, and a booster vaccine was administered at 21 dpv. Blood samples were collected at 0, 21, 28, 35, and 118 dpv to measure M. hyo -specific IgG levels. Fecal samples for 16S rRNA gene amplicon sequencing were collected at 0, 21, 35, and 118 dpv. The results showed variability in antibody response among individual pigs, whilst pre-vaccination operational taxonomic units (OTUs) primarily belonging to Prevotella , [ Prevotella ], Anaerovibrio , and Sutterella appeared to best-predict vaccine response. Microbiota composition did not differ between the vaccinated and non-vaccinated pigs at post-vaccination time points, but the time effect was significant irrespective of the animals' vaccination status. Our study provides insight into the role of pre-vaccination gut microbiota composition in vaccine response and emphasizes the importance of studies on full metagenomes and microbial metabolites aimed at deciphering the role of specific bacteria and bacterial genes in the modulation of vaccine response.

Background: Early-life malnutrition may have long-lasting effects on microbe-host interactions that affect health and disease susceptibility later in life. Diet quality and quantity in conjunction with toxin and pathogen exposure are key contributors to microbe-host physiology and malnutrition. Consequently, it is important to consider both diet- and microbe-induced pathologies as well as their interactions underlying malnutrition., Main Body: Gastrointestinal immunity and digestive function are vital to maintain a symbiotic relationship between the host and microbiota. Childhood malnutrition can be impacted by numerous factors including gestational malnutrition, early life antibiotic use, psychological stress, food allergy, hygiene, and exposure to other chemicals and pollutants. These factors can contribute to reoccurring environmental enteropathy, a condition characterized by the expansion of commensal pathobionts and environmental pathogens. Reoccurring intestinal dysfunction, particularly during the critical window of development, may be a consequence of diet-microbe interactions and may lead to life-long immune and metabolic programming and increased disease risk. We provide an overview of the some key factors implicated in the progression of malnutrition (protein, fat, carbohydrate, iron, vitamin D, and vitamin B12) and discuss the microbiota during early life that may contribute health risk later in life., Conclusion: Identifying key microbe-host interactions, particularly those associated with diet and malnutrition requires well-controlled dietary studies. Furthering our understanding of diet-microbe-host interactions will help to provide better strategies during gestation and early life to promote health later in life.

Antibiotic exposure during neonatal development may result in transient or persistent alterations of key microbes that are vital for normal development of local and systemic immunity, potentially impairing immune competence later in life. To further elucidate the relationship between antibiotic exposure and immune development, newborn pigs were exposed to a therapeutic pediatric dose (30 mg/kg/day) of amoxicillin (AB) or placebo (PL) from post-natal day (PND) 0-14. Subsequently, immune cell phenotype, microbial composition, and immune response to an intraperitoneal (IP) challenge with Salmonella enterica serovar Typhimurium were evaluated. AB exposure caused significant changes in fecal microbial composition on PND 3 ( P = 0.025). This stemmed from a 2-fold increase in Enterobacteriaceae with live cecal coliforms on PND 7 indicating at 10-fold increase ( P = 0.036). Alterations in microbial composition were transient, and successional patterns were normalizing by PND 14 ( P = 0.693). Differences in PBMC (peripheral blood mononuclear cell) immune cell subtypes were detected, with the percentage of CD3 + CD4 + T cells among the broader T cell population (CD3 + CD4 + /CD3 + ) being significantly higher ( P = 0.031) in AB pigs and the numbers of CD4+CD45RA+ (naïve) T cells per liter of blood were lower on PND 21 in AB pigs ( P = 0.036). Meanwhile, PBMCs from AB pigs produced significantly more IFNγ upon stimulation with a T-cell mitogen on PND 21 and 49 ( P = 0.021). When AB pigs were challenged with heat-killed Salmonella (IP) on PND 49, IFNγ gene expression in peripheral blood was upregulated compared to those treated with PL ( P = 0.043). Additionally, AB pigs showed stronger activation among neutrophils infiltrating the peritoneal cavity after in vivo immune challenge, based on higher levels of NF-κB nuclear translocation ( P = 0.001). Overall, our results indicate that early life treatment with a therapeutically relevant dose of a commonly prescribed antibiotic has a programming effect on the immune system. Despite antibiotics only causing a transient disruption in gut-associated microbial communities, implications were long-term, with antibiotic treated pigs mounting an upregulated response to an immune challenge. This research adds to the growing body of evidence indicating adverse immune outcomes of early life antibiotic exposures.

