Adaptation of the cecal bacterial microbiome of growing pigs in response to resistant starch type 4

Large intestinal dynamics differ between fowl and swine: Anatomical modifications, microbial collaboration, and digestive advantages from fibrolytic enzymes

The large intestinal systems of fowl and swine recover nutrients from ileal indigesta by a strategically different manner. Indigesta with fowl enter a short colon where retro-peristalsis using urine from the urodeum carries small particulates and solutes into both ceca while coarse materials collect in the cloaca. Fowl repetitively add fine and soluble materials into both ceca to continue fermentation until complexity of the remainder exceeds microbial action, then contents apart from faeces are entirely evacuated. Indigesta with swine initially enter a short cecum followed by a lengthy progression through to the rectal ampulla. Wall out-pocketings of circular muscle or haustrae occur throughout the length of the pig's cecum and helicoidal colon. Each pocket carries contents acquired earlier in the cecum. Motility collects fines and solutes into haustrae during their progression through the colon whereas coarse particulates assemble in the core. Haustrae contents continually ferment during movement to the distal colon with resulting volatile fatty acids (VFA) and electrolytes being absorbed. Mucin loosely covers the lumen surface in caeca as well as helicoidal colon that may capture microbes from active intestinal contents as well as release others to sustain fermentation. The microbial community continually modifies to accommodate fibre complexity as encountered. Resistant starches (RS) and simple oligosaccharides rapidly ferment to yield VFA while encouraging butyric acid in the cecum and anterior colon, whereas non-starch polysaccharides (NSP) complexity requires extended durations through the remaining colon that enhance acetic acid. Residual fibre eventually results in undue complexity for fermentation and consolidates at termination of the colon. These compact pellets are placed on core contents to form faeces having a nodular surface. Acetic, propionic, and butyric acids represent the bulk of VFA and are derived from non-digestible carbohydrates. Fibrolytic enzymes, when supplemented to feed, may increase the proportion of oligosaccharides and simpler NSP to further the rate as well as extent of fermentation. Active absorption of VFA by mucosal enterocytes employs its ionized form together with Na⁺, whereas direct membrane passage occurs when non-dissociated. Most absorbed VFA favour use by the host with a portion of butyric acid together with by-products from protein digestion being retained to reform mucin and sustain mucosal integrity.

Lycopene Affects Intestinal Barrier Function and the Gut Microbiota in Weaned Piglets via Antioxidant Signaling Regulation

BACKGROUND

In pig production, early and abrupt weaning frequently causes weaning stress, which manifests as oxidative damage, barrier disruption, and digestion and absorption capacity declines. Lycopene exhibits beneficial antioxidant capacity in both humans and other animal models.

OBJECTIVES

The present study aimed to investigate the effects of lycopene supplementation on early weaning stress in piglets and the underlying mechanisms by examining the oxidative stress state, gut intestinal barrier function, and the gut microbiota.

METHODS

Twenty-four 21-day-old weaned piglets [Duroc × (Landrace × Yorkshire); castrated males; 5.48 ± 0.10 kg initial body weight] were randomly assigned to 2 treatments. The piglets were fed a basal diet (control treatment) or a basal diet supplemented with 50 mg/kg lycopene (lycopene treatment) for 28 days. The serum lipid levels, serum and jejunum enzyme activities, jejunum morphology, mRNA and protein expression, and gut microbiota were determined.

RESULTS

Compared with the control treatment, lycopene supplementation increased the serum catalase activity (P = 0.042; 62.0%); serum total cholesterol concentration (P = 0.020; 14.1%); and jejunum superoxide dismutase activity (P = 0.032; 21.4%), whereas it decreased serum (P = 0.039, 23.0%) and jejunum (P = 0.047; 20.9%) hydrogen peroxide concentrations. Additionally, lycopene increased the mRNA and protein expression of NFE2-like bZIP transcription factor 2 (214.0% and 102.4%, respectively) and CD36 (100.8% and 145.2%, respectively) in the jejunum, whereas it decreased the mRNA and protein expression of Kelch-like ECH-associated protein 1 (55.6% and 39.8%, respectively ). Lycopene also improved jejunal morphology, increasing the villus height (P = 0.018; 27.5%) and villus:crypt ratio (P < 0.001; 57.9%). Furthermore, it increased the abundances of potentially beneficial bacterial groups, including Phascolarctobacterium and Parasutterella, and decreased those of potentially pathogenic bacterial groups, including Treponema_2 and Prevotellaceae_unclassified.

CONCLUSIONS

Lycopene supplementation strengthens the intestinal barrier function and improves the gut microbiota in weaned piglets by regulating intestinal antioxidant signaling.

Effects of Dietary Supplementation of Black Soldier Fly (Hermetia illucens) Larvae Oil on Broiler Health

Insects are a potential source of proteins and fats which can be incorporated into diets of broiler chickens. Accordingly, black soldier fly larvae oil (BSFLO) needs to be tested as an appropriate fat source to produce healthy chickens for consumers. Therefore, the objective of the present study was to evaluate the effects of the replacement of soybean oil (SBO) with BSFLO in broiler diets on intestinal health and blood profiles. A total of 210 one-day-old male broilers were randomly allocated to three dietary treatments (10 replicates of seven birds per group): a control diet and two experimental diets in which SBO was replaced with 50% (50 BSFLO) or 100% (100 BSFLO) BSFLO. At the end of the study (35 days), 18 birds (six broilers per treatment) were slaughtered to determine the intestinal morphology, digestibility, and volatile fatty acid (VFA) profile. Blood samples were collected from 24 randomly selected birds (eight broilers per treatment) to determine the blood profiles. BSFLO supplementation positively affected villus height but did not affect digestibility. BSFLO showed no adverse effects on the VFA and blood profiles. In conclusion, the results of this study suggest that SBO can be replaced by BSFLO without any adverse effects on broiler health.

Milk replacer supplementation in early life optimizes the development of intestinal microbes in goats

Colonization and development of the gut microbiome during early life is important in establishing a host-microbial symbiotic relationship. It contributes to maintaining health and well-being throughout the life span. To date, early longitudinal development of intestinal microflora in the ileum micro-ecology of the Yimeng black goats (YBGs) is rare. The purpose of this research was to study the effect of milk replacer with age on the ileal microbiota growth and maturation in YBGs throughout the post-weaning phase. The newborn YBGs (n = 24) were divided into two groups, i.e., milk replacer (R group) and control group (B group). The microbiome of Ileum was observed on days 15, 25, 45, and 75. When compared with baseline (B group), the R group's alpha diversity was lower (day 15, 25, 45), but it gradually approached and exceeded the baseline in the later stages (day 75). On the time axis, the richness of intestinal microflora was increased with age, but there was no statistically significant difference. The relative abundances of Proteobacteria, Firmicutes, Peptoclustridium, Lachnospiraceae, and Prevotellaceae showed a continuous trend of increase initially. They then decreased except Ruminococcaceae, which reflected the gradual maturity of intestinal microbial development. Milk replacer treatment temporarily increased the abundance of Actinomycetes (day 25 and 45), while the relative proportion of several intestinal bacteria such as Parasutterella, Megasphaera, Prevotellaceae, Akkermansia, and Subdoligranulum species were significantly higher in R group than in B group. The major changes in gut microflora composition might reflect positive effect of milk replacer on the development and maturation of the intestine during the early stage, connecting with substrate availability in the gut. Our study provides an effective strategy to promote the development of the gut microbiome, which is helpful for a smooth transition during the early-weaning period in YBGs.

Functional enrichment of gut microbiome by early supplementation of Bacillus based probiotic in cage free hens: a field study

BACKGROUND

The chicken gut microbiota passes through different stages of maturation; therefore, strengthening it with well characterised probiotics increases its resilience required for optimum gut health and wellbeing. However, there is limited information on the interaction of Bacillus based probiotics with gut microbial community members in cage free laying chickens both in rearing and production phases of life. In the current study, we investigated the changes in the gut microbiome of free range hens in the field after Bacillus based probiotic supplementation.

RESULTS

Overall, at phylum level, probiotic supplementation increased the populations of Bacteroidetes and Proteobacteria mainly at the expense of Firmicutes. The population of Bacteroidetes significantly increased during the production as compared to the rearing phase, and its higher population in the probiotic-supplemented chickens reflects the positive role of Bacillus based probiotic in gut health. Core differences in the beta diversity suggest that probiotic supplementation decreased microbial compositionality. The non-significant difference in alpha diversity between the probiotic and control chickens showed that the composition of community structure did not change. No Salmonella spp. were isolated from the probiotic supplemented birds. Egg internal quality was significantly higher, while egg production and body weight did not differ. Functional prediction data showed that probiotic supplementation enriched metabolic pathways, such as vitamin B6 metabolism, phenylpropanoid biosynthesis, monobactam biosynthesis, RNA degradation, retinol metabolism, pantothenate and CoA biosynthesis, phosphonate and phosphinate metabolism, AMPK signaling pathway, cationic antimicrobial peptide (CAMP) resistance and tyrosine metabolism.

CONCLUSIONS

Overall, age was the main factor affecting the composition and diversity of gut microbiota, where probiotic supplementation improved the abundance of many useful candidates in the gut microbial communities. The generated baseline data in the current study highlights the importance of the continuous use of Bacillus based probiotic for optimum gut health and production.

Effect of feeding acidified or fermented barley using Limosilactobacillus reuteri with or without supplemental phytase on diet nutrient digestibility in growing pigs

Fermentation of cereal grains may degrade myo-inositol 1,2,3,4,5,6-hexakis (dihydrogen phosphate) (InsP6) thereby increasing nutrient digestibility. Effects of chemical acidification or fermentation with Limosilactobacillus (L.) reuteri with or without phytase of high β-glucan hull-less barley grain on apparent ileal digestibility (AID) and apparent total tract digestibility (ATTD) of nutrients and gross energy (GE), standardized ileal digestibility (SID) of crude protein (CP) and amino acids (AAs), and standardized total tract digestibility (STTD) of P were assessed in growing pigs. Pigs were fed four mash barley-based diets balanced for water content: 1) unfermented barley (Control); 2) chemically acidified barley (ACD) with lactic acid and acidic acid (0.019 L/kg barley grain at a ratio of 4:1 [vol/vol]); 3) barley fermented with L. reuteri TMW 1.656 (Fermented without phytase); and 4) barley fermented with L. reuteri TMW 1.656 and phytase (Fermented with phytase; 500 FYT/kg barley grain). The acidification and fermentation treatments occurred for 24 h at 37 °C in a water bath. The four diets were fed to eight ileal-cannulated barrows (initial body weight [BW], 17.4 kg) for four 11-d periods in a double 4 × 4 Latin square. Barley grain InsP6 content of Control, ACD, Fermented without phytase, or Fermented with phytase was 1.12%, 0.59%, 0.52% dry matter (DM), or not detectable, respectively. Diet ATTD of DM, CP, Ca, and GE, digestible energy (DE), predicted net energy (NE) value, and urinary excretion of P were greater (P < 0.05) for ACD than Control. Diet ATTD of DM, CP, Ca, GE, DE and predicted NE value, urinary excretion of P was greater (P < 0.05), and diet AID of Ca and ATTD and STTD of P tended to be greater (P < 0.10) for Fermented without phytase than Control. Diet ATTD of GE was lower (P < 0.05) and diet ATTD and STTD of P, AID and ATTD of Ca was greater (P < 0.05) for Fermented with phytase than Fermented without phytase. Acidification or fermentation with/without phytase did not affect diet SID of CP and AA. In conclusion, ACD or Fermented without phytase partially degraded InsP6 in barley grain and increased diet ATTD of DM, CP, and GE, but not SID of CP and most AA in growing pigs. Fermentation with phytase entirely degraded InsP6 in barley grain and maximized P and Ca digestibility, thereby reducing the need to provide inorganic dietary P to meet P requirements of growing pigs.

Comparative study of growth performance, nutrient digestibility, and ruminal and fecal bacterial community between yaks and cattle-yaks raised by stall-feeding

The experiment was conducted to compare the growth performance, rumen fermentation, nutrient digestibility, and ruminal and fecal bacterial community between yaks and cattle-yaks. Ten male yaks (36-month-old) were used as the yak (YAK) group and 10 male cattle-yaks with similar age were selected as the cattle-yak (CAY) group. All the animals were fed same ration and the experiment lasted for 60 days. The results showed that the average daily gain and dry matter intake of CAY group were higher (P < 0.05) than those of YAK group. The ruminal concentrations of total volatile fatty acids, acetate, and butyrate were higher (P < 0.05) in CAY group than those in YAK group. However, the neutral detergent fiber and acid detergent fiber digestibility exhibited an opposite between two groups. In the rumen, the relative abundances of Prevotella 1 and Prevotellaceae UCG-001 were higher (P < 0.05) and Succiniclasticum and Butyrivibrio 2 were lower (P < 0.05) in YAK group compared to CAY group. In the feces, the unclassified Lachnospiraceae, Lachnospiraceae NK4A136 group, and Lachnospiraceae AC2044 group were significantly enriched (P < 0.05) in YAK group, whereas the Ruminococcaceae UCG-010, Ruminococcaceae UCG-013, and Succiniclasticum were significantly enriched (P < 0.05) in CAY group. Overall, under the same diet, the yaks have higher fiber utilization and cattle-yaks have higher energy utilization.

Individual and Site-Specific Variation in a Biogeographical Profile of the Coyote Gastrointestinal Microbiota

Most knowledge of the vertebrate gut microbiota comes from fecal samples; due to difficulties involved in sample collection, the upper intestinal microbiota is poorly understood in wild animals despite its potential to inform broad interpretations about host-gut microbe relationships under natural conditions. Here, we used 16S rRNA gene sequencing to characterize the microbiota of wild coyotes (Canis latrans) along the gastrointestinal tract, including samples from the duodenum, jejunum, ileum, caecum, ascending and descending colon, and feces. We used this intestinal profile to (1) quantify how intestinal site and individual identity interact to shape the microbiota in an uncontrolled setting, and (2) evaluate whether the fecal microbiota adequately represent other intestinal sites. Microbial communities in the large intestine were distinct from those in the small intestine, with higher diversity and a greater abundance of anaerobic taxa. Within each of the small and large intestine, individual identity explained significantly more among-sample variation than specific intestinal sites, revealing the importance of individual variation in the microbiota of free-living animals. Fecal samples were not an adequate proxy for studying upper intestinal environments, as they contained only half the amplicon sequence variants (ASVs) present in the small intestine at three- to four-fold higher abundances. Our study is a unique biogeographical investigation of the microbiota using free-living mammals rather than livestock or laboratory organisms and provides a foundational understanding of the gastrointestinal microbiota in a wild canid.

Dietary Phytase- and Lactic Acid-Treated Cereals Caused Greater Taxonomic Adaptations than Functional Adaptations in the Cecal Metagenome of Growing Pigs

Phosphorus (P) is an essential nutrient for the gut bacteria and the host. Nevertheless, little information exists that indicates to what extent an improved level of P availability in the small intestine leads to functional adaptations in bacterial metabolic pathways in the large intestine. Therefore, we investigated the changes in the taxonomic and functional bacterial metagenome in cecal digesta of growing pigs fed diets containing phytase and/or cereals treated with 2.5% lactic acid (LA) for 19 days (n = 8/diet) using shotgun metagenome sequencing. The phytase supplementation resulted in strikingly distinct bacterial communities, affecting almost all major bacterial families, whereas functional changes were less dramatic among the feeding groups. While phytase treatment decreased predominant Prevotellaceae levels, it seemed that Clostridiaceae, Ruminococcaceae, and Lachnospiraceae filled the opening metabolic niches (P < 0.05). The LA-treated cereals mediated reduced levels of Bacteroidaceae and increased levels of Veillonellaceae, but those results were mainly seen when the cereals were fed as a single treatment (P < 0.05). In association with the taxonomic alterations, phytase caused changes within the major functional pathways corresponding to amino acid metabolism; translation; membrane transport; folding, sorting, and degradation; and energy metabolism, whereas the LA treatment of cereals resulted in decreased enzymatic capacities within the carbohydrate metabolism and energy metabolism pathways (P < 0.05). Metabolic dependencies corresponding to the starch and sucrose metabolism, glycolysis/gluconeogenesis, and citrate cycle pathways were indicated by diet-associated changes in enzymatic capacities related to short-chain fatty acid, methane, vitamin, and bacterial antigen synthesis. Accordingly, the present results support the idea of the importance of the availability of intestinal P for bacterial metabolism. However, the functional profiles were less different than the taxonomic profiles among the dietary treatment results, indicating a certain degree of metabolic plasticity within the cecal metagenome.IMPORTANCE Dietary strategies (e.g., phytase supplementation and lactic acid [LA] treatment of cereals) used to improve the availability of phytate-phosphorus (P) from pig feed reduce the amount of P flowing into the large intestine, whereas LA treatment-induced changes in nutrient fractions alter the substrate being available to the microbiota. In ruminants, lower intestinal P availability compromises the fibrolytic activity of the microbiome. Here, we report that the functional capacities were less dramatically affected than the taxonomic composition by phytase-supplemented and LA-treated cereals. The bacterial community appeared to be partly capable of functionally compensating for the altered flow of P by replacing taxa with higher P needs by those with lower P needs. Therefore, by acting as mucosal immune stimulants, alterations in microbiota-associated molecular patterns (MAMPs) due to the taxonomic shifts may play a greater role for host physiology and health than functional differences caused by differing intestinal P availabilities, which merits further research.

Integration of culture-dependent and independent methods provides a more coherent picture of the pig gut microbiome

Bacterial communities resident in the hindgut of pigs, have profound impacts on health and disease. Investigations into the pig microbiome have utilized either culture-dependent, or far more commonly, culture-independent techniques using next generation sequencing. We contend that a combination of both approaches generates a more coherent view of microbiome composition. In this study, we surveyed the microbiome of Tamworth breed and feral pigs through the integration high throughput culturing and shotgun metagenomics. A single culture medium was used for culturing. Selective screens were added to the media to increase culture diversity. In total, 46 distinct bacterial species were isolated from the Tamworth and feral samples. Selective screens successfully shifted the diversity of bacteria on agar plates. Tamworth pigs are highly dominated by Bacteroidetes primarily composed of the genus Prevotella whereas feral samples were more diverse with almost equal proportions of Firmicutes and Bacteroidetes. The combination of metagenomics and culture techniques facilitated a greater retrieval of annotated genes than either method alone. The single medium based pig microbiota library we report is a resource to better understand pig gut microbial ecology and function. It allows for assemblage of defined bacterial communities for studies in bioreactors or germfree animal models.

Maturational Changes Alter Effects of Dietary Phytase Supplementation on the Fecal Microbiome in Fattening Pigs

Age-related successions in the porcine gut microbiome may modify the microbial response to dietary changes. This may especially affect the bacterial response to essential nutrients for bacterial metabolism, such as phosphorus (P). Against this background, we used phytase supplementation (0 or 650 phytase units/kg complete feed) to alter the P availability in the hindgut and studied the dietary response of the fecal bacterial microbiome from the early to late fattening period. Fecal DNA were isolated after 0, 3, 5 and 10 weeks and the V3-V4 region of the 16S rRNA gene was sequenced. Permutational analysis of variance showed distinct bacterial communities for diet and week. Alpha-diversity and taxonomy indicated progressing maturation of the bacterial community with age. Prevotellaceae declined, whereas Clostridiaceae and Ruminococcaceae increased from weeks 0 to 3, 5, and 10, indicating changes in fiber-digesting capacities with age. Phytase affected all major bacterial taxa but reduced species richness (Chao1) and diversity (Shannon and Simpson). To conclude, present results greatly support the importance of available P for bacterial proliferation, including fibrolytic, lactic acid- and butyrate-producing genera, in pigs. Results also emphasize the necessity to assess bacterial responses to dietary manipulation at several time points throughout the fattening period.

Early Parenteral Administration of Ceftiofur has Gender-Specific Short- and Long-Term Effects on the Fecal Microbiota and Growth in Pigs from the Suckling to Growing Phase

Simple Summary

Antibiotics are commonly used in prevention and therapy of bacterial diseases in pig production. Although the main target of antibiotics are the pathogenic bacteria, they often disrupt the commensal gut microbiota as a whole, leading to intestinal disturbances. These detrimental effects have been well established for oral administration of antibiotics, whereas knowledge about potential disturbing effects of single parenteral antibiotic treatments on the gut microbiota development is limited. In this research, the impact of a single antibiotic injection on the first day of life on the maturation of the fecal microbiome and host growth performance was evaluated from the suckling to the growing phase. Results showed that a single antibiotic injection early in life influenced the bacterial community development in the short- and long-term and that this disturbance in the bacterial community was sex-specific. Present results further demonstrated that changes in the bacterial ecosystem of the gut may impair the growth performance of the growing pig. Thus, the results of the present study emphasize the importance of a proper and strict use of antibiotics in swine herds.

Abstract

Using ceftiofur during the first days of life is a common preventative strategy against several bacterial diseases in pig production. This study aimed to evaluate short- and long-term effects of early use of ceftiofur on the fecal microbiota development in suckling and growing pigs. Sixty-four piglets from eight litters were assigned to the antibiotic (AB; n = 32) or control group (control; n = 32). Twelve hours postpartum (day 0) AB piglets received an intramuscular injection of ceftiofur (5.0 mg/kg body weight) or a placebo. DNA was extracted from fecal samples collected on days 0, 12, 28, and 97 for deep-sequencing of the 16S rRNA gene. The AB administration disturbed the maturational changes in the fecal microbiome, whereby effects were sex-specific. Sex-related differences in AB metabolism in females and males may have caused these diverging AB-effects on the fecal microbiota. Especially the loss of bacterial diversity and of certain taxa in female AB pigs may have contributed to the decreased body weight of these females on day 97 of life. Taken together, this study showed that an AB injection with ceftiofur 12 h postpartum markedly affected the successional changes in the fecal microbiota composition in male and female pigs, with long-term consequences for host performance.

Investigating the relationship between vaginal microbiota and host genetics and their impact on immune response and farrowing traits in commercial gilts

Our objectives were to evaluate the interaction between host genetics and vaginal microbiota and their relationships with antibody (Ab) response to porcine reproductive and respiratory syndrome virus (PRRSV) vaccination and farrowing performance in commercial gilts. The farrowing performance traits were number born alive, number weaning (NW), total number born, number born dead, stillborn, mummies and preweaning mortality (PWM). The vaginal microbiota was collected on days 4 (D4) and 52 (D52) after vaccination for PRRSV. Blood samples were collected on D52 for Ab measurement. Actinobacteria, Bacterioidetes, Firmicutes, Proteobacteria and Tenericutes were the most abundant Phyla identified in the vaginal microbiota. Heritability ranged from ~0 to 0.60 (Fusobacterium) on D4 and from ~0 to 0.63 (Terrisporobacter) on D52, with 43 operational taxonomic units (OTUs) presenting moderate to high heritability. One major QTL on chromosome 12 was identified for 5 OTUs (Clostridiales, Acinetobacter, Ruminococcaceae, Campylobacter and Anaerococcus), among other 19 QTL. The microbiability for Ab response to PRRSV vaccination was low for both days (<0.07). For farrowing performance, microbiability varied from <0.001 to 0.15 (NW on D4). For NW and PWM, the microbiability was greater than the heritability estimates. Actinobacillus, Streptococcus, Campylobacter, Anaerococcus, Mollicutes, Peptostreptococcus, Treponema and Fusobacterium showed different abundance between low and high Ab responders. Finally, canonical discriminant analyses revealed that vaginal microbiota was able to classify gilts in high and low Ab responders to PRRSV vaccination with a misclassification rate of <0.02. Although the microbiota explained limited variation in Ab response and farrowing performance traits, there is still potential to explore the use of vaginal microbiota to explain variation in traits such as NW and PWM. In addition, these results revealed that there is a partial control of host genetic over vaginal microbiota, suggesting a possibility for genetic selection on the vaginal microbiota.

Effects of dietary supplementation of Lycium barbarum polysaccharides on growth performance, immune status, antioxidant capacity and selected microbial populations of weaned piglets

Lycium barbarum polysaccharides (LBPs) are a complex mixture of highly branched and partially characterised polysaccharides and proteoglycans extracted from the goji berry. This mixture has great potential as a novel feed supplement for pigs. Two trials were conducted to evaluate the effects of supplementation with LBPs on the growth performance, immune status, antioxidant capacity and selected intestinal microbial populations in weaned piglets. In trial 1, a total of 400 weaned piglets [(Yorkshire × Landrace) × Duroc] with an average body weight (BW) of 6.34 ± 0.16 kg (21 days of age) were divided into five groups and fed a basal diet (control group) or a basal diet containing 1,000, 2,000, 4,000 or 6,000 mg/kg LBPs (supplemented at the expense of corn). Supplementation with 4,000 or 6,000 mg/kg LBPs for 2 weeks significantly increased the average daily gain (ADG) and average daily feed intake (ADFI) of the pigs compared with the control group (p < .05). In trial 2, thirty-two 21-days-old weaned piglets (BW: 6.33 ± 0.11 kg) were allotted to a control group (fed with a basal diet) or an experimental group (basal diet containing 4,000 mg/kg LBPs). The experiment lasted for 14 days. Pigs fed LBP diets exhibited an increased ADG and ADFI, and a decreased diarrhoeal incidence compared with those fed the basal diets (p < .05). Supplementation with LBPs increased the serum IgG and IgM levels (p < .05). Dietary LBPs effectively promoted antioxidant defence properties through enhancing the activities of serum, liver superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GSH-Px), in addition to decreasing the malondialdehyde (MDA) content (p < .05). The addition of LBPs increased the amounts of Bacteroidetes in the ileum and caecum and the caecal contents of Lactobacillus spp. and Bifidobacterium spp. (p < .05), while decreased the populations of Escherichia coli and Firmicutes in the ileum and caecum (p < .05) compared with the control group. Our results suggest that dietary supplementation with LBPs can enhance growth performance, immune status and antioxidant capacity, and improve the intestinal microbial populations of weaned piglets.

The preparation, formation, fermentability, and applications of resistant starch

Resistant starch (RS) cannot be digested in the small intestine but can be fermented by microflora in the colon. To meet the demand for RS, effective methods and advanced equipment for preparing RS have emerged, but further development is needed. RS contents are affected by different prepared methods, starch source and certain nutrients such as protein, phenols, and hydrocolloids interacted with RS. As a beneficial fermentation substrate, RS modifies and stabilizes the intestinal flora to balance the intestinal environment and improve intestinal tract health and function. RS is also a kind of ingredient with potential physiological function, even better than that dietary fiber, but also in terms of providing various health benefits. RS has good food-processing characteristics as well and can thus be widely used in the food industry.

Age-related compositional and functional changes in micro-pig gut microbiome

Age-related changes in human gut microbiota composition have been reported, and such changes might be influenced by the intake of nutrients or diets. To investigate the effects of aging on the gut microbiota independent of nutrient effects, we analyzed the gut microbiomes of 126 micro-pigs at a wide range of ages from newborns to 10 years old. The micro-pigs were reared in a constantly controlled environment. The diversity of the gut microbiome was found to continuously change with age. We also found associations between age and specific members and functions of the gut microbiome. Consistent with previous studies on the human gut microbiome, beneficial microbes including probiotic bacteria and short-chain fatty acid-producers decreased in older pigs, whereas Bacteroides increased with age. Based on the correlation network, Bacteroides seemed to have an important role in determining the relative abundances of other beneficial microbes. Our results suggest that maintaining beneficial gut microbes at a specific ratio corresponding to a certain age might contribute to a younger gut microbiome-age. Furthermore, due to similarities with the human system, micro-pigs are a useful animal model to elucidate the links between aging and the microbiome.

Fermentation characteristics of resistant starch, arabinoxylan, and β-glucan and their effects on the gut microbial ecology of pigs: A review

Dietary fibers (DF) contain an abundant amount of energy, although the mammalian genome does not encode most of the enzymes required to degrade them. However, a mutual dependence is developed between the host and symbiotic microbes, which has the potential to extract the energy present in these DF. Dietary fibers escape digestion in the foregut and are fermented in the hindgut, producing short-chain fatty acids (SCFA) that alter the microbial ecology in the gastrointestinal tract (GIT) of pigs. Most of the carbohydrates are fermented in the proximal part, allowing protein fermentation in the distal part, resulting in colonic diseases. The structures of resistant starch (RS), arabinoxylan (AX), and β-glucan (βG) are complex; hence, makes their way into the hindgut where these are fermented and provide energy substrates for the colonic epithelial cells. Different microbes have different preferences of binding to different substrates. The RS, AX and βG act as a unique substrate for the microbes and modify the relative composition of the gut microbial community. The granule dimension and surface area of each substrate are different, which influences the penetration capacity of microbes. Arabinose and xylan are 2 different hemicelluloses, but arabinose is substituted on the xylan backbone and occurs in the form of AX. Fermentation of xylan produces butyrate primarily in the small intestine, whereas arabinose produces butyrate in the large intestine. Types of RS and forms of βG also exert beneficial effects by producing different metabolites and modulating the intestinal microbiota. Therefore, it is important to have information of different types of RS, AX and βG and their roles in microbial modulation to get the optimum benefits of fiber fermentation in the gut. This review provides relevant information on the similarities and differences that exist in the way RS, AX, and βG are fermented, and their positive and negative effects on SCFA production and gut microbial ecology of pigs. These insights will help nutritionists to develop dietary strategies that can modulate specific SCFA production and promote beneficial microbiota in the GIT of swine.

The effects of dietary supplementation with porous zinc oxide on growth performance, intestinal microbiota, morphology, and permeability in weaned piglets

The objective of this experiment was to evaluate the effects of dietary supplementation with porous zinc oxide (HiZox) on growth performance, intestinal microbiota, morphology, and permeability in weaned piglets. A total of 128 weaned piglets [(Landrace × Yorkshire) × Duroc] with an average body weight (BW) of (6.55 ± 0.25 kg; 21 d of age) were randomly assigned to four dietary treatments: (1) a corn-soybean basal diet; (2) basal diet + 3,000 mg/kg conventional ZnO; (3) basal diet + 200 mg/kg HiZox; (4) basal diet + 500 mg/kg HiZox. The experiments lasted for 28 days. Incremental HiZox in the diet increased ADG (linear p = 0.015; quadratic p = 0.043) and ADFI (linear p = 0.027; quadratic p = 0.038), and the diarrhea index decreased linearly and quadratically (p < 0.01) as HiZox supplemented increased. Furthermore, supplementation with HiZox increased the amounts of Lactobacillus spp. (p < 0.05) in the ileum and cecum in comparison with that of control treatment or 3,000 mg/kg ZnO treatment, while decreased the populations of Escherichia coli, Clostridium coccoides, and Clostridium. leptum subgroup (p < 0.05) in the ileum and cecum relative to those in control treatment. The addition of HiZox increased the villus height and villus-to-crypt ratio (VC) of duodenum, jejunum, and ileum (p < 0.05), while decreased the crypt depth of jejunum (p < 0.05) and tended to reduce the crypt depth of duodenum (p < 0.10) compared with the control treatment. Piglets fed with 500 mg/kg HiZox had lower serum D-lactate and diamine oxidase (DAO) than those fed with basal control diet or 3,000 mg/kg ZnO diet (p < 0.01). The results suggested that supplementation with HiZox modulated intestinal microbial composition and improved intestinal morphology, which may exert protective effects on the integrity of the mucosal barrier function of weaned piglets, was as efficacious as pharmaceutical doses of ZnO in enhancing growth performance, indicating that the HiZox may be a promising alternative to pharmaceutical doses of ZnO.

Porcine Feed Efficiency-Associated Intestinal Microbiota and Physiological Traits: Finding Consistent Cross-Locational Biomarkers for Residual Feed Intake

Optimal feed efficiency (FE) in pigs is important for economic and environmental reasons. Previous research identified FE-associated bacterial taxa within the intestinal microbiota of growing pigs. This study investigated whether FE-associated bacteria and selected FE-associated physiological traits were consistent across geographic locations (Republic of Ireland [ROI] [two batches of pigs, ROI1 and ROI2], Northern Ireland [NI], and Austria [AT]), where differences in genetic, dietary, and management factors were minimized. Pigs (n = 369) were ranked, within litter, on divergence in residual feed intake (RFI), and 100 extremes were selected (50 with high RFI and 50 with low RFI) across geographic locations for intestinal microbiota analysis using 16S rRNA amplicon sequencing and examination of FE-associated physiological parameters. Microbial diversity varied by geographic location and intestinal sampling site but not by RFI rank, except in ROI2, where more-feed-efficient pigs had greater ileal and cecal diversity. Although none of the 188 RFI-associated taxonomic differences found were common to all locations/batches, Lentisphaerae, Ruminococcaceae, RF16, Mucispirillum, Methanobrevibacter, and two uncultured genera were more abundant within the fecal or cecal microbiota of low-RFI pigs in two geographic locations and/or in both ROI batches. These are major contributors to carbohydrate metabolism, which was reflected in functional predictions. Fecal volatile fatty acids and salivary cortisol were the only physiological parameters that differed between RFI ranks. Despite controlling genetics, diet specification, dietary phases, and management practices in each rearing environment, the rearing environment, encompassing maternal influence, herd health status, as well as other factors, appears to impact intestinal microbiota more than FE.IMPORTANCE Interest in the role of intestinal microbiota in determining FE in pigs has increased in recent years. However, it is not known if the same FE-associated bacteria are found across different rearing environments. In this study, geographic location and intestinal sampling site had a greater influence on the pig gut microbiome than FE. This presents challenges when aiming to identify consistent reliable microbial biomarkers for FE. Nonetheless, seven FE-associated microbial taxa were common across two geographic locations and/or two batches within one location, and these indicated a potentially "healthier" and metabolically more capable microbiota in more-feed-efficient pigs. These taxa could potentially be employed as biomarkers for FE, although bacterial consortia, rather than individual taxa, may be more likely to predict FE. They may also merit consideration for use as probiotics or could be targeted by dietary means as a strategy for improving FE in pigs in the future.

Functional adaptations in the cecal and colonic metagenomes associated with the consumption of transglycosylated starch in a pig model

Background

Both phylogeny and functional capabilities within the gut microbiota populations are of great importance for influencing host health. As a novel type of resistant starch, transglycosylated starch (TGS) modifies the microbial community and metabolite profiles along the porcine gut, but little is known about the related functional adaptations in key metabolic pathways and their taxonomic identity.

Results

Metagenomic sequencing was used to characterize the functional alterations in the cecal and colonic microbiomes of growing pigs fed TGS or control starch (CON) diets for 10 days (n = 8/diet). Bacterial communities were clearly distinguishable at taxonomic and functional level based on the dietary starch, with effects being similar at both gut sites. Cecal and colonic samples from TGS-fed pigs were enriched in Prevotella, Bacteroides, Acidaminoccus and Veillonella, whereas Treponema, Ruminococcus, and Aeromonas declined at both gut sites compared to CON-fed pigs (log₂ fold change > ±1; p < 0.001 (q < 0.05)). This was associated with increased enzymatic capacities for amino acid metabolism, galactose, fructose and mannose metabolism, pentose and glucuronate interconversions, citrate cycle and vitamin metabolism for samples from TGS-fed pigs. However, TGS-fed pigs comprised fewer reads for starch and sucrose metabolism and genetic information processing. Changes in key catabolic steps were found to be the result of changes in taxa associated with each type of starch. Functional analysis indicated steps in the breakdown of TGS by the action of α- and β-galactosidases, which mainly belonged to Bacteroides and Prevotella. Reads mapped to alpha-amylase were less frequent in TGS- compared to CON-fed pigs, with the major source of this gene pool being Bacillus, Aeromonas and Streptococcus. Due to the taxonomic shifts, gene abundances of potent stimulants of the mucosal innate immune response were altered by the starches. The cecal and colonic metagenomes of TGS-fed pigs comprised more reads annotated in lipopolysaccharides biosynthesis, whereas they became depleted of genes for flagellar assembly compared to CON-fed pigs.

Conclusions

Metagenomic sequencing revealed distinct cecal and colonic bacterial communities in CON- and TGS-fed pigs, with strong discrimination among samples by functional capacities related to the respective starch in each pig’s diet.

Electronic supplementary material

The online version of this article (10.1186/s12866-019-1462-2) contains supplementary material, which is available to authorized users.

High-Amylose Maize, Potato, and Butyrylated Starch Modulate Large Intestinal Fermentation, Microbial Composition, and Oncogenic miRNA Expression in Rats Fed A High-Protein Meat Diet

High red meat intake is associated with the risk of colorectal cancer (CRC), whereas dietary fibers, such as resistant starch (RS) seemed to protect against CRC. The aim of this study was to determine whether high-amylose potato starch (HAPS), high-amylose maize starch (HAMS), and butyrylated high-amylose maize starch (HAMSB)—produced by an organocatalytic route—could oppose the negative effects of a high-protein meat diet (HPM), in terms of fermentation pattern, cecal microbial composition, and colonic biomarkers of CRC. Rats were fed a HPM diet or an HPM diet where 10% of the maize starch was substituted with either HAPS, HAMS, or HAMSB, for 4 weeks. Feces, cecum digesta, and colonic tissue were obtained for biochemical, microbial, gene expression (oncogenic microRNA), and immuno-histochemical (O⁶-methyl-2-deoxyguanosine (O⁶MeG) adduct) analysis. The HAMS and HAMSB diets shifted the fecal fermentation pattern from protein towards carbohydrate metabolism. The HAMSB diet also substantially increased fecal butyrate concentration and the pool, compared with the other diets. All three RS treatments altered the cecal microbial composition in a diet specific manner. HAPS and HAMSB showed CRC preventive effects, based on the reduced colonic oncogenic miR17-92 cluster miRNA expression, but there was no significant diet-induced differences in the colonic O⁶MeG adduct levels. Overall, HAMSB consumption showed the most potential for limiting the negative effects of a high-meat diet.

Predicting Growth and Carcass Traits in Swine Using Microbiome Data and Machine Learning Algorithms

In this paper, we evaluated the power of microbiome measures taken at three time points over the growth test period (weaning, 15 and 22 weeks) to foretell growth and carcass traits in 1039 individuals of a line of crossbred pigs. We measured prediction accuracy as the correlation between actual and predicted phenotypes in a five-fold cross-validation setting. Phenotypic traits measured included live weight measures and carcass composition obtained during the trial as well as at slaughter. We employed a null model excluding microbiome information as a baseline to assess the increase in prediction accuracy stemming from the inclusion of operational taxonomic units (OTU) as predictors. We further contrasted performance of models from the Bayesian alphabet (Bayesian Lasso) as well machine learning approaches (Random Forest and Gradient Boosting) and semi-parametric kernel models (Reproducing Kernel Hilbert space). In most cases, prediction accuracy increased significantly with the inclusion of microbiome data. Accuracy was more substantial with the inclusion of microbiome information taken at weeks 15 and 22, with values ranging from approximately 0.30 for loin traits to more than 0.50 for back fat. Conversely, microbiome composition at weaning resulted in most cases in marginal gains of prediction accuracy, suggesting that later measures might be more useful to include in predictive models. Model choice affected predictions marginally with no clear winner for any model/trait/time point. We, therefore, suggest average prediction across models as a robust strategy in fitting microbiome information. In conclusion, microbiome composition can effectively be used as a predictor of growth and composition traits, particularly for fatness traits. The inclusion of OTU predictors could potentially be used to promote fast growth of individuals while limiting fat accumulation. Early microbiome measures might not be good predictors of growth and OTU information might be best collected at later life stages. Future research should focus on the inclusion of both microbiome as well as host genome information in predictions, as well as the interaction between the two. Furthermore, the influence of the microbiome on feed efficiency as well as carcass and meat quality should be investigated.

Consumption of transglycosylated starch down-regulates expression of mucosal innate immune response genes in the large intestine using a pig model

Benefits of resistant starch (RS) consumption on host physiology encompass microbial activity-derived attenuation of intestinal inflammation. However, little is known about anti-inflammatory properties of RS of type 4. This study compared the effects of transglycosylated starch (TGS) consumption on the jejunal barrier function and expression of genes related to inflammation, barrier function and the mucosal defence in jejunum, ileum, caecum and colon of pigs. Moreover, interactions of TGS-induced alterations in bacterial metabolites and composition with host mucosal responses were assessed using sparse partial least squares regression and relevance network analysis. Intestinal samples were collected after pigs (n 8/diet; 4 months of age) were fed the experimental diets for 10 d. Consumption of TGS did not modify jejunal barrier function and gene expression. By contrast, TGS down-regulated the caecal expression of zonula occludens-1 and mucin 2 and of genes within the toll-like receptor 4 and NF-κB pro-inflammatory signalling cascade. Relevance networks revealed a microbiome signature on ileal, caecal and colonic mucosal signalling as TGS-derived changes in bacterial genera and fermentation acids, such as propionic acid, correlated with the differently expressed genes in ileum, caecum and colon of pigs. In conclusion, the present findings suggest certain anti-inflammatory capabilities of TGS by down-regulating the expression of pro-inflammatory pathways in the caecal mucosa, which seems to be mediated, at least in part, by TGS-induced changes in microbial action in the large intestine.

Metagenomic reconstructions of gut microbial metabolism in weanling pigs

BACKGROUND

The piglets' transition from milk to solid feed induces a succession of bacterial communities, enhancing the hosts' ability to harvest energy from dietary carbohydrates. To reconstruct microbial carbohydrate metabolism in weanling pigs, this study combined 16S rRNA gene sequencing (n = 191) and shotgun metagenomics (n = 72).

RESULTS

Time and wheat content in feed explained most of the variation of the microbiota as assessed by 16S rRNA gene sequencing in weanling pigs. De novo metagenomic binning reconstructed 360 high-quality genomes that represented 11 prokaryotic and 1 archaeal phylum. Analysis of carbohydrate metabolism in these genomes revealed that starch fermentation is carried out by a consortium of Firmicutes expressing extracellular α-(1 → 4)-glucan branching enzyme (GH13) and Bacteroidetes expressing periplasmic neopullulanase (GH13) and α-glucosidase (GH97). Fructans were degraded by extracellular GH32 enzymes from Bacteriodetes and Lactobacillus. Lactose fermentation by β-galactosidases (GH2 and GH42) was identified in Firmicutes. In conclusion, the assembly of 360 high-quality genomes as the first metagenomic reference for swine intestinal microbiota allowed identification of key microbial contributors to degradation of starch, fructans, and lactose.

CONCLUSIONS

Microbial consortia that are responsible for degradation of these glycans differ substantially from the microbial consortia that degrade the same glycans in humans. Our study thus enables improvement of feeding models with higher feed efficiency and better pathogen control for weanling pigs.

Defining the role of Parasutterella, a previously uncharacterized member of the core gut microbiota

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.

Feed Restriction Modifies Intestinal Microbiota-Host Mucosal Networking in Chickens Divergent in Residual Feed Intake

The impact of the FE-associated differences in feed intake on intestinal bacterial and host physiological parameters has so far not been clarified. Understanding the underlying principles is essential for the development of cost-effective strategies to improve FE in chicken production. Under conditions of quantitative feed restriction, low- and high-RFI chickens ate the same amount of feed. Therefore, this research helps in distinguishing intestinal bacterial taxa and functions that were highly reliant on feed intake from those that were associated with physiological adaptations to RFI-associated differences in host nutritional needs and intestinal nutrient availability. This work provides a background for further research to assess manipulation of the intestinal microbiota, host physiology, and FE in chickens by dietary intervention.

Differences in chickens’ feed intake may be the underlying factor influencing feed-efficiency (FE)-associated variation in intestinal microbiota and physiology. In chickens eating the same amount of feed, quantitative feed restriction may create similar intestinal conditions and help clarify this cause-and-effect relationship. This study investigated the effect of ad libitum versus restrictive feeding (85% of ad libitum) on ileal and cecal microbiota, concentrations of short-chain fatty acids, visceral organ size, intestinal morphology, permeability, and expression of genes related to nutrient uptake, barrier function, and innate immune response in broiler chickens with divergent residual feed intake (RFI; metric for FE). On day 30 posthatch, 28 low-RFI (good FE) and 29 high-RFI (poor FE) chickens across both feeding-level groups (n = 112) were selected. Supervised multigroup data integration and relevance network analyses showed that especially Lactobacillus (negative) in ileal digesta, Turicibacter (positive) in cecal digesta, and Enterobacteriaceae (positive) in both intestinal segments depended on chicken’s feed intake, whereas the level of Anaerotruncus in cecal digesta was most discriminative for high RFI. Moreover, shallower crypts and fewer goblet cells in ceca indicated host-related energy-saving mechanisms with low RFI, whereas greater tissue resistance suggested a stronger jejunal barrier function in low-RFI chickens. Values corresponding to feed intake level × RFI interactions indicated larger pancreas and lower levels of ileal and cecal short-chain fatty acids in restrictively fed high-RFI chickens than in the other 3 groups, suggesting host physiological adaptations to support greater energy and nutrient needs of high-RFI chickens compensating for the restricted feeding.

