Effect of fermentable carbohydrates on piglet faecal bacterial communities as revealed by denaturing gradient gel electrophoresis analysis of 16S ribosomal DNA

Supplementation with Antimicrobial Peptides or a Tannic Acid Can Effectively Replace the Pharmacological Effects of Zinc Oxide in the Early Stages of Weaning Piglets

Zinc oxide (ZnO) harms the environment and can potentially increase the number of drug-resistant bacteria. Therefore, there is an urgent need to find safe and effective alternatives to improve gut health and reduce the incidence of diarrhea in weaned piglets. This study conducted an antibacterial test of ZnO, antibacterial peptides (AMPs), and tannic acid (TA) in vitro. Thirty piglets were randomly allotted to one of the following three dietary treatments: ZnO (2000 mg/kg ZnO diet), AMPs (700 mg/kg AMPs diet), and TA (1000 mg/kg TA diet). The results showed that the minimum inhibitory concentrations of ZnO and TA against Escherichia coli and Salmonella were lower than those of AMPs, and the minimum inhibitory concentrations of ZnO, AMPs, and TA against Staphylococcus aureus were the same. Compared to ZnO, AMPs increased the digestibility of dry, organic matter and the crude fat. Additionally, TA significantly (p < 0.05) increased the digestibility of dry and organic matter. On experimental day 14, the plasma interleukin-6 (IL-6) content of piglets supplemented with AMPs and TA was increased significantly (p < 0.05). On experimental day 28, alanine aminotransferase activity in the plasma of weaned piglets in the ZnO and TA groups was significantly (p < 0.05) higher than in piglets in the AMPs group. The levels of plasma IL-6 and immunoglobulin M (IgM) were significantly higher (p < 0.05) in the ZnO and AMPs groups than in the TA group. On experimental days 14 and 28, no significant differences were observed in the antioxidant capacity among the three experimental groups. Intestinal microbial diversity analysis showed that the Chao1 and ACE indices of piglets in the AMPs group were significantly higher (p < 0.05) than those in the ZnO and TA groups. At the genus level, the relative abundance of Treponema_2 was higher in the feces of piglets fed a diet supplemented with TA than in those fed diet supplemented with ZnO (p < 0.05). The relative abundance of Lachnospiraceae was higher in the feces of piglets fed a diet supplemented with AMPs than in those fed diet supplemented with ZnO or TA. Overall, AMPs and TA could be added to feed as substitutes for ZnO to reduce diarrhea, improve nutrient digestibility and immunity, and increase the abundance of beneficial intestinal bacteria in weaned piglets.

Dietary micro-fibrillated cellulose improves growth, reduces diarrhea, modulates gut microbiota, and increases butyrate production in post-weaning piglets

Dietary fiber (DF) supplementation is one of the strategies to prevent on-farm infections; it has the capability to improve gut health and piglet performance. Among the beneficial DFs, micro-fibrillated cellulose (MFC) is a new-generation plant-derived innovative feed ingredient; MFC, originating from sugar-beet pulp, has a hyper-branched structure with the ability to form shear-thinning hydrogel and has a high water-binding capacity. We aimed to determine the effects of MFC supplementation on piglets' performance before and after weaning. We included 45 sows and their piglets in this trial and monitored the results until the piglets were 7 weeks old. Piglets supplemented with MFC had higher body weight and average daily growth (ADG) than did control piglets, both pre- and post-weaning. In addition, MFC supplementation in post-weaning piglets improved butyrate content, and reduced diarrhea incidence. These phenomena, perhaps due to the MFC supplementation at different stages until age 7 weeks. In addition, after weaning, MFC supplementation stimulated the growth of butyrate-producing bacteria such as Ruminococcus.2, Ruminococcaceae.UCG.014, Intestinibacter, Roseburia, and Oribacterium genera, as well as reduced the pathogenic bacteria, such as Campylobacter, and Escherichia. Evidently, supplementation of MFC in feed to young piglets can improve growth performance and butyric acid content and reduce post-weaning diarrhea.

Dietary Effects of a Short-Term Administration of Microalgae Blend on Growth Performance, Tissue Fatty Acids, and Predominant Intestinal Microbiota in Sparus aurata

Given the potential of microalgae as new aquafeed ingredients, this study focuses on using a blend of microalgae, Tisochrysis lutea, Nannochloropsis gaditana, and Scenedesmus almeriensis, as a dietary ingredient for feeding Sparus aurata juveniles. The growth performance, carcass composition, tissue fatty acid profile, and intestinal microbiota were evaluated after a 30 day-feeding period. A microalgae-free diet was used as control, and three experimental diets were formulated containing 5%, 15%, and 25% of the microalgae blend (MB-5%, MB-15%, and MB-25%, respectively). After 7, 15, and 30 days of feeding experimental diets, biological samples were taken. Growth performance and nutrient utilization were not significantly modified at the end of the experiment. Microalgae inclusion tended to decrease body lipids and affected the fatty acid profile, especially MB-25 diet increased DHA levels. Diet MB-25 promoted appropriate microbial diversity, favoring the presence of probiotic bacteria, such as Lactobacillus, and significantly influencing the fatty acid composition and lipid metabolism in fish. In conclusion, using a short pulse of dietary administration of 25% microalgal blend in S. aurata modulates the intestinal microbiota and lipid composition while maintaining growth performance.

Maintenance of gut microbiome stability for optimum intestinal health in pigs - a review

Pigs are exposed to various challenges such as weaning, environmental stressors, unhealthy diet, diseases and infections during their lifetime which adversely affects the gut microbiome. The inability of the pig microbiome to return to the pre-challenge baseline may lead to dysbiosis resulting in the outbreak of diseases. Therefore, the maintenance of gut microbiome diversity, robustness and stability has been influential for optimum intestinal health after perturbations. Nowadays human and animal researches have focused on more holistic approaches to obtain a robust gut microbiota that provides protection against pathogens and improves the digestive physiology and the immune system. In this review, we present an overview of the swine gut microbiota, factors affecting the gut microbiome and the importance of microbial stability in promoting optimal intestinal health. Additionally, we discussed the current understanding of nutritional interventions using fibers and pre/probiotics supplementation as non-antibiotic alternatives to maintain microbiota resilience to replace diminished species.

Fate of undigested proteins in the pig large intestine: What impact on the colon epithelium?

Apart from its obvious agronomic interest in feeding billions of people worldwide, the porcine species represents an irreplaceable experimental model for intestinal physiologists and nutritionists. In this review, we give an overview on the fate of proteins that are not fully digested in the pig small intestine, and thus are transferred into the large intestine. In the large intestine, dietary and endogenous proteins are converted to peptides and amino acids (AA) by the action of bacterial proteases and peptidases. AA, which cannot, except in the neonatal period, be absorbed to any significant level by the colonocytes, are used by the intestinal microbes for protein synthesis and for the production of numerous metabolites. Of note, the production of the AA-derived metabolites greatly depends on the amount of undigested polysaccharides in the pig's diet. The effects of these AA-derived bacterial metabolites on the pig colonic epithelium have not yet been largely studied. However, the available data, performed on colonic mucosa, isolated colonic crypts and colonocytes, indicate that some of them, like ammonia, butyrate, acetate, hydrogen sulfide (H₂S), and p-cresol are active either directly or indirectly on energy metabolism in colonic epithelial cells. Further studies in that area will certainly gain from the utilization of the pig colonic organoid model, which allows for disposal of functional epithelial unities. Such studies will contribute to a better understanding of the potential causal links between diet-induced changes in the luminal concentrations of these AA-derived bacterial metabolites and effects on the colon epithelial barrier function and water/electrolyte absorption.

Effect of fiber source and crude protein level on nursery pig performance and fecal microbial communities

Reduction in dietary crude protein and addition of fiber could mitigate the incidence and severity of post-weaning diarrhea, a common gastrointestinal condition in newly weaned pigs. Therefore, 360 weanling pigs, initially 5.0 ± 0.10 kg, were used to evaluate the effects of crude protein (CP) level and fiber source on growth performance and fecal microbial communities. At weaning, pigs were randomly assigned to pens and allotted to 1 of 8 dietary treatments in a 2 × 4 factorial with main effects of CP (21 or 18%) and fiber source (none, coarse wheat bran, oat hulls, or cellulose). There were 5 pigs per pen and 9 pens per treatment. Experimental diets were formulated in two dietary phases from d 0 to 10 and 10 to 24, with a common post-treatment diet fed from 24 to 45. The 21% CP diets contained 1.40% standardized ileal digestible (SID) Lys in phase 1 and 1.35% SID Lys in phase 2. By using a maximum SID Lys:digestible CP ratio of 6.35%, the 18% CP diets contained 1.25% SID Lys in both phases. Diets containing a fiber source were formulated to the level of insoluble fiber provided by 4% coarse wheat bran, resulting in the addition of 1.85% oat hulls and 1.55% cellulose. No fiber source × CP level interactions (P > 0.05) were observed. Decreasing CP (and subsequently SID lysine) decreased (P = 0.05) ADG and G:F during the experimental period. From d 0 to 45, ADG decreased (P = 0.05) for pigs fed 18% CP diets compared to pigs fed 21% CP. No effect of fiber source was observed for growth performance. Fecal DM on d 17 increased (P < 0.001) for pigs fed 18% CP diets compared to pigs fed 21% CP diets. Pigs fed diets with added cellulose had increased (P < 0.05) fecal dry matter during the experimental period compared to pigs fed no fiber source or wheat bran. Bacterial community structure was investigated by sequencing the V4 region of the 16S rRNA gene. Analysis indicated a significant difference between CP content at d 24 (P = 0.023) using a Weighted UniFrac distance matrix. Further investigation identified five differential Amplicon Sequence Variants associated with CP content at d 24. In conclusion, reducing crude protein (and subsequently SID Lys) decreased growth performance but increased fecal dry matter content. The source of dietary fiber in nursery diets had no impact on growth performance; but pigs fed added cellulose had increased fecal DM compared with other treatments. Microbial analysis identified differential taxa associated with CP content.

Gut microbiome colonization and development in neonatal ruminants: Strategies, prospects, and opportunities

Colonization and development of the gut microbiome is a crucial consideration for optimizing the health and performance of livestock animals. This is mainly attributed to the fact that dietary and management practices greatly influence the gut microbiota, subsequently leading to changes in nutrient utilization and immune response. A favorable microbiome can be implanted through dietary or management interventions of livestock animals, especially during early life. In this review, we explore all the possible factors (for example gestation, colostrum, and milk feeding, drinking water, starter feed, inoculation from healthy animals, prebiotics/probiotics, weaning time, essential oil and transgenesis), which can influence rumen microbiome colonization and development. We discuss the advantages and disadvantages of potential strategies used to manipulate gut development and microbial colonization to improve the production and health of newborn calves at an early age when they are most susceptible to enteric disease. Moreover, we provide insights into possible interventions and their potential effects on rumen development and microbiota establishment. Prospects of latest techniques like transgenesis and host genetics have also been discussed regarding their potential role in modulation of rumen microbiome and subsequent effects on gut development and performance in neonatal ruminants.

Early-Life Intake of an Isotonic Protein Drink Improves the Gut Microbial Profile of Piglets

Simple Summary

The gut microbiota plays a key role in maintaining the overall health and homeostasis of mammals. Developing blends of nutrients that contribute to a diverse and balanced gut microbiota community thus contributes to improve pig health, particularly at weaning when rapid dietary and environmental changes occur. As shown in the present study, Tonisity Px, an isotonic protein drink that provides key nutrients for nourishing the enterocytes, increased the abundance of beneficial bacteria and decreased that of potentially-pathogenic bacteria when provided to piglets aged 2 to 8 days. This isotonic protein drink also improved the overall gut environment, both pre-weaning and post-weaning, as revealed by 16S rRNA gene sequencing and semiquantitative Escherichia coli culture.

Abstract

A healthy microbial community in the gut of piglets is critical to minimize the negative performance consequences associated with dietary and environmental changes that occur at weaning. Tonisity Px, an isotonic protein drink, is a potential alternative to balance the gut microbiota as it contains key ingredients for nourishing the small intestine. In the present study, 16 litters comprising 161 piglets were randomly allocated to a group to which Tonisity Px was provided from days 2 to 8 of age (TPX group) or to a control group, to which no Tonisity Px was provided. The TPX group also received Tonisity Px in the 3 days before and after weaning. At days 9, 17, and 30 of age, fecal and ileum samples were collected from piglets belonging to both groups and analyzed using 16S rRNA gene sequencing, semiquantitative PCR of Rotavirus serogroups, and semiquantitative Escherichia coli culture. Overall, Tonisity Px increased the abundance of beneficial bacterial populations (Lactobacillus and Bacteroides species) and reduced potentially pathogenic bacterial populations (E. coli and Prevotellaceae), in both the pre-weaning and post-weaning periods.

Effect of a direct-fed microbial and prebiotic on performance and intestinal histomorophology of turkey poults challenged with Salmonella and Campylobacter

Salmonella and Campylobacter are leading human foodborne pathogens commonly associated with poultry and poultry products, and several methods to control these pathogens have been applied to poultry production. This study was conducted to evaluate the effect of CALSPORIN, (CSP), a direct-fed microbial (DFM), and yeast cell wall (Saccharomyces cervisiae, IMW50, a mannanoligosaccharide (MOS)-based prebiotic, on performance, levels of Salmonella and Campylobacter in the feces, and intestinal histomorphometry in turkey poults. A 21-day battery cage study was conducted using 4 dietary treatments, including: an unsupplemented basal diet (corn and soybean-based) as negative control (NC); basal diet supplemented with 0.05% DFM; basal diet supplemented with 0.05% MOS; and basal diet supplemented with 0.05% mixture of DFM and MOS at equal proportions. Female Large White turkey poults (n = 336) were randomly distributed in 6 electrically-heated battery cages with 4 treatments and 12 replicates per treatment (7 poults per replicate pen). The first 16 pens were not inoculated with bacteria, while poults in pens 17 to 32 were orally challenged at day 7 with 105 CFU Salmonella Heidelberg and the poults in pens 33 to 48 were orally challenged at day 7 with 105 CFU Campylobacter jejuni. Feed consumption, body weight, and feed conversion ratio were measured weekly and at the end of the experiment. At day 21, fresh fecal samples from each pen were collected for Salmonella and Campylobacter enumeration and ileal tissue samples were collected from 1 bird per pen for histomorphology examination. DFM and MOS supplementation was accompanied with reduced levels of Salmonella shed by the treated birds compared to the control group, and with increased body weight (P ≤ 0.05). The surface area of villi increased in the MOS-supplemented group compared to the control group (P ≤ 0.05). There was a significant difference in V:C ratio between supplemented groups and control group (P ≤ 0.05). Based on these results, there is potential for CALSPORIN and IMW50 to reduce Salmonella shedding in feces, enhance ileal mucosal health, and improve growth performance of turkey poults.

Effect of cereal soaking and carbohydrase supplementation on growth, nutrient digestibility and intestinal microbiota in liquid-fed grow-finishing pigs

Soaking the cereal fraction of a liquid diet prior to feeding (C_soak), and/or carbohydrase enzyme supplementation (ENZ) are likely to modulate both feed and intestinal microbial populations and improve feed efficiency (FE) in pigs. To test this hypothesis, a total of 392 grow-finisher pigs (~33.4 kg, 7 pigs/pen) were randomly allocated to 4 treatments in a 2 × 2 factorial arrangement for 70 days as follows: (1) fresh liquid feed (Fresh); (2) Cereal soaked liquid feed (Soak); (3) Fresh + ENZ and (4) Soak + ENZ. An interaction between ENZ and C_soak was found for average daily gain (ADG) during the growing phase (day 0 to 21; P < 0.05) where pigs fed the Soak + ENZ diet had higher ADG than pigs fed the Fresh + ENZ diet. No treatment effect was found for ADG thereafter. Enzyme supplementation increased total tract nutrient digestibility (P < 0.05) and reduced caecal VFA concentrations (P < 0.05) but did not improve pig growth or FE. Both C_soak and ENZ modulated intestinal microbiota composition; increasing abundance of bacterial taxa that were negatively correlated with pig growth and reducing abundance of taxa positively correlated with pig growth and caecal butyrate concentration. In conclusion, both strategies (C_soak and ENZ) improved nutrient digestibility in pigs and modulated intestinal microbiota composition.

Zearalenone Biodegradation by the Combination of Probiotics with Cell-Free Extracts of Aspergillus oryzae and its Mycotoxin-Alleviating Effect on Pig Production Performance

In order to remove zearalenone (ZEA) detriment—Bacillus subtilis, Candida utilis, and cell-free extracts from Aspergillus oryzae were used to degrade ZEA in this study. The orthogonal experiment in vitro showed that the ZEA degradation rate was 92.27% (p < 0.05) under the conditions that Candida utilis, Bacillus subtilis SP1, and Bacillus subtilis SP2 were mixed together at 0.5%, 1.0%, and 1.0%. When cell-free extracts from Aspergillus oryzae were combined with the above probiotics at a ratio of 2:1 to make mycotoxin-biodegradation preparation (MBP), the ZEA degradation rate reached 95.15% (p < 0.05). In order to further investigate the MBP effect on relieving the negative impact of ZEA for pig production performance, 120 young pigs were randomly divided into 5 groups, with 3 replicates in each group and 8 pigs for each replicate. Group A was given the basal diet with 86.19 μg/kg ZEA; group B contained 300 μg/kg ZEA without MBP addition; and groups C, D, and E contained 300 μg/kg ZEA added with 0.05%, 0.10%, and 0.15% MBP, respectively. The results showed that MBP addition was able to keep gut microbiota stable. ZEA concentrations in jejunal contents in groups A and D were 89.47% and 80.07% lower than that in group B (p < 0.05), indicating that MBP was effective in ZEA biodegradation. In addition, MBP had no significant effect on pig growth, nutrient digestibility, and the relative mRNA abundance of estrogen receptor alpha (ERα) genes in ovaries and the uterus (p > 0.05).

Growth performance, carcass quality characteristics and colonic microbiota profiles in finishing pigs fed diets with different inclusion levels of rice distillers' by-product

The aim of this study was to evaluate the effects of diets containing rice distillers' by-product (RDP) on growth performance, carcass characteristics, meat quality, and gut microbiota of fattening pigs. Twenty-four crossbred finishing pigs (Duroc × Landrace × Yorkshire), 56.9 ± 3.1 kg initial body weight, were randomly allocated to three groups. For 56 days, pigs were fed one of three diets including RDP0 (control), RDP15 (15% RDP in DM), and RDP30 (30% RDP in DM). With RDP level in diet, average daily gain and backfat thickness linearly increased (p < 0.05), and drip loss tended to increase (p ≤ 0.08). In addition, 16S ribosomal RNA gene amplicon profiling showed that RDP was associated with modulation of colonic microbiota composition, especially at family and genus levels. Relative abundance of Porphyromonadaceae and Erysipelotrichaceae families in colonic digesta increased with inclusion of RDP, while that of Enterobacteriaceae decreased. The proportion of genera unclassified Erysipelotrichaceae, and Butyrivibrio increased as inclusion of RDP. These results indicate that up to 30% inclusion in diet of finishing pigs, RDP can modulate colonic microbiota composition, and induces an improvement of animal growth and fat deposition.

Dietary Supplementation With Chinese Herbal Residues or Their Fermented Products Modifies the Colonic Microbiota, Bacterial Metabolites, and Expression of Genes Related to Colon Barrier Function in Weaned Piglets

To explore the feasibility of dietary Chinese herbal residue (CHR) supplementation in swine production with the objective of valorization, we examined the effects of dietary supplementation with CHR or fermented CHR products on the colonic ecosystem (i.e., microbiota composition, luminal bacterial metabolites, and expression of genes related to the intestinal barrier function in weaned piglets). We randomly assigned 120 piglets to one of four dietary treatment groups: a blank control group, CHR group (dose of supplement 4 kg/t), fermented CHR group (dose of supplement 4 kg/t), and a positive control group (supplemented with 0.04 kg/t virginiamycin, 0.2 kg/t colistin, and 3000 mg/kg zinc 0.04 kg/t virginiamycin, 0.2 kg/t colistin, and 3000 mg/kg zinc oxide). Our results indicate that dietary supplementation with CHR increased (P < 0.05) the mRNA level corresponding to E-cadherin compared with that observed in the other three groups, increased (P < 0.05) the mRNA level corresponding to zonula occludens-1, and decreased (P < 0.05) the quantity of Bifidobacterium spp. When compared with the blank control group. Dietary supplementation with fermented CHR decreased (P < 0.05) the concentration of indole when compared to the positive control group; increased (P < 0.05) the concentrations of short-chain fatty acids compared with the values measured in the CHR group, as well as the mRNA levels corresponding to interleukin 1 alpha, interleukin 2, and tumor necrosis factor alpha. However, supplementation with fermented CHR decreased (P < 0.05) interleukin 12 levels when compared with the blank control group. Collectively, these findings suggest that dietary supplementation with CHR or fermented CHR modifies the gut environment of weaned piglets.

Dietary or supplemental fermentable fiber intake reduces the presence of Clostridium XI in mouse intestinal microbiota: The importance of higher fecal bacterial load and density

OBJECTIVES

Clostridium difficile infection is a public health concern. C. difficile was found in healthy human intestine as a member of Clostridium XI. Because soluble fermentable fiber ingestion affects intestinal microbiota, we used fiber-containing diets to determine the intestinal microbial condition that could reduce the presence of Clostridium XI.

METHODS

Newly weaned male mice were assigned to three published diets: Control AIN-93G purified diet with only poorly fermented cellulose; Control plus 5% purified fermentable fiber inulin; Chow with wheat, soybean and corn that provide a mixture of unpurified dietary fibers. Methods were developed to quantify 24-hour fecal microbial load and microbial DNA density. The relative abundance of bacterial genera and the bacterial diversity were determined through 16S rRNA sequence-based fecal microbiota analysis.

RESULTS

Mice adjusted food intake to maintain the same energy intake and body weight under these three moderate-fat (7% w:w) diets. Chow-feeding led to higher food intake but also higher 24-h fecal output. Chow-feeding and 1-8 wk ingestion of inulin-supplemented diet increased daily fecal microbial load and density along with lowering the prevalence of Clostridium XI to undetectable. Clostridium XI remained undetectable until 4 weeks after the termination of inulin-supplemented diet. Fermentable fiber intake did not consistently increase probiotic genera such as Bifidobacterium or Lactobacillus. Chow feeding, but not inulin supplementation, increased the bacterial diversity.

CONCLUSIONS

Increase fecal microbial load/density upon fermentable fiber ingestion is associated with a lower and eventually undetectable presence of Clostridium XI. Higher bacterial diversity or abundance of particular genera is not apparently essential. Future studies are needed to see whether this observation can be translated into the reduction of C. difficile at the species level in at-risk populations.

Development of the Tonsil Microbiome in Pigs and Effects of Stress on the Microbiome

Tonsils, lympho-epithelial tissues located at the junction of the oropharynx and nasopharynx, play a key role in surveillance, colonization, and persistence of inhaled and ingested pathogens. In pigs, the tonsils are a reservoir for numerous bacteria and viruses, including host-specific pathogens and potential zoonotic pathogens as well as commensal organisms. However, there are no in depth studies of the development of the tonsillar microbiome in pigs, or any mammal, over time. The goal of this study was to follow the development of the tonsil microbiome in healthy pigs from birth to market weight. Samples were collected using tonsil brushes from 16 piglets (4 each from 4 sows) at newborn, 1, 2, 3, and 4 weeks of age, and from 8 of those piglets at 6, 8, 10, 12, 16, and 19 weeks of age. Bacterial DNA was isolated from each sample and 16S rDNA genes were amplified and sequenced. Sequence analysis showed that members of the Streptococcaceae, Pasteurellaceae, and Moraxellaceae were present at all time points and represent the three most abundant families identified. Other community members appeared transiently or increased or decreased significantly with disruption events or stress. We observed four significant shifts in the tonsil community that coincided with well-defined disruption events: weaning plus addition of Carbadox plus movement to the nursery at week 3, removal of Carbadox and addition of Tylan at week 5, removal of Tylan and habitat change at week 9, and habitat change at week 16. Weaning triggered a bloom of Streptococcaeae and decrease of Moraxellaceae. The shift from Carbadox to Tylan led to reduction in Proteobacteria and Streptococcaceae but an increase in other Firmicutes, accompanied by a dramatic increase in community richness. Cessation of Tylan coincided with a return to a less rich community, and a bloom in Clostridiales. The final shift in habitat was accompanied by a decrease in Clostridiales and increase in Proteobacteria. The tonsillar microbiome of older pigs resembled the previously described mature core tonsillar microbiome. This study demonstrates a temporal succession in the development of the pig tonsillar microbiome, and significant community shifts that correlate with disruption events.

In vitro effects of inulin and soya bean oligosaccharide on skatole production and the intestinal microbiota in broilers

The experiment was conducted to investigate the in vitro effects of inulin and soya bean oligosaccharide (SBO) on the metabolism of L-tryptophan (L-try) to skatole production, and the intestinal microbiota in broilers. Treatments were as follows: caecal microbiota control (Cc), Cc + inulin, Cc + SBO, rectal microbiota control (Rc), Rc + inulin and Rc + SBO. Microbial suspensions were anaerobically incubated at 38°C for 24 hr. The results showed that concentrations of skatole and acetic acid were significantly lower in caecal microbiota fermentation broth (MFB) than those in rectal MFB (p < .05). Addition of inulin or SBO significantly decreased the concentrations of indole and skatole and rate of L-try degradation (p < .05). Inulin groups had lower indole than SBO groups (p < .05). PCR-DGGE analysis revealed that addition of inulin or SBO decreased the microbiota richness (p < .05), but no significant differences in Shannon index (p > .05). Four distinct bands were detected in inulin and SBO groups, which were related to two of Bacteroides, one of Firmicutes and Bifidobacteria. Six bands were detected only in control groups, which represented uncultured Rikenellaceae, Roseburia, Escherichia/Shigella dysenteriae, Bacteroides uniformis (T), Parabacteroides distasonis and Enterobacter aerogenes. Populations of Lactobacilli, Bifidobacteria and total bacteria in inulin groups were higher than those in control groups (p < .05). For SBO groups, only population of total bacteria increased (p < .05). However, there were no significant differences in Escherichia coli population among treatments (p > .05). These results suggest that reduced concentrations of skatole and indole in the presence of inulin and SBO may be caused by decrease in L-try degradation rate, which were caused by change in microbial ecosystem and pH value. Uncultured B. uniformis (T) and E. aerogenes may be responsible for degradation of L-try to skatole.

Development of the tonsillar microbiome in pigs from newborn through weaning

Background

Porcine tonsils are lympho-epithelial tissues, colonized by numerous bacteria and viruses, that act as a reservoir for both host-specific pathogens and zoonotic pathogens with a high potential of transmission to humans. There are no existing studies describing the development of the tonsillar microbiome. We sequenced 16S rRNA genes from tonsillar samples of pigs to follow the development of the microbial communities from birth through weaning. Samples derived from sows were also analyzed to determine potential sources for the tonsil microbiome in piglets.

Results

The composition of the newborn piglet tonsil microbiome could be differentiated by litter and had strong similarity to the sow teat skin as well as sow vaginal microbiome. The tonsil microbiome in these young piglets was mainly dominated by members of the Pasteurellaceae, Moraxellaceae, and Streptococcaceae families, while there were some transient members of the microbiome that were abundant at specific times, such as Staphylococcaceae in newborns and Fusobacteriaceae and Leptotrichiaceae in weeks 2 and 3. The microbiome initially differed between litters but over the following 3 weeks the communities of different litters converged in composition and then diverged in week 4 due to a combination of changes and stresses associated with weaning, including a shift from milk to a solid diet, in-feed Carbadox^® and room change.

Conclusions

A significant portion of the tonsil microbiome was acquired either at birth from the sow vaginal tract or within a few hours post-birth from the sow teat skin. Our data demonstrate a temporal succession in the development of the pig tonsillar microbiome through the first weeks of life, with a convergence in the composition of the microbiome in all piglets by 3 weeks of age. The combination of management practices associated with weaning coincided with dramatic shifts in the tonsillar microbiome.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1176-x) contains supplementary material, which is available to authorized users.

Global restriction of using antibiotic growth promoters and alternative strategies in poultry production

A growing global concern of antibiotic use in poultry diets due to its potential adverse effects on birds and human health, food safety and the environment has led to a complete ban or restricted use in some countries, and, at the same time, expanding options for the use of alternative feed additives. Multiple, rather than a single additive may replace antibiotic growth promoters (AGPs) in poultry. Blending of feeding additives and hygienic farm management, vaccination and biosecurity may help achieve good intestinal health, stabilise enteric ecosystems and result in sustainable and cost effective production performance of birds. Moreover, controlling unsolicited ingredients at the production level must have the support of different markets responsible for the supply of safe and quality poultry products for consumers. This requires the further increase and diversification of value added poultry products and the expansion of their markets through strategic planning and gradual limitation of live bird markets. More research is warranted in order to explore suitable, reliable and cost effective alternatives to AGPs for commercial use, and strategic poultry value chain development.

Dietary pea fibre alters the microbial community and fermentation with increase in fibre degradation-associated bacterial groups in the colon of pigs

This study was attempted to investigate the influence of dietary pea fibre (PF) on the community and quantity of colonic bacteria of piglets and finisher pigs using pyrosequencing data and real-time PCR. The concentration of acetate in colonic digesta from PF-fed piglets was significantly higher than that from control (p < .05). Feeding PF diet to finisher pigs increased the ratio of acetate to total volatile fatty acids (VFAs) but decreased the ratio of butyrate, as compared with the control pigs (p < .05 in both cases). The lower ratio of butyrate in samples from finisher pigs receiving PF suggested that this dietary fibre did not favour butyrate production in the hindgut. Supplementation of PF to piglets reduced abundance of Bacteroidetes, as compared with control animals. However, PF had opposite effects in finisher pigs, higher abundance of Bacteroidetes but lower of Firmicutes. Lactobacillus and Prevotella were found as the predominant genera in PF piglets. Prevotella accounted for nearly half of the total bacteria in the colon of finisher pigs in the PF group, but only one-third in the control animals. Quantitative PCR showed that Firmicutes/Bacteroidetes were significantly increased in the colon of PF piglets (p < .05) as compared with control animals, but decreased in PF finisher pigs. Bacteroidetes-Prevotella-Porphyromonas and Desulfovibrio desulfuricans which are involved in degradation of dietary fibres were more abundant in the PF finisher pigs than in the controls (p < .05), suggesting mutualism between host and its gut microbes.

Does Modification of the Large Intestinal Microbiome Contribute to the Anti-Inflammatory Activity of Fermentable Fiber?

Fiber is an inadequately understood and insufficiently consumed nutrient. This review examines the possible causal relation between fiber-induced microbiome changes and the anti-inflammatory activity of fiber. To demonstrate the dominant role of fermentable plant fiber in shaping the intestinal microbiome, animal and human fiber-feeding studies are reviewed. Using culture-, PCR-, and sequencing-based microbial analyses, a higher prevalence of Bifidobacterium and Lactobacillus genera was observed from the feeding of different types of fermentable fiber. This finding was reported in studies performed on several host species including human. Health conditions and medications that are linked to intestinal microbial alterations likely also change the nutrient environment of the large intestine. The unique gene clusters of Bifidobacterium and Lactobacillus that enable the catabolism of plant glycans and the ability of Bifidobacterium and Lactobacillus to reduce the colonization of proteobacteria probably contribute to their prevalence in a fiber-rich intestinal environment. The fiber-induced microbiome changes could contribute to the anti-inflammatory activity of fiber. Although most studies did not measure fecal microbial density or total daily fecal microbial output (colon microbial load), limited evidence suggests that the increase in intestinal commensal microbial load plays an important role in the anti-inflammatory activity of fiber. Various probiotic supplements, including Bifidobacterium and Lactobacillus, showed anti-inflammatory activity only in the presence of fiber, which promoted microbial growth as indicated by increasing plasma short-chain fatty acids. Probiotics alone or pure fiber administered under sterile conditions showed no anti-inflammatory activity. The potential mechanisms that could mediate the anti-inflammatory effect of common microbial metabolites are reviewed, but more in vivo trials are needed. Future studies including simultaneous microbial composition and load measurements are also important.

Effects of Lactobacillus casei and Enterococcus faecalis on growth performance, immune function and gut microbiota of suckling piglets

This study was carried out to investigate the effects of orally administrated Lactobacillus casei and Enterococcus faecalis on performance, immune function and gut microbiota of suckling piglets. Neonatal piglets (n = 120) were randomly assigned to 4 groups, with 30 suckling piglets in each group. The piglets were from 15 litters, one male and one female piglet were selected for each group in each litter. The Control group was administrated with normal saline, the other groups with L. casei or E. faecalis or a combination of L. casei and E. faecalis at a ratio of 3:1. Each piglet was orally administrated with 1, 2, 3 and 4 ml probiotics or normal saline at the age of 1, 7, 14 and 21 d, respectively. The piglets were weaned at the age of 21 d. The results showed that compared with the Control group, the average daily gain of piglets administrated with probiotics was significantly increased, and the diarrhoea rate and mortality were significantly decreased (p < 0.05). After supplementation of the combined probiotics, the protease activity in stomach, duodenum and colon was increased and in all supplemented groups, the immunoglobulin A concentration in plasma was significantly higher (p < 0.05). The combined probiotics significantly increased villus length and the expression level of transforming growth factor-β in the jejunum (p < 0.05) but decreased the expression level of the jejunal tumour necrosis factor-α (p < 0.05). In addition, probiotics could regulate gut microbiota and increase microbial similarity coefficients for keeping piglet gut microbiota stable.

Effect of varying the energy density on growth performance, meat quality, caecum fermentation and microbiota of growing Rex rabbits

An experiment was conducted to determine the effects of varying the digestible energy (DE) density on growth performance, meat quality, caecum fermentation and microbiota in 3–5-month-old Rex rabbits. One-hundred and eighty 3-month-old Rex rabbits were allocated in individual cages to five treatments with diets having DE levels (MJ/kg as-fed basis) of 9.46, 9.97, 10.46, 10.94 and 11.43, respectively. The results showed as follows: with increasing DE concentration the average daily gain, muscle pH value of 45 min post-mortem, caecal pH value and NH3-N concentration increased (P < 0.05). Bacterial denaturing gradient gel electrophoresis (denaturing gradient gel electrophoresis) of partial 16S rRNA genes profiles were clearly different among different treatments, which suggests that the population of microorganism in the caecum was influenced by the dietary DE density.

Effects of fiber inclusion on growth performance and nutrient digestibility of piglets reared under optimal or poor hygienic conditions

Two experiments were conducted to study the effects of inclusion of additional fiber in the Phase I diet on growth performance and nutrient digestibility in piglets reared under "optimal" or "poor" hygienic conditions. In both experiments, the design was completely randomized with a control diet that contained 2.2% crude fiber and 8 additional isonutritive diets that included 2.5 or 5.0% of sugar beet pulp (SBP), straw, oat hulls (OH), or wheat middlings (WHM). Preplanned polynomial contrasts were used to study the effects of 1) fiber inclusion (control diet vs. average of the 8 fiber-containing diets), 2) source of fiber, 3) level of fiber, and 4) interaction between source and level of fiber. In Exp. 1 (clean barn), fiber inclusion increased ( < 0.01) the incidence of postweaning diarrhea (PWD) and reduced ( < 0.05) feed efficiency and apparent total tract digestibility (ATTD) of all nutrients except that of CP, which was not affected. Piglet performance was not affected by source or level of dietary fiber. The ATTD of all nutrients decreased ( < 0.05) as the level of fiber increased and was lower in pigs fed straw or OH than in pigs fed SBP or WHM. The apparent ileal digestibility of GE and DM decreased ( < 0.05) with fiber inclusion, a reduction that was more pronounced ( < 0.05) with straw or SBP than with OH inclusion, with WHM inclusion being intermediate. Fiber inclusion did not affect villous height to crypt depth ratio of the ileum mucosa. The inclusion of 5% of a fiber source increased and counts in the cecum ( < 0.001) but the to ratio was not affected. In Exp. 2 (dirty barn), fiber inclusion did not affect piglet performance but tended to increase PWD ( = 0.07). Also, fiber inclusion reduced ( < 0.05) the ATTD of all dietary components except that of CP, which was not affected. Source and level of fiber did not affect ATTD of nutrients except for DM, which was greater for pigs fed SBP than for pigs fed straw ( < 0.05). In conclusion, in the current research, pigs reared under optimal hygienic conditions had lower incidence of PWD, better growth performance, and greater DM and GE digestibility than pigs reared under poor hygienic conditions. An excess of dietary fiber was more detrimental for all these traits in piglets reared under optimal hygienic conditions. The effects of the source and level of fiber on piglet performance was limited in the 2 experiments.

Lactobacillus rhamnosus GG modulates innate signaling pathway and cytokine responses to rotavirus vaccine in intestinal mononuclear cells of gnotobiotic pigs transplanted with human gut microbiota

Background

A better understanding of mechanisms underlying dose-effects of probiotics in their applications as treatments of intestinal infectious or inflammatory diseases and as vaccine adjuvant is needed. In this study, we evaluated the modulatory effects of Lactobacillus rhamnosus GG (LGG) on transplanted human gut microbiota (HGM) and on small intestinal immune cell signaling pathways in gnotobiotic pigs vaccinated with an oral attenuated human rotavirus (AttHRV) vaccine.

Results

Neonatal HGM transplanted pigs were given two doses of AttHRV on 5 and 15 days of age and were divided into three groups: none-LGG (AttHRV), 9-doses LGG (AttHRV + LGG9X), and 14-doses LGG (AttHRV + LGG14X) (n = 3–4). At post-AttHRV-inoculation day 28, all pigs were euthanized and intestinal contents and ileal tissue and mononuclear cells (MNC) were collected. AttHRV + LGG14X pigs had significantly increased LGG titers in the large intestinal contents and shifted structure of the microbiota as indicated by the formation of a cluster that is separated from the cluster formed by the AttHRV and AttHRV + LGG9X pigs. The increase in LGG titers concurred with significantly increased ileal HRV-specific IFN-γ producing T cell responses to the AttHRV vaccine reported in our previous publication, suggesting pro-Th1 adjuvant effects of the LGG. Both 9- and 14-doses LGG fed pig groups had significantly higher IkBα level and p-p38/p38 ratio, while significantly lower p-ERK/ERK ratio than the AttHRV pigs, suggesting activation of regulatory signals during immune activation. However, 9-doses, but not 14-doses LGG fed pigs had enhanced IL-6, IL-10, TNF-α, TLR9 mRNA levels, and p38 MAPK and ERK expressions in ileal MNC. Increased TLR9 mRNA was in parallel with higher mRNA levels of cytokines, p-NF-kB and higher p-p38/p38 ratio in MNC of the AttHRV + LGG9X pigs.

Conclusions

The relationship between modulation of gut microbiota and regulation of host immunity by different doses of probiotics is complex. LGG exerted divergent dose-dependent effects on the intestinal immune cell signaling pathway responses, with 9-doses LGG being more effective in activating the innate immunostimulating TLR9 signaling pathway than 14-doses in the HGM pigs vaccinated with AttHRV.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-016-0727-2) contains supplementary material, which is available to authorized users.

Impairment of rumen biohydrogenation and bacteria of the Butyrivibrio group in the rumen of goats through a 20:5 n-3 (EPA) rich supplement

BACKGROUND

Marine products can inhibit biohydrogenation in the rumen, but the mechanism is not clear. This study investigated a 20:5 n-3 rich supplement effects on rumen biohydrogenation, microbial change and fermentation characteristics in goats.

RESULTS

The supplementation decreased 18:0 proportions in rumen fatty acids (P < 0.001), while it increased cis-9, trans-11 conjugated linoleic acid (CLA) (P < 0.001) and trans-10, cis-12 CLA proportions (P < 0.001). The supplement reduced the number of Butyrivibrio spp. and B. proteoclasticus (P < 0.01). Denaturing gradient gel electrophoresis redundancy analysis indicated that some species, mainly from the rumen of goats receiving the 2.5 and 5.0 g d(-1) supplement, were positively correlated with cis-9, trans-11 CLA proportions; some species, mainly from the rumen of control goats, were positively correlated with 18:0 proportions. The supplement reduced the NH3 -N concentrations and acetate molar proportions in the rumen (P < 0.05), but increased propionate and butyrate molar proportions (P < 0.01), and had no effect on total volatile fatty acid concentration.

CONCLUSION

The supplement rich in 20:5 n-3 reduced the biohydrogenation of 18-carbon unsaturated fatty acids with a significant reduction of the 18:0 proportion and this was coupled with the suppression of the abundance of biohydrogenating bacteria and unknown bacteria.

Characterization of the Intestinal Lactobacilli Community following Galactooligosaccharides and Polydextrose Supplementation in the Neonatal Piglet

Recently, prebiotic supplementation of infant formula has become common practice; however the impact on the intestinal microbiota has not been completely elucidated. In this study, neonatal piglets were randomized to: formula (FORM, n = 8), formula supplemented with 2 g/L each galactooligosaccharides (GOS) and polydextrose (PDX, F+GP, n = 9) or a sow-reared (SOW, n = 12) reference group for 19 days. The ileal (IL) and ascending colon (AC) microbiota were characterized using culture-dependent and -independent methods. 16S amplicon sequencing identified no differences at the genera level in the IL. Interestingly, six genera in the AC were significantly different between FORM and F+GP (P<0.05): Lactobacillus, Ruminococcus, Parabacteroides, Oscillospira, Hydrogenoanaerobacterium and Catabacter. In particular, the relative abundance of AC Lactobacillus was higher (P = 0.04) in F+GP as compared to FORM. Culture-dependent analysis of the IL and AC lactobacilli communities of FORM and F+GP revealed a Lactobacillus spp. composition similar to 16S amplicon sequencing. Additional analysis demonstrated individual Lactobacillus isolates were unable to ferment PDX. Conversely, a majority of lactobacilli isolates could ferment GOS, regardless of piglet diet. In addition, the ability of lactobacilli isolates to ferment the longer chain GOS fragments (DP 3 or greater), which are expected to be present in the distal intestine, was not different between FORM and F+GP. In conclusion, prebiotic supplementation of formula impacted the AC microbiota; however, direct utilization of GOS or PDX does not lead to an increase in Lactobacillus spp.

Effects of low dietary protein on the metabolites and microbial communities in the caecal digesta of piglets

Thirty-six healthy piglets (weighing 10 ± 1 kg; three animals per pen) were randomly allocated to two treatments: (i) a low protein diet (14% crude protein [CP]) supplemented with lysine, methionine, threonine and tryptophan (Group LP) and (ii) a normal protein diet (20% CP, Group NP), resulting in six replicate pens per treatment. One piglet from each pen was slaughtered at days 10, 25 and 45 of the experiment. For the whole experimental period of 45 d, Group LP had lower feed intake and daily gain and a higher feed-to-gain ratio compared with Group NP. At day 10, no effects on measured caecum metabolites were observed, but at days 25 and 45 in Group LP the concentration of ammonia-N, cadaverine, branched chain fatty acids and acetate were reduced. This was also true for the concentration of short chain fatty acids at day 45. The results of denaturing gradient gel electrophoresis showed that microbial diversity in Group LP was less abundant at day 25, but there was no difference at days 10 and 45. An unweighted pair group mean average analysis showed that the similarities were lower between Groups LP and NP at day 10 and higher at days 25 and 45. Quantitation results indicated that the numbers of Firmicutes and Clostridium cluster IV were lower in Group LP than in Group NP at day 25, but there were no differences at days 10 and 45. In conclusion, the low protein diet markedly reduced the metabolites of protein and carbohydrate fermentation and altered microbial communities in the caecal digesta of piglets.

Changes in Fecal and Colonic Mucosal Microbiota of Patients with Refractory Constipation after a Subtotal Colectomy

The purpose of this study was to investigate the changes in gut microbiota of patients with refractory constipation 6 months after a subtotal colectomy. Feces and mucosal samples of five healthy volunteers and 17 patients with refractory constipation before and six months after subtotal colectomy were collected. Denaturing gradient gel electrophoresis (DGGE) and polymerase chain reaction techniques were used for quantitative analysis of main bacterial groups and archeal methanogens. No significant differences were found in the DGGE profiles among the three groups. After subtotal colectomy, a significantly decreased similarity coefficient was observed in the fecal. The Shannon diversity indices had no significant differences among the three groups. The numbers of predominant bacteria (Bacteriodetes, Clostridium coccoides group, and Clostridium leptum group) did not significantly change in patients before and after surgery compared with healthy control subjects, and the number of total bacteria, Firmicutes, Bacteriodetes, and Clostridium leptum group bacteria in the feces decreased after surgery. However, the numbers of these bacteria remained the same in mucosa from postoperative patients. The numbers of Bifidobacteria and Lactobacilli in feces and the number of Bifidobacteria in mucosa were significantly lower in preoperative compared with healthy control subjects and increased after the surgery. The number of methanogens in the mucosa was decreased in preoperative patients but returned to normal levels postoperatively. In conclusion, although there was no difference in the structure of the predominant bacteria between refractory constipated patients and healthy control subjects, the number of probiotics ( Bifidobacteria and Lactobacilli) was significantly lower in refractory constipated patients. However, subtotal colectomy can significantly normalize the number of intestinal flora.

Dietary Enterococcus faecalis LAB31 improves growth performance, reduces diarrhea, and increases fecal Lactobacillus number of weaned piglets

Lactic acid bacteria (LAB) have been shown to enhance performance of weaned piglets. However, few studies have reported the addition of LAB Enterococcus faecalis as alternatives to growth promoting antibiotics for weaned piglets. This study evaluated the effects of dietary E. faecalis LAB31 on the growth performance, diarrhea incidence, blood parameters, fecal bacterial and Lactobacillus communities in weaned piglets. A total of 360 piglets weaned at 26 ± 2 days of age were randomly allotted to 5 groups (20 pens, with 4 pens for each group) for a trial of 28 days: group N (negative control, without antibiotics or probiotics); group P (Neomycin sulfate, 100 mg/kg feed); groups L, M and H (supplemented with E. faecalis LAB31 0.5×109, 1.0×109, and 2.5×109 CFU/kg feed, respectively). Average daily gain and feed conversion efficiency were found to be higher in group H than in group N, and showed significant differences between group H and group P (P0 < 0.05). Furthermore, groups H and P had a lower diarrhea index than the other three groups (P0 < 0.05). Denaturing gradient gel electrophoresis (DGGE) showed that the application of probiotics to the diet changed the bacterial community, with a higher bacterial diversity in group M than in the other four groups. Real-time PCR revealed that the relative number of Lactobacillus increased by addition of probiotics, and was higher in group H than in group N (P0 < 0.05). However, group-specific PCR-DGGE showed no obvious difference among the five groups in Lactobacillus composition and diversity. Therefore, the dietary addition of E. faecalis LAB31 can improve growth performance, reduce diarrhea, and increase the relative number of Lactobacillus in feces of weaned piglets.

Temporal analysis of the effect of extruded flaxseed on the swine gut microbiota

Flaxseed is a rich source of α-linolenic acid, an essential ω-3 fatty acid reported to have beneficial health effects in humans. Feeding swine a diet supplemented with flaxseed has been found to enrich pork products with ω-3 fatty acids. However, the effect of flaxseed supplementation on the swine gut microbiota has not been assessed to date. The purpose of this study was to investigate if extruded flaxseed has any impact on the bacterial and archaeal microbiota in the feces of growing–finishing pigs over a 51-day period, using denaturing gradient gel electrophoresis (DGGE) and real-time PCR. Bacterial DGGE profile analysis revealed major temporal shifts in the bacterial microbiota with only minor ones related to diet. The archaeal microbiota was significantly less diverse than that of Bacteria. The majority of bacterial DGGE bands sequenced belonged to the Firmicutes phylum while the archaeal DGGE bands were found to consist of only 2 species, Methanobrevibacter smithii and Methanosphaera stadtmanae. The abundance of Bacteroidetes decreased significantly from day 0 to day 21 in all diet groups while the abundance of Firmicutes was relatively stable across all diet cohorts and sampling times. There was also no significant correlation between pig mass and the ratio of Firmicutes to Bacteroidetes. While the addition of extruded flaxseed to the feed of growing–finishing pigs was beneficial for improving ω-3 fatty acid content of pork, it had no detectable impact on the fecal bacterial and archaeal microbiota, suggesting that extruded flaxseed may be used to improve meat quality without adverse effect on the swine gut microbiota or animal performance.

Fermentable non-starch polysaccharides increases the abundance of Bacteroides-Prevotella-Porphyromonas in ileal microbial community of growing pigs

Most plant-origin fiber sources used in pig production contains a mixture of soluble and insoluble non-starch polysaccharides (NSP). The knowledge about effects of these sources of NSP on the gut microbiota and its fermentation products is still scarce. The aim of this study was to investigate effects of feeding diets with native sources of NSP on the ileal and fecal microbial composition and the dietary impact on the concentration of short-chain fatty acids (SCFA) and lactic acid. The experiment comprised four diets and four periods in a change-over design with seven post valve t-cecum cannulated growing pigs. The four diets were balanced to be similar in NSP content and included one of four fiber sources, two diets were rich in pectins, through inclusion of chicory forage (CFO) and sugar beet pulp, and two were rich in arabinoxylan, through inclusion of wheat bran (WB) and grass meal. The gut microbial composition was assessed with terminal restriction fragment (TRF) length polymorphism and the abundance of Lactobacillus spp., Enterobacteriaceae, Bacteroides-Prevotella-Porphyromonas and the β-xylosidase gene, xynB, were assessed with quantitative PCR. The gut microbiota did not cluster based on NSP structure (arabinoxylan or pectin) rather, the effect was to a high degree ingredient specific. In pigs fed diet CFO, three TRFs related to Prevotellaceae together consisted of more than 25% of the fecal microbiota, which is about 3 to 23 times higher (P<0.05) than in pigs fed the other diets. Whereas pigs fed diet WB had about 2 to 22 times higher abundance (P<0.05) of Megasphaera elsdenii in feces and about six times higher abundance (P<0.05) of Lactobacillus reuteri in ileal digesta than pigs fed the other diets. The total amount of digested NSP (r=0.57; P=0.002), xylose (r=0.53; P=0.004) and dietary fiber (r=0.60; P=0.001) in ileal digesta were positively correlated with an increased abundance of Bacteroides-Prevotella-Porphyromonas. The effect on SCFA was correlated to specific neutral sugars where xylose increased the ileal butyric acid proportion, whereas arabinose increased the fecal butyric acid proportion. Moreover, chicory pectin increased the acetic acid proportion in both ileal digesta and feces.

Lactulose increases equol production and improves liver antioxidant status in barrows treated with Daidzein

Equol, one of the intestinal microflora metabolites of daidzein, has gained much attention for having greater bioactivity than its precursor (daidzein and daidzin) and seeming to be promoted by hydrogen gas. The effects of lactulose on the equol-producing capacity and liver antioxidant status of barrows treated with daidzein were investigated in this study. Male castrated piglets (barrows) of Landrace × Duroc, aged 40 days, were randomly divided into the following three groups: control group (C, n = 12, fed an isoflavones-free basic diet), daidzein group (D, n = 12, fed an isoflavones-free basic diet with 50 mg/kg of daidzein supplementation) and daidzein+lactulose group (D+L, n = 12, fed an isoflavones-free basic diet with 1% of lactulose and 50 mg/kg of daidzein supplementation). After 20 days, the profile of short-chain fatty acids in the colon digesta showed that lactulose significantly increased the fermented capacity in the gastrointestinal tract of the barrows. First-void urinary equol concentrations were significantly higher in the D+L group than in the D group (3.13 ± 0.93 compared to 2.11 ± 0.82 μg/ml, respectively). Furthermore, fecal equol levels were also significantly higher in the D+L group than in the D group (12.00 ± 2.68 compared to 10.00 ± 2.26 μg/g, respectively). The population of bacteroidetes and the percentage of bacteroidetes to bacteria in feces were higher in the D+L group than in the D group. The DGGE profiles results indicate that lactulose might shift the pathways of hydrogen utilization, and changing the profiles of SRB in feces. Moreover, the D+L group had weak enhancement of T-SOD and CuZn-SOD activities in the livers of barrows treated with daidzein.

Effect of dietary protein supply originating from soybean meal or casein on the intestinal microbiota of piglets

Dietary composition is a major factor influencing the intestinal microbial ecosystem of pigs. To alleviate weaning-associated disorders, variations in dietary protein supply may beneficially affect microbial composition in the gastrointestinal tract of piglets. A total of 48 piglets, fitted with simple ileal T-cannulas, was used to examine the effect of protein supply of either highly digestible casein or less digestible, fiber-rich soybean meal (SBM) on the composition of the intestinal microbiota. Gene copies of 7 bacteria groups were determined by real-time PCR in ileal digesta and feces. Ileal counts of total eubacteria, the Bacteroides-Prevotella-Porphyromonas group, Enterobacteriaceae and Clostridium Cluster XIVa were higher (P < 0.001) in the casein-based diets. Fecal counts of all analyzed bacterial groups were higher for the SBM-based diets (P < 0.001), apart from Enterobacteriaceae (P < 0.05) which were higher in the casein-based diets. Ileal counts of lactobacilli linearly increased as the crude protein level was increased up to 335 g/kg (P < 0.01). The Bacteroides-Prevotella-Porphyromonas group linearly decreased in ileal samples (P < 0.01) and increased in fecal samples (P < 0.05) as the crude protein level in the SBM-based diet was increased. Both, protein level and protein source may affect intestinal microbial balance. Higher dietary protein levels in combination with diets low in fiber contents might stimulate proliferation of protein fermenting bacteria in piglet's large intestine. Further studies are warranted to clarify, whether this would be associated with intestinal disturbances.

Dietary probiotic supplementation (Shewanella putrefaciens Pdp11) modulates gut microbiota and promotes growth and condition in Senegalese sole larviculture

Probiotic supplementation in fish aquaculture has significantly increased in the last decade due to its beneficial effect on fish performance. Probiotic use at early stages of fish development may contribute to better face metamorphosis and weaning stress. In the present work, we studied the influence of Shewanella putrefaciens Pdp11 supplementation on growth, body composition and gut microbiota in Senegalese sole (Solea senegalensis) during larval and weaning development. S. putrefaciens Pdp11 was incorporated using Artemia as live vector (2.5 × 10⁷ cfu mL⁻¹) and supplied to sole specimens in a co-feeding regime (10-86 DAH) by triplicate. Probiotic addition promoted early metamorphosis and a significantly higher growth in length at 24 DAH larvae. S. putrefaciens Pdp11 also modulated gut microbiota and significantly increased protein content and DHA/EPA ratios in sole fry (90 DAH). This nutritional enhancement is considered especially important after weaning, where significantly higher growth in length and weight was observed in probiotic fish. Moreover, a less heterogeneous fish size in length was detected since metamorphosis till the end of weaning, being of interest for sole aquaculture production. After weaning, fish showed significantly higher growth (length and weight) and less variable lengths in fish when supplemented with probiotics. Both the enhancement of nutritional condition and the decrease in size variability associated with probiotic addition are highly interesting for sole aquaculture production.

Broad diversity and newly cultured bacterial isolