In vitro fermentation of feed ingredients by fresh or frozen pig fecal inocula

Effect of in vitro cultivation on human gut microbiota composition using 16S rDNA amplicon sequencing and metabolomics approach

Gut microbiota (GM) plays many key functions and helps maintain the host's health. Consequently, the development of GM cultivation under in vitro stimulating physiological conditions has gained extreme interest in different fields. In this study, we evaluated the impact of four culture media: Gut Microbiota Medium (GMM), Schaedler Broth (SM), Fermentation Medium (FM), and Carbohydrate Free Basal Medium (CFBM) on preserving the biodiversity and metabolic activity of human GM in batch in vitro cultures using PMA treatment coupled with 16S rDNA sequencing (PMA-seq) and LC-HR-MS/MS untargeted metabolomics supplemented with GC-MS SCFA profiling. Before the experiments, we determined the possibility of using the pooled faecal samples (MIX) from healthy donors (n = 15) as inoculum to reduce the number of variables and ensure the reproducibility of in vitro cultivation tests. Results showed the suitability of pooling faecal samples for in vitro cultivation study. Non-cultured MIX inoculum was characterized by higher α-diversity (Shannon effective count, and Effective microbial richness) compared to inocula from individual donors. After 24 h of cultivation, a significant effect of culture media composition on GM taxonomic and metabolomic profiles was observed. The SM and GMM had the highest α-diversity (Shannon effective count). The highest number of core ASVs (125) shared with non-cultured MIX inoculum and total SCFAs production was observed in the SM. These results might contribute to the development of standardized protocols for human GM in vitro cultivation by preventing methodological bias in the data.

Weaning-associated feed deprivation stress causes microbiota disruptions in a novel mucin-containing in vitro model of the piglet colon (MPigut-IVM)

BACKGROUND

Risk factors for the etiology of post-weaning diarrhea, a major problem in swine industry associated with enormous economic losses, remain to be fully elucidated. In concordance with the ethical concerns raised by animal experiments, we developed a new in vitro model of the weaning piglet colon (MPigut-IVM) including a mucin bead compartment to reproduce the mucus surface from the gut to which gut microbes can adhere.

RESULTS

Our results indicated that the MPigut-IVM is able to establish a representative piglet archaeal and bacterial colon microbiota in terms of taxonomic composition and function. The MPigut-IVM was consequently used to investigate the potential effects of feed deprivation, a common consequence of weaning in piglets, on the microbiota. The lack of nutrients in the MPigut-IVM led to an increased abundance of Prevotellaceae and Escherichia-Shigella and a decrease in Bacteroidiaceae and confirms previous in vivo findings. On top of a strong increase in redox potential, the feed deprivation stress induced modifications of microbial metabolite production such as a decrease in acetate and an increase in proportional valerate, isovalerate and isobutyrate production.

CONCLUSIONS

The MPigut-IVM is able to simulate luminal and mucosal piglet microbiota and represent an innovative tool for comparative studies to investigate the impact of weaning stressors on piglet microbiota. Besides, weaning-associated feed deprivation in piglets provokes disruptions of MPigut-IVM microbiota composition and functionality and could be implicated in the onset of post-weaning dysbiosis in piglets.

Measures Matter-Determining the True Nutri-Physiological Value of Feed Ingredients for Swine

Many types of feed ingredients are used to provide energy and nutrients to meet the nutritional requirements of swine. However, the analytical methods and measures used to determine the true nutritional and physiological ("nutri-physiological") value of feed ingredients affect the accuracy of predicting and achieving desired animal responses. Some chemical characteristics of feed ingredients are detrimental to pig health and performance, while functional components in other ingredients provide beneficial health effects beyond their nutritional value when included in complete swine diets. Traditional analytical procedures and measures are useful for determining energy and nutrient digestibility of feed ingredients, but do not adequately assess their true physiological or biological value. Prediction equations, along with ex vivo and in vitro methods, provide some benefits for assessing the nutri-physiological value of feed ingredients compared with in vivo determinations, but they also have some limitations. Determining the digestion kinetics of the different chemical components of feed ingredients, understanding how circadian rhythms affect feeding behavior and the gastrointestinal microbiome of pigs, and accounting for the functional properties of many feed ingredients in diet formulation are the emerging innovations that will facilitate improvements in precision swine nutrition and environmental sustainability in global pork-production systems.

Preservation of Human Gut Microbiota Inoculums for In Vitro Fermentations Studies

The use of fecal inoculums for in vitro fermentation models requires a viable gut microbiota, capable of fermenting the unabsorbed nutrients. Fresh samples from human donors are used; however, the availability of fresh fecal inoculum and its inherent variability is often a problem. This study aimed to optimize a method of preserving pooled human fecal samples for in vitro fermentation studies. Different conditions and times of storage at −20 °C were tested. In vitro fermentation experiments were carried out for both fresh and frozen inoculums, and the metabolic profile compared. In comparison with the fresh, the inoculum frozen in a PBS and 30% glycerol solution, had a significantly lower (p < 0.05) bacterial count (<1 log CFU/mL). However, no significant differences (p < 0.05) were found between the metabolic profiles after 48 h. Hence, a PBS and 30% glycerol solution can be used to maintain the gut microbiota viability during storage at −20 °C for at least 3 months, without interfering with the normal course of colonic fermentation.

Heat Stress Increases In Vitro Hindgut Fermentation of Distinct Substrates in Iberian Pigs

Simple Summary

Heat stress is a major concern in pig production in summer, as pigs have a limited number of functional sweat glands to transfer body heat. Above 25 °C pigs are out of their comfort zone and mechanisms such as decreasing feed intake or diverting blood from the internal organs to the skin are triggered. Intestinal microbiota is also affected by high ambient temperature but the consequences on fermentation capacity are poorly known. Short-chain fatty acids are the end-products of bacterial metabolism of carbohydrates and protein mainly in the hindgut and, in addition to being a source of energy, they have beneficial effects on immune status and health. An understanding of the effects of heat stress on intestinal fermentation could help to develop strategies mitigating intestinal disorders. We used an in vitro method to assess gas and short-chain fatty acid production, utilizing as inoculum feces from Iberian pigs fed a commercial diet for 28 days under neutral (20 °C) or heat stress (30 °C) conditions. Four substrates with dissimilar fermentation characteristics were incubated in vitro with fecal inoculum for 24 h. Chronic heat stress increased in vitro production of short-chain fatty acids, suggesting a modification of intestinal microbiota activity.

Abstract

Heat stress reduces the feed intake and growth of pigs. We hypothesized that heat stress affects the intestinal fermentation capacity of pigs. Sixteen Iberian pigs (44 ± 1.0 kg) were randomly assigned to one of two treatments (eight pigs/treatment) for 4 weeks—heat stress (HS; 30 °C) ad libitum or thermoneutral (TN; 20 °C) pair feeding. Frozen rectum contents were used as inocula for 24 h in vitro incubations in which a mixture of starches, citrus pectin, inulin from chicory, and cellulose were the substrates. Cellulose was poorly degraded, whereas pectin and the mixture of starches were the most fermentable substrates according to total short-chain fatty acid (SCFA) production. The mixture of starches and inulin produced the greatest amount of gas. For all substrates, heat stress enhanced gas production (8%, p = 0.001), total SCFA production (16%, p = 0.001), and the production of acetate and propionate (12% and 42%, respectively; p = 0.001). The increased isoacid production (33%, p = 0.001) and ammonia concentration (12%, p = 0.001) may indicate protein fermentation under heat stress. In conclusion, the in vitro intestinal fermentation capacity of pigs under heat stress was increased compared to thermoneutral conditions, which may indicate an adaptive response to heat stress.

Effects of Gas Production Recording System and Pig Fecal Inoculum Volume on Kinetics and Variation of In Vitro Fermentation using Corn Distiller's Dried Grains with Solubles and Soybean Hulls

Simple Summary

Various in vitro methodologies have been developed and used to estimate the digestibility of feed ingredients, such as corn distillers dried grains with solubles (cDDGS) and soybean hulls (SBH) which contain high concentrations of dietary fiber. This study evaluated two in vitro gas production recording systems (manual vs. automated) and two initial fecal inoculum volumes (30 vs. 75 mL) on the parameters of in vitro fermentation of cDDGS and SBH. The results showed that the use of 75-mL inoculum volume with 0.5 g substrate tended to reduce the variation of measurements compared to the 30-mL inoculum volume with 0.2 g substrate regardless of the gas production recording system. These findings suggest that using larger inoculum volume with more substrate increases the precision of measurements. Furthermore, the automated system decreases labor for conducting the assay.

Abstract

An experiment was conducted to investigate the effect of inoculum volume (IV), substrate quantity, and the use of a manual or automated gas production (GP) recording system for in vitro determinations of fermentation of corn distillers dried grains with solubles (cDDGS) and soybean hulls (SBH). A 2 × 2 × 2 factorial arrangement of treatments was used and included the factors of (1) ingredients (cDDGS or SBH), (2) inoculum volume and substrate quantity (IV30 = 0.2 g substrate + 30 mL inoculum or IV75 = 0.5 g substrate + 75 mL inoculum), and (3) GP recording system (MRS = manual recording system or ARS = automated recording system). Feed ingredient samples were pre-treated with pepsin and pancreatin, and the hydrolyzed residues were subsequently incubated with fresh pig feces in a buffered mineral solution. The GP recording was monitored for 72 h, and the kinetics were estimated by fitting data using an exponential model. Compared with SBH, cDDGS yielded less (p < 0.01) maximal gas production (G_f), required more time (p < 0.02) to achieve half gas accumulation (T/2), and had less (p < 0.01) fractional rate of degradation (µ) and in vitro fermentability of dry matter (IVDMF). Using the ARS resulted in less IVDMF (p < 0.01) compared with MRS (79.0% vs. 81.2%, respectively). Interactions were observed between GP recording system and inoculum volume and substrate quantity for Gf (p < 0.04), µ (p < 0.01), and T/2 (p < 0.04) which implies that increasing inoculum volume and substrate quantity resulted in decreased Gf (332 mL/g from IV30 vs. 256 mL/g from IV75), µ (0.05 from IV30 vs. 0.04 from IV75), and T/2 (34 h for IV30 vs. 25 h for IV75) when recorded with ARS but not MRS. However, the recorded cumulative GP at 72 h was not influenced by the inoculum volume nor recording system. The precision of G_f (as measured by the coefficient of variation of G_f) tended to increase for IV30 compared with IV75 (p < 0.10), indicating that using larger inoculum volume and substrate quantity (IV75) reduced within batch variation in GP kinetics. Consequently, both systems showed comparable results in GP kinetics, but considering convenience and achievement of consistency, 75 mL of inoculum volume with 0.5 g substrate is recommended for ARS.

Challenges in simulating the human gut for understanding the role of the microbiota in obesity

There is an elevated incidence of cases of obesity worldwide. Therefore, the development of strategies to tackle this condition is of vital importance. This review focuses on the necessity of optimising in vitro systems to model human colonic fermentation in obese subjects. This may allow to increase the resolution and the physiological relevance of the information obtained from this type of studies when evaluating the potential role that the human gut microbiota plays in obesity. In light of the parameters that are currently used for the in vitro simulation of the human gut (which are mostly based on information derived from healthy subjects) and the possible difference with an obese condition, we propose to revise and improve specific standard operating procedures.

Evaluation of an optimal preparation of human standardized fecal inocula for in vitro fermentation studies

This study investigated the optimal preservation approach to prepare human feces as inoculum for in vitro fermentations as an alternative to the use of fresh feces. The four treatments studied were: Treatment 1) fresh feces resuspended in dialysate solution+glycerol; Treatment 2) fresh feces resuspended in dialysate solution+glycerol and then stored at -80°C; Treatment 3) fecal sample frozen with 1.5 g glycerol; and Treatment 4) fecal sample frozen. All the treatments contained 8.75 g of feces, 3.5 ml dialysate and 4.9 ml glycerol when inoculated in TIM-2 in vitro system. Treatment 1 (fresh fecal preparation) was used as a reference. The effects were evaluated in terms of i) metabolic activity and ii) composition of the microbiota using fermentation experiments in the TIM-2 in vitro system. In all treatments, high levels of acetate were produced followed by n-butyrate and propionate. However, the metabolic activity of the bacteria, in terms of short-chain fatty acid production, was affected by the different treatments. Microbiota composition was analyzed using the IS-pro profiling technique. Diversity in Actinobacteria, Firmicutes, Fusobacteria and Verrucomicrobia and Proteobacteria groups seemed to be preserved in all treatments whereas it was observed to decline in the Bacteroidetes group. Preparing a human fecal inoculum resuspended in dialysate solution with glycerol and then stored at -80°C showed high similarities to the results obtained with fresh feces, and is proposed as the optimal way to freeze fecal material as an alternative to fresh feces for in vitro fermentation studies.