Use of reconstituted kefir consortia to determine the impact of microbial composition on kefir metabolite profiles.

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 log2(fold change) higher levels of esters and the consortium fermented kefir having between 1 and 3 log2(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 log2(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.

A blend of medium-chain fatty acids, butyrate, organic acids, and a phenolic compound accelerates microbial maturation in newly weaned piglets.

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 ß-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.

Comparing the impact of mixed-culture microbial communities and fecal transplant on the intestinal microbiota and metabolome of weaned piglets.

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.

Maternal Mycobiome, but Not Antibiotics, Alters Fungal Community Structure in Neonatal Piglets.

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 ß-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.

Dietary benzoic acid and supplemental enzymes alter fiber-fermenting taxa and metabolites in the cecum of weaned pigs.

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, ß-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.

Feeding weaned pigs diets containing benzoic acid or supplemental enzymes for 21 d after weaning changed the gut microbiota and metabolome. Benzoic acid increased feed intake, weight gain, and the presence of 1,2-propanediol in cecal digesta, which is an important microbial cross-feeding product. Dietary enzymes altered microbiota composition, increasing the presence of fiber-fermenting microbes including Prevotellaceae. Pigs fed a combination of both benzoic acid and enzymes showed improved resolution of postweaning diarrhea. These differences demonstrate the role of these feed additives in the establishment of gut microbes and metabolic pathways for the degradation of complex dietary components in the weaned pig. This study provides new information about alterations in microbial function and community composition using microbiota sequencing and metabolomic analysis.

Characterization of whole blood transcriptome and early-life fecal microbiota in high and low responder pigs before, and after vaccination for Mycoplasma hyopneumoniae.

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.

Microbial Fermentation of Dietary Protein: An Important Factor in Diet⁻Microbe⁻Host Interaction.

Protein fermentation by gut microbiota contributes significantly to the metabolite pool in the large intestine and may contribute to host amino acid balance. However, we have a limited understanding of the role that proteolytic metabolites have, both in the gut and in systemic circulation. A review of recent studies paired with findings from previous culture-based experiments suggests an important role for microbial protein fermentation in altering the gut microbiota and generating a diverse range of bioactive molecules which exert wide-ranging host effects. These metabolic products have been shown to increase inflammatory response, tissue permeability, and colitis severity in the gut. They are also implicated in the development of metabolic disease, including obesity, diabetes, and non-alcoholic fatty liver disease (NAFLD). Specific products of proteolytic fermentation such as hydrogen sulfide, ammonia, and p-Cresol may also contribute to the development of colorectal cancer. These findings are in conflict with other studies showing that tryptophan metabolites may improve gut barrier function and attenuate severity in a multiple sclerosis model. Further research examining proteolytic fermentation in the gut may be key to our understanding of how microbial and host metabolism interact affecting health.