The gastrointestinal tract microbiome plays a critical role in regulating host innate and adaptive immune responses against pathogenic bacteria. Disease associated dysbiosis and environmental induced insults, such as antibiotic treatments can lead to increased susceptibility to infection, particularly in a hospital setting. Dietary intervention is the greatest tool available to modify the microbiome and support pathogen resistance. Some dietary components can maintain a healthy disease resistant microbiome, whereas others can contribute to an imbalanced microbial population, impairing intestinal barrier function and immunity. Characterizing the effects of dietary components through the host-microbe axis as it relates to gastrointestinal health is vital to provide evidence-based dietary interventions to mitigate infections. This review will cover the effect of dietary components (carbohydrates, fiber, proteins, fats, polyphenolic compounds, vitamins, and minerals) on intestinal integrity and highlight their ability to modulate host-microbe interactions as to improve pathogen resistance.

The development of nutritional strategies to improve microbial homeostasis and gut health of piglets post-weaning is required to mitigate the high prevalence of post-weaning diarrhea and subsequent growth checks typically observed during the weaning transition. Therefore the objective of this study was to determine the effect of supplementing piglet creep and nursery feed with a yeast-derived mannan-rich fraction (MRF) on piglet growth performance, cecal microbial profiles, and jejunal morphology and gene expression. Ten litters of piglets (n=106) were selected on postnatal day (PND) 7 and assigned to diets with or without MRF (800 mg/kg) until weaning (n=5 litters/treatment; initial weight 3.0±0.1 kg). On PND 21, 4 piglets per litter (n=40) were selected and weaned into the nursery where they remained on their respective diets until PND 42. A two-phase feeding program was used to meet nutrient requirements, and pigs were switched from phase 1 to phase 2 on PND 28. Feed intake and piglet weights were recorded on PND 7, 14, 21, 28, 35 and 42. On PND 28 and 42, ten piglets per treatment were euthanized to collect intestinal tissue and digesta. Piglets supplemented with MRF had 21.5% greater (P&lt;0.05) average daily feed intake between PND 14-21. However, MRF supplementation did not affect piglet growth performance compared to control. On PND 28, jejunal villus height was 16.8% greater (P&lt;0.05) in piglets consuming MRF supplemented diets. Overall microbial community structure in cecal digesta on PND 28 tended to differ in pigs supplemented with MRF (P=0.076; analysis of similarities (ANOSIM)) with increased (P&lt;0.05) relative abundance of Paraprevotellaceae genera YRC22 and CF231, and reduced (P&lt;0.05) relative abundance of Sutterella and Prevotella. Campylobacter also tended to reduce (P&lt;0.10) in MRF supplemented piglets. On PND 28 differential gene expression in jejunal tissue signified an overall effect of supplementing MRF to piglets. Downstream analysis of gene expression data revealed piglets supplemented with MRF had enriched biological pathways involved in intestinal development, function and immunity, supporting the observed improvement in jejunal villus architecture on PND 28. On PND 42 there was no effect of MRF supplementation on jejunal morphology or overall cecal microbial community structure. In conclusion, supplementing Actigen™, a MRF, to piglets altered cecal microbial community structure and improved jejunal morphology early post-weaning on PND 28, which is supported by enrichment of intestinal development pathways.

Low birth weight (LBW) and postnatal nutrition are risk factors for adult metabolic diseases. However, the interactions between LBW, diet, and intestinal lipid absorption and secretion leading to adult metabolic disease remain unclear. The current study determined the impact of LBW on intestinal lipid and carbohydrate metabolism under both control and Western diet (high fat, high fructose, and cholesterol) conditions in 5-wk-old LBW and normal birth weight (NBW) Landrace-Large White × Duroc pigs. A 2-step modified oral glucose and fat challenge test was performed. Mesenteric lymph, jejunal mucosal scrapings, and cecal digesta samples were also collected. LBW offspring were lower in weight and gained less weight per day. LBW pigs on either control or Western diets displayed increased triglyceride (TG) secretion into lymph ( P = 0.0135). Western diet-fed LBW pigs developed fasting ( P = 0.03) and postprandial ( P < 0.05) hypertriglyceridemia, muscle steatosis ( P = 0.0072), had higher insulin excursion ( P < 0.01), increased jejunal stearoyl-CoA desaturase 1 mRNA and increased hepatic fibrosis ( P = 0.0017) compared with NBW piglets. Gut microbiota showed significant dysbiosis on Western diet independent of birth weight. In conclusion, LBW pigs fed a Western diet specifically up-regulate TG absorption and secretion, develop dyslipidemia, muscular steatosis, and display early signs of insulin resistance. Interestingly, this study does not provide evidence of altered intestinal microbiome in LBW pigs contributing to increased severity of metabolic diseases.-Fontaine, M. A., Diane, A., Singh, V. P., Mangat, R., Krysa, J. A., Nelson, R., Willing, B. P., Proctor, S. D. Low birth weight causes insulin resistance and aberrant intestinal lipid metabolism independent of microbiota abundance in Landrace-Large White pigs.

Background: Neonates with intestinal failure dependent on parenteral nutrition (PN) are at risk of intestinal failure-associated liver disease (IFALD). PN lipid composition relates to the risk of IFALD, but the mechanisms are poorly understood. We investigated the effects of soybean oil (SO), a mixed-lipid (ML) emulsion containing fish oil (FO), and a pure FO. We hypothesized FO-containing PN lipids would result in increased gene expression of canalicular bile acid transporters and a larger, more hydrophilic bile acid pool, predictive of increased bile flow., Methods: Neonatal piglets were allocated to receive 1 of SO, ML, or FO throughout 14 days of PN feeding. Relative expression of genes involved in bile acid synthesis and transport were determined through quantitative polymerase chain reaction. Bile secreted from the liver was collected and measured. Bile acid composition was determined using tandem mass spectrometry. Regression analysis was used to determine predictors of bile flow., Results: PN reduced bile acid secretion (P < .001). FO-containing PN lipids were associated with greater expression of bile acid and organic solute transport genes (P < .05) and greater secretion of hydrophobic bile acids (P < .001). Farnesoid X receptor (P = .01), bile salt export pump (P < .01), multidrug resistant protein 2 (P < .01), and unconjugated hyocholic acid (P < .001) independently predicted bile flow., Conclusions: PN lipid modulation altered bile acid metabolism and composition. These alterations may explain the hepatoprotective effects of FO-containing PN lipids and support their use in the prevention and treatment of IFALD., (© 2018 American Society for Parenteral and Enteral Nutrition.)

The genus of Parasutterella has been defined as a core component of the human and mouse gut microbiota, and has been correlated with various health outcomes. However, like most core microbes in the gastrointestinal tract (GIT), very little is known about the biology of Parasutterella and its role in intestinal ecology. In this study, Parasutterella was isolated from the mouse GIT and characterized in vitro and in vivo. Mouse, rat, and human Parasutterella isolates were all asaccharolytic and producers of succinate. The murine isolate stably colonized the mouse GIT without shifting bacterial composition. Notable changes in microbial-derived metabolites were aromatic amino acid, bilirubin, purine, and bile acid derivatives. The impacted bile acid profile was consistent with altered expression of ileal bile acid transporter genes and hepatic bile acid synthesis genes, supporting the potential role of Parasutterella in bile acid maintenance and cholesterol metabolism. The successful colonization of Parasutterella with a single environmental exposure to conventional adult mice demonstrates that it fills the ecological niche in the GIT and contributes to metabolic functionalities. This experiment provides the first indication of the role of Parasutterella in the GIT, beyond correlation, and provides insight into how it may contribute to host health.

Health benefits associated with pea consumption have been attributed to the fiber and polyphenolic content concentrated within the pea seed coat. However, the amount of pea polyphenols can vary between cultivars, and it has yet to be studied whether pea polyphenols impact the intestinal microbiota. We hypothesized that pea polyphenols promote a healthy microbiome that supports intestinal integrity and pathogen colonization resistance. To investigate the effects of pea polyphenols, pea cultivars rich and poor in proanthocyanidins were supplemented in raw or acid hydrolyzed form to an isocaloric diet in mice. Acid hydrolysis increases the absorption of pea polyphenols by cleaving polymeric proanthocyanidins to their readily absorbable anthocyanidin monomers. After 3 weeks of diet, mice were challenged with Citrobacter rodentium and pathogen colonization and inflammation were assessed. Counter to our hypothesis, pea seed coat fraction supplementation, especially the non-hydrolyzed proanthocyanidin-rich fraction diet adversely increased C. rodentium pathogen load and inflammation. Ileal, cecal and colon microbial communities were notably distinct between pea seed cultivar and hydrolysis processing. The consumption of intact proanthocyanidins decreased microbial diversity indicating that proanthocyanidins have antimicrobial properties. Together our results indicate supplementation of raw pea seed coat rich in proanthocyanidins adversely affect intestinal integrity. However, acid hydrolysis processing restored community structure and colonization resistance, and the anthocyanidin-rich fractions reduced weight gain on a high fat diet. Establishing a clear understanding of the effects of pea fiber and polyphenolic form on health will help to develop research-based pea products and dietary recommendations., (Copyright © 2019 Elsevier Inc. All rights reserved.)

We investigated gene expression patterns in whole blood and fecal microbiota profile as potential predictors of immune response to vaccination, using healthy M. hyopneumoniae infection free piglets (n = 120). Eighty piglets received a dose of prophylactic antibiotics during the first two days of life, whereas the remaining 40 did not. Blood samples for RNA-Seq analysis were collected on experimental Day 0 (D0; 28 days of age) just prior to vaccination, D2, and D6 post-vaccination. A booster vaccine was given at D24. Fecal samples for microbial 16SrRNA sequencing were collected at 7 days of age, and at D0 and D35 post-vaccination. Pigs were ranked based on the levels of M. hyopneumoniae-specific antibodies in serum samples collected at D35, and groups of 'high' (HR) and 'low' (LR) responder pigs (n = 15 each) were selected. Prophylactic antibiotics did not influence antibody titer levels and differential expression analysis did not reveal differences between HR and LR at any time-point (FDR > 0.05); however, based on functional annotation with Ingenuity Pathway Analysis, D2 post-vaccination, HR pigs were enriched for biological terms relating to increased activation of immune cells. In contrast, the immune activation decreased in HR, 6 days post-vaccination. No significant differences were observed prior to vaccination (D0). Two days post-vaccination, multivariate analysis revealed that ADAM8, PROSER3, B4GALNT1, MAP7D1, SPP1, HTRA4, and ENO3 genes were the most promising potential biomarkers. At D0, OTUs annotated to Prevotella, CF21, Bacteroidales and S24-7 were more abundant in HR, whereas Fibrobacter, Paraprevotella, Anaerovibrio, [Prevotella], YRC22, and Helicobacter positively correlated with the antibody titer as well as MYL1, SPP1, and ENO3 genes. Our study integrates gene differential expression and gut microbiota to predict vaccine response in pigs. The results indicate that post-vaccination gene-expression and early-life gut microbiota profile could potentially predict vaccine response in pigs, and inform a direction for future research., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Animal performance, feed efficiency, and overall health are heavily dependent on gut health. Changes in animal production systems and feed regulations away from the use of antibiotic growth promoters (AGP) have necessitated the identification of strategies to optimize gut health in novel and effective ways. Among alternatives to AGP, the inclusion of dietary fibers (DF) in monogastric diets has been attempted with some success. Alternative feedstuffs and coproducts are typically rich in fiber and can be used in the diets to reduce feed costs and optimize gut health. DF are naturally occurring compounds with a diverse composition and are present in all plant-based feedstuffs. DF stimulate the growth of health-promoting gut bacteria, are fermented in the distal small intestine and large intestine to short-chain fatty acids and have beneficial effects on the immune system. Maternal DF supplementation is one novel strategy suggested to have a beneficial programming effect on the microbial and immune development of their offspring. One mechanism by which DF improves gut health is through maintenance of an anaerobic intestinal environment that subsequently prevents facultative anaerobic pathogens from flourishing. Studies with pigs and poultry have shown that fermentation characteristics and their beneficial effects on gut health vary widely based on type, form, and the physico-chemical properties of the DF. Therefore, it is important to have information on the different types of DF and their role in optimizing gut health. This review will provide information and updates on different types of DF used in monogastric nutrition and its contribution to gut health including microbiology, fermentation characteristics, and innate and adaptive immune responses.