IMPORTANCE The impact of the FE-associated differences in feed intake on intestinal bacterial and host physiological parameters has so far not been clarified. Understanding the underlying principles is essential for the development of cost-effective strategies to improve FE in chicken production. Under conditions of quantitative feed restriction, low- and high-RFI chickens ate the same amount of feed. Therefore, this research helps in distinguishing intestinal bacterial taxa and functions that were highly reliant on feed intake from those that were associated with physiological adaptations to RFI-associated differences in host nutritional needs and intestinal nutrient availability. This work provides a background for further research to assess manipulation of the intestinal microbiota, host physiology, and FE in chickens by dietary intervention.

Canine endometrial and vaginal microbiomes reveal distinct and complex ecosystems

The objective of this study was to characterize the normal microbiome of healthy canine vagina and endometrium and to determine the effect of the stage of estrous, on the resident microbiome. Cranial vaginal swabs and uterine biopsy samples were collected from twenty-five bitches in five different stages of estrous at elective ovariohysterectomy (OVH). Over 4 million reads of the V4 region of 16S rDNA gene were obtained and used for further analyses. A total of 317 genera belonging to 24 known phyla were identified. The endometrium was higher in bacterial diversity while the vagina was higher in richness. Proteobacteria, Bacteroidetes and Firmicutes were the most abundant phyla observed across all samples. Hydrotalea, Ralstonia, and Fusobacterium accounted for nearly 60% of the OTUs identified in the vagina while organisms identified in the endometrium were more evenly distributed. Pseudomonas, Staphylococcus, and Corynebacterium were the prominent genera in the endometrium. The microbiome of the endometrium was distinctly different from that of the vagina. There was large animal-to-animal variation. Other than the vaginal microbiome of bitches in estrus (i.e. in heat), there were no distinct clustering of the organisms based on the stage of estrous. These findings establish the presence of a resident microbiome of the endometrium throughout all stages of estrous cycle.

Effects of dietary intake of potatoes on body weight gain, satiety-related hormones, and gut microbiota in healthy rats

Potatoes, as a prominent staple food, have exerted diverse intestinal health benefits, but few studies have addressed the gut microecology modulatory effects of consuming potatoes in realistic quantities. The objective of this study was to evaluate the effects of ingesting potatoes in different doses on body weight gain (BWG), food intake, short chain fatty acids (SCFAs), fecal microbiota, gut hormones, and colon morphology of healthy rats. Male Sprague-Dawley rats of 6–8 weeks old were randomized to five groups and fed AIN-93 G or diets containing graded concentrations of potato powder (low, medium, high, and higher) for 7 weeks. Accordingly, the final body weight was significantly lower for rats fed the high and/or higher potato diets than their control counterparts (P < 0.05). Potato intervention caused a significant dose-dependent increment in full cecum, and SCFAs production. The relative abundance of “S24-7” (order Bacteroidales), Bifidobacterium, “NK3B31” (family Prevotellaceae), Parasutterella, and Ruminococcus_1 increased in high and higher potato diets. Furthermore, a Spearman's correlation analysis revealed that Parasutterella was negatively correlated with BWG, triglyceride (TG), and low-density lipoproteins (LDL). The maximum number of goblet cells, longest crypt depth, and highest level of PYY were found in the distal colon of rats fed higher potato diets. The results suggested that potato powder could provide the potential for hopeful impact on weight control.

Supplementation of potato powders with 54.88 g kg⁻¹ would significantly reduce the body weight gain by enriching Bifidobacterium and Parasutterella.

Application of resistant starch in swine and poultry diets with particular reference to gut health and function

The immediate post-weaning period poses a major challenge on the survival of piglets. Similarly, newly hatched chicks face life threatening challenges due to enteric infections. In the past several years, in-feed antibiotics have been used to reduce these production problems and improve growth. However, in-feed antibiotics have been banned in many jurisdictions and therefore the most effective alternatives to in-feed antibiotics must be developed. To date, several studies have been conducted to develop alternatives to antibiotics. One of the potential candidates as alternatives to in-feed antibiotics is resistant starch (RS). Resistance starch is a type of starch that resists enzymatic digestion in the upper parts of the gastrointestinal tract and therefore passes to hindgut where it can be fermented by resident microorganisms. Microbial fermentation of RS in the hindgut results in the production of short chain fatty acids (SCFA). Production of SCFA in turn results in growth and proliferation of colonic and cecal cells, increased expression of genes involved in gut development, and creation of an acidic environment. The acidic environment suppresses the growth of pathogenic microorganisms while selectively promoting the growth of beneficial microbes. Thus, RS has the potential to improve gut health and function by modifying and stabilising gut microbial community and by improving the immunological status of the host. In this review, we discussed the roles of RS in modifying and stabilising gut microbiota, gut health and function, carcass quality, and energy metabolism and growth performance in pigs and poultry.

Effects of natural dietary supplementation with Macleaya cordata extract containing sanguinarine on growth performance and gut health of early-weaned piglets

This study was conducted to investigate the effects of dietary supplementation with Sangrovit^® (SAG; minimum of 1.5% sanguinarine, a quaternary benzo[c]phenanthridine alkaloid extracted from Macleaya cordata) on growth performance, intestinal morphology, intestinal microflora and its metabolites of early-weaned piglets. A total of 20 healthy weaned piglets (Duroc× [Large White×Landrace]), weaned at 21 days of age with an average body weight (BW) of 6.52 ± 0.23 kg, were randomly assigned to receive either a corn-soybean meal basal diet (CTR) or a basal diet supplemented with 50 mg/kg SAG (SAG). During the 21-days trial, we collected and analysed intestinal tissues and the luminal digesta for their morphology and populations of gut microbiota, as well as for measuring the concentrations of short-chain fatty acids (SCFAs) and ammonia. Compared with the CTR group, supplementation with SAG improved average daily gains (p = 0.011) and average daily feed intake (p = 0.037). Piglets fed the SAG diet had an average lower value for crypt depth of the jejunum (p = 0.011) and greater values for villus height in the ileum (p = 0.015) and ratios of villus height to crypt depth in the jejunum (p < 0.01) and in the ileum (p = 0.027) than did animals receiving the CTR diet. The addition of SAG increased the amounts of Lactobacillus in the ileum (p = 0.033) and caecum (p < 0.01), and tended to increase the amounts of Bifidobacterium (p = 0.058) in the caecum, while decreasing the amounts of Escherichia coli (p = 0.046) and Salmonella spp. (p = 0.035) in the ileum, as well as Salmonella spp. (p = 0.029) in the caecum. Dietary supplementation with SAG enhanced (p < 0.05) the concentrations of acetate, propionate, butyrate and total SCFAs, and also tended to increase the level of valerate (p = 0.055 and p = 0.052) in the ileal and caecal contents when compared with the CTR group. Concentrations of ammonia also declined in the caecal (p = 0.037) and ileal (p = 0.046) digesta in response to SAG. These results indicate that feeding early-weaned piglets a SAG-supplemented diet can potentially improve their growth performance and intestinal morphology, and can modify the intestinal luminal environment in a beneficial manner.

Alpha-Ketoglutarate in Low-Protein Diets for Growing Pigs: Effects on Cecal Microbial Communities and Parameters of Microbial Metabolism

Alpha-ketoglutarate (AKG), a critical molecule in the tricarboxylic acid cycle, is beneficial to intestinal functions. However, its influence on intestinal microbiota and metabolism is not fully understood. We investigated the effects of a low-protein (LP) diet supplemented with AKG on cecal microbial communities and the parameters of microbial metabolism in growing pigs. Twenty-seven young pigs (Large White × Landrace) with an average initial body weight of 11.96 ± 0.18 kg were randomly allotted into three groups (n = 9): a normal protein (NP) diet containing 20% crude protein (CP); LP diet formulated with 17% CP (LP diet); or LP diet supplemented with 10 g kg^-1 of AKG (ALP diet). After a 35-day trial period, the digesta of the cecum were collected to analyze the concentrations of ammonia and short-chain fatty acids (SCFAs). We also performed a microbial analysis. Although no significant differences were found in performance among the diet groups, pigs fed the ALP diet had greater average daily gain (ADG) when compared with those in the LP group. Experimental diet did not affect cecal bacterial richness or diversity, as determined by Chao1 and ACE species richness measures and Shannon and Simpson indices, respectively. The predominant phyla Firmicutes, Bacteroidetes, and Proteobacteria increased in relative abundances in the cecum of pigs fed ALP diet. At the genus level, compared to the LP diet, the ALP diet significantly increased the abundances of Lachnospiraceae UCG-005, Lachnospiraceae NK4A136 group, Phascolarctobacterium and Parabacteroides, while decreased Vibrio and Maritalea. Pigs fed the ALP diet increased Oribacterium and Lachnoclostridium when compared with the NP diet. Non-metric multidimensional scaling analysis revealed that the distribution of microbiota at each group was distinctly clustered separately along principal coordinate. In addition, quantitative PCR revealed that the ALP diet was also associated with increases in the amounts of Bacteroides, Bifidobacterium, and Lactobacillus, but a decrease in the level of Escherichia coli. Compared with the NP diet, the ALP diet enhanced the concentrations of valerate and propionate. This ALP diet also increased the concentrations of valerate and isobutyrate when compared with the LP diet. Moreover, the ALP diet was linked with a significant decline in the concentration of ammonia in the cecum. These results indicate that a LP diet supplemented with AKG can alter the balance in microbial communities, increasing the population of SCFA-producing bacteria and the amounts of Bacteroides and Bifidobacterium, while reducing the counts of Escherichia coli and the amount of ammonia in the cecum.

Dietary Deoxynivalenol Contamination and Oral Lipopolysaccharide Challenge Alters the Cecal Microbiota of Broiler Chickens

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

Efficacy of Various Preservatives on Extending Shelf Life of Vacuum-Packaged Raw Pork during 4°C Storage

Uncontrolled bacterial growth and metabolic activities are responsible for the short shelf life of raw pork. Culture-independent analysis by 16S ribosome cDNA could reveal viable bacteria in raw pork. This study investigated microbial growth and volatile organic compounds of raw pork supplemented with various preservatives. Vacuum-packaged raw pork was stored at 4°C, after soaking in solutions of potassium sorbate, ε-poly-l-lysine, kojic acid (KA), or sodium diacetate, individually. Spoilage of raw pork was monitored by determining pH and total volatile basic nitrogen, whereas bacterial growth was determined by culture-dependent and culture-independent analyses. Data indicated that all the preservatives were able to inhibit bacterial growth and extend the shelf life of pork. High-throughput sequencing of 16S ribosome cDNA indicated that Pseudomonas was inhibited under vacuum conditions, whereas facultative anaerobes ( Acinetobacter, Photobacterium, Brochothrix, and Myroides) were the most active genera in the spoiled pork. Photobacterium was further inhibited by each preservative. The inhibition of Acinetobacter, Photobacterium, and Myroides could be responsible for the extended shelf life of vacuum-packaged pork; they were effectively inhibited by KA, which also induced the longest shelf life. Moreover, 19 types of volatile organic compounds were detected. 3-Methylbutanol, 3-methylbutanol acetate, 2-butanone, toluene, benzeneacetaldehyde, dimethyl trisulfide, and acetoin were associated with spoilage. Furthermore, KA is a potential preservative in raw pork; because no phenol was detectable within 35 days, excessive intake of phenol induced by preservatives was avoided.

Transglycosylated Starch Modulates the Gut Microbiome and Expression of Genes Related to Lipid Synthesis in Liver and Adipose Tissue of Pigs

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

Host contributes to longitudinal diversity of fecal microbiota in swine selected for lean growth

BACKGROUND

In pigs, gut bacteria have been shown to play important roles in nutritional, physiological, and immunological processes in the host. However, the contribution of their metagenomes or part of them, which are normally reflected by fragments of 16S rRNA-encoding genes, has yet to be fully investigated.

RESULTS

Fecal samples, collected from a population of crossbred pigs at three time points, including weaning, week 15 post weaning (hereafter "week 15"), and end-of-feeding test (hereafter "off-test"), were used to evaluate changes in the composition of the fecal microbiome of each animal over time. This study used 1205, 1295, and 1283 samples collected at weaning, week 15, and off-test, respectively. There were 1039 animals that had samples collected at all three time points and also had phenotypic records on back fat thickness (BF) and average daily body weight gain (ADG). Firmicutes and Bacteroidetes were the most abundant phyla at all three time points. The most abundant genera at all three time points included Clostridium, Escherichia, Bacteroides, Prevotella, Ruminococcus, Fusobacterium, Campylobacter, Eubacterium, and Lactobacillus. Two enterotypes were identified at each time point. However, only enterotypes at week 15 and off-test were significantly associated with BF. We report herein two novel findings: (i) alpha diversity and operational taxonomic unit (OTU) richness were moderately heritable at week 15, h2 of 0.15 ± 0.06 to 0.16 ± 0.07 and 0.23 ± 0.09 to 0.26 ± 0.08, respectively, as well as at off-test, h2 of 0.20 ± 0.09 to 0.33 ± 0.10 and 0.17 ± 0.08 to 0.24 ± 0.08, respectively, whereas very low heritability estimates for both measures were detected at weaning; and (ii) alpha diversity at week 15 had strong and negative genetic correlations with BF, - 0.53 ± 0.23 to - 0.45 ± 0.25, as well as with ADG, - 0.53 ± 0.32 to - 0.53 ± 0.29.

CONCLUSIONS

These results are important for efforts to genetically improve the domesticated pig because they suggest fecal microbiota diversity can be used as an indicator trait to improve traits that are expensive to measure.

Intestinal microbiota profiles associated with low and high residual feed intake in chickens across two geographical locations

Intestinal microbe-host interactions can affect the feed efficiency (FE) of chickens. As inconsistent findings for FE-associated bacterial taxa were reported across studies, the present objective was to identify whether bacterial profiles and predicted metabolic functions that were associated with residual feed intake (RFI) and performance traits in female and male chickens were consistent across two different geographical locations. At six weeks of life, the microbiota in ileal, cecal and fecal samples of low (n = 34) and high (n = 35) RFI chickens were investigated by sequencing the V3-5 region of the 16S rRNA gene. Location-associated differences in α-diversity and relative abundances of several phyla and genera were detected. RFI-associated bacterial abundances were found at the phylum and genus level, but differed among the three intestinal sites and between males and females. Correlation analysis confirmed that, of the taxonomically classifiable bacteria, Lactobacillus (5% relative abundance) and two Lactobacillus crispatus-OTUs in feces were indicative for high RFI in females (P < 0.05). In males, Ruminococcus in cecal digesta (3.1% relative abundance) and Dorea in feces (<0.1% relative abundance) were best indicative for low RFI, whereas Acinetobacter in feces (<1.5% relative abundance) related to high RFI (P < 0.05). Predicted metabolic functions in feces of males confirmed compositional relationships as functions related to amino acid, fatty acid and vitamin metabolism correlated with low RFI, whereas an increasing abundance of bacterial signaling and interaction (i.e. cellular antigens) genes correlated with high RFI (P < 0.05). In conclusion, RFI-associated bacterial profiles could be identified across different geographical locations. Results indicated that consortia of low-abundance taxa in the ileum, ceca and feces may play a role for FE in chickens, whereby only bacterial FE-associations found in ileal and cecal digesta may serve as useful targets for dietary strategies.

Exploring a Possible Link between the Intestinal Microbiota and Feed Efficiency in Pigs

Feed efficiency (FE) is critical in pig production for both economic and environmental reasons. As the intestinal microbiota plays an important role in energy harvest, it is likely to influence FE. Therefore, our aim was to characterize the intestinal microbiota of pigs ranked as low, medium, and high residual feed intake ([RFI] a metric for FE), where genetic, nutritional, and management effects were minimized, to explore a possible link between the intestinal microbiota and FE. Eighty-one pigs were ranked according to RFI between weaning and day 126 postweaning, and 32 were selected as the extremes in RFI (12 low, 10 medium, and 10 high). Intestinal microbiota diversity, composition, and predicted functionality were assessed by 16S rRNA gene sequencing. Although no differences in microbial diversity were found, some RFI-associated compositional differences were revealed, principally among members of Firmicutes, predominantly in feces at slaughter (albeit mainly for low-abundance taxa). In particular, microbes associated with a leaner and healthier host (e.g., Christensenellaceae, Oscillibacter, and Cellulosilyticum) were enriched in low RFI (more feed-efficient) pigs. Differences were also observed in the ileum of low RFI pigs; most notably, Nocardiaceae (Rhodococcus) were less abundant. Predictive functional analysis suggested improved metabolic capabilities in these animals, especially within the ileal microbiota. Higher ileal isobutyric acid concentrations were also found in low RFI pigs. Overall, the differences observed within the intestinal microbiota of low RFI pigs compared with that of their high RFI counterparts, albeit relatively subtle, suggest a possible link between the intestinal microbiota and FE in pigs.IMPORTANCE This study is one of the first to show that differences in intestinal microbiota composition, albeit subtle, may partly explain improved feed efficiency (FE) in low residual feed intake (RFI) pigs. One of the main findings is that, although microbial diversity did not differ among animals of varying FE, specific intestinal microbes could potentially be linked with porcine FE. However, as the factors impacting FE are still not fully understood, intestinal microbiota composition may not be a major factor determining differences in FE. Nonetheless, this work has provided a potential set of microbial biomarkers for FE in pigs. Although culturability could be a limiting factor and intervention studies are required, these taxa could potentially be targeted in the future to manipulate the intestinal microbiome so as to improve FE in pigs. If successful, this has the potential to reduce both production costs and the environmental impact of pig production.

Meta-analysis To Define a Core Microbiota in the Swine Gut

The swine gut microbiota encompasses a large and diverse population of bacteria that play a significant role in pig health. As such, a number of recent studies have utilized high-throughput sequencing of the 16S rRNA gene to characterize the composition and structure of the swine gut microbiota, often in response to dietary feed additives. It is important to determine which factors shape the composition of the gut microbiota among multiple studies and if certain bacteria are always present in the gut microbiota of swine, independently of study variables such as country of origin and experimental design. Therefore, we performed a meta-analysis using 20 publically available data sets from high-throughput 16S rRNA gene sequence studies of the swine gut microbiota. Next to the "study" itself, the gastrointestinal (GI) tract section that was sampled had the greatest effect on the composition and structure of the swine gut microbiota (P = 0.0001). Technical variation among studies, particularly the 16S rRNA gene hypervariable region sequenced, also significantly affected the composition of the swine gut microbiota (P = 0.0001). Despite this, numerous commonalities were discovered. Among fecal samples, the genera Prevotella, Clostridium, Alloprevotella, and Ruminococcus and the RC9 gut group were found in 99% of all fecal samples. Additionally, Clostridium, Blautia, Lactobacillus, Prevotella, Ruminococcus, Roseburia, the RC9 gut group, and Subdoligranulum were shared by >90% of all GI samples, suggesting a so-called "core" microbiota for commercial swine worldwide. IMPORTANCE The results of this meta-analysis demonstrate that "study" and GI sample location are the most significant factors in shaping the swine gut microbiota. However, in comparisons of results from different studies, some biological factors may be obscured by technical variation among studies. Nonetheless, there are some bacterial taxa that appear to form a core microbiota within the swine GI tract regardless of country of origin, diet, age, or breed. Thus, these results provide the framework for future studies to manipulate the swine gut microbiota for potential health benefits.

Transglycosylated Starch Improves Insulin Response and Alters Lipid and Amino Acid Metabolome in a Growing Pig Model

Due to the functional properties and physiological effects often associated with chemically modified starches, significant interest lies in their development for incorporation in processed foods. This study investigated the effect of transglycosylated cornstarch (TGS) on blood glucose, insulin, and serum metabolome in the pre- and postprandial phase in growing pigs. Eight jugular vein-catheterized barrows were fed two diets containing 72% purified starch (waxy cornstarch (CON) or TGS). A meal tolerance test (MTT) was performed with serial blood sampling for glucose, insulin, lipids, and metabolome profiling. TGS-fed pigs had reduced postprandial insulin (p < 0.05) and glucose (p < 0.10) peaks compared to CON-fed pigs. The MTT showed increased (p < 0.05) serum urea with TGS-fed pigs compared to CON, indicative of increased protein catabolism. Metabolome profiling showed reduced (p < 0.05) amino acids such as alanine and glutamine with TGS, suggesting increased gluconeogenesis compared to CON, probably due to a reduction in available glucose. Of all metabolites affected by dietary treatment, alkyl-acyl-phosphatidylcholines and sphingomyelins were generally increased (p < 0.05) preprandially, whereas diacyl-phosphatidylcholines and lysophosphatidylcholines were decreased (p < 0.05) postprandially in TGS-fed pigs compared to CON. In conclusion, TGS led to changes in postprandial insulin and glucose metabolism, which may have caused the alterations in serum amino acid and phospholipid metabolome profiles.

Enzymatically Modified Starch Favorably Modulated Intestinal Transit Time and Hindgut Fermentation in Growing Pigs

Aside from being used as stabilizing agents in many processed foods, chemically modified starches may act as functional dietary ingredients. Therefore, development of chemically modified starches that are less digestible in the upper intestinal segments and promote fermentation in the hindgut receives considerable attention. This study aimed to investigate the impact of an enzymatically modified starch (EMS) on nutrient flow, passage rate, and bacterial activity at ileal and post-ileal level. Eight ileal-cannulated growing pigs were fed 2 diets containing 72% purified starch (EMS or waxy cornstarch as control) in a cross-over design for 10 d, followed by a 4-d collection of feces and 2-d collection of ileal digesta. On d 17, solid and liquid phase markers were added to the diet to determine ileal digesta flow for 8 h after feeding. Reduced small intestinal digestion after the consumption of the EMS diet was indicated by a 10%-increase in ileal flow and fecal excretion of dry matter and energy compared to the control diet (P<0.05). Moreover, EMS feeding reduced ileal transit time of both liquid and solid fractions compared to the control diet (P<0.05). The greater substrate flow to the large intestine with the EMS diet increased the concentrations of total and individual short-chain fatty acids (SCFA) in feces (P<0.05). Total bacterial 16S rRNA gene abundance was not affected by diet, whereas the relative abundance of the Lactobacillus group decreased (P<0.01) by 50% and of Enterobacteriaceae tended (P<0.1) to increase by 20% in ileal digesta with the EMS diet compared to the control diet. In conclusion, EMS appears to resemble a slowly digestible starch by reducing intestinal transit and increasing SCFA in the distal large intestine.

Enzymatically modified starch up-regulates expression of incretins and sodium-coupled monocarboxylate transporter in jejunum of growing pigs

Dietary effects on the host are mediated via modulation of the intestinal mucosal responses. The present study investigated the effect of an enzymatically modified starch (EMS) product on the mucosal expression of genes related to starch digestion, sugar and short-chain fatty acid (SCFA) absorption and incretins in the jejunum and cecum in growing pigs. Moreover, the impact of the EMS on hepatic expression of genes related to glucose and lipid metabolism, and postprandial serum metabolites were assessed. Barrows (n=12/diet; initial BW 29 kg) were individually fed three times daily with free access to a diet containing either EMS or waxy corn starch as control (CON) for 10 days. The enzymatic modification led to twice as many α-1,6-glycosidic bonds (~8%) in the amylopectin fraction in the EMS in comparison with the non-modified native waxy corn starch (4% α-1,6-glycosidic bonds). Linear discriminant analysis revealed distinct clustering of mucosal gene expression for EMS and CON diets in jejunum. Compared with the CON diet, the EMS intake up-regulated jejunal expression of sodium-coupled monocarboxylate transporter (SMCT), glucagon-like peptide-1 (GLP1) and gastric inhibitory polypeptide (GIP) (P<0.05) and intestinal alkaline phosphatase (ALPI) (P=0.08), which may be related to greater luminal SCFA availability, whereas cecal gene expression was unaffected by diet. Hepatic peroxisome proliferator-activated receptor γ (PPARγ) expression tended (P=0.07) to be down-regulated in pigs fed the EMS diet compared with pigs fed the CON diet, which may explain the trend (P=0.08) of 30% decrease in serum triglycerides in pigs fed the EMS diet. Furthermore, pigs fed the EMS diet had a 50% higher (P=0.03) serum urea concentration than pigs fed the CON diet potentially indicating an increased use of glucogenic amino acids for energy acquisition in these pigs. Present findings suggested the jejunum as the target site to influence the intestinal epithelium and altered lipid and carbohydrate metabolism by EMS feeding.

High-Throughput Sequencing of Viable Microbial Communities in Raw Pork Subjected to a Fast Cooling Process

This study aimed to investigate the effect of the fast cooling process on the microbiological community in chilled fresh pork during storage. We established a culture-independent method to study viable microbes in raw pork. Tray-packaged fresh pork and chilled fresh pork were completely spoiled after 18 and 49 d in aseptic bags at 4 °C, respectively. 16S/18S ribosomal RNAs were reverse transcribed to cDNA to characterize the activity of viable bacteria/fungi in the 2 types of pork. Both cDNA and total DNA were analyzed by high-throughput sequencing, which revealed that viable Bacteroides sp. were the most active genus in rotten pork, although viable Myroides sp. and Pseudomonas sp. were also active. Moreover, viable fungi were only detected in chilled fresh pork. The sequencing results revealed that the fast cooling process could suppress the growth of microbes present initially in the raw meat to extend its shelf life. Our results also suggested that fungi associated with pork spoilage could not grow well in aseptic tray-packaged conditions.

Microbiome-Metabolome Responses in the Cecum and Colon of Pig to a High Resistant Starch Diet

Currently, knowledge about the impact of long-term intake of high resistant starch diet on pig hindgut microbiota and metabolite profile is limited. In this study, a combination of the pyrosequencing and the mass spectrometry (MS)-based metabolomics techniques were used to investigate the effects of a raw potato starch (RPS, high in resistant starch) diet on microbial composition and microbial metabolites in the hindgut of pig. The results showed that Coprococcus, Ruminococcus, and Turicibacter increased significantly, while Sarcina and Clostridium decreased in relative abundances in the hindgut of pigs fed RPS. The metabolimic analysis revealed that RPS significantly affected starch and sucrose metabolites, amino acid turnover or protein biosynthesis, lipid metabolites, glycolysis, the pentose phosphate pathway, inositol phosphate metabolism, and nucleotide metabolism. Furthermore, a Pearson's correlation analysis showed that Ruminococcus and Coprococcus were positively correlated with glucose-6-phosphate, maltose, arachidonic acid, 9, 12-octadecadienoic acid, oleic acid, phosphate, but negatively correlated with α-aminobutyric acid. However, the correlation of Clostridium and Sarcina with these compounds was in the opposite direction. The results suggest that RPS not only alters the composition of the gut microbial community but also modulates the metabolic pathway of microbial metabolism, which may further affect the hindgut health of the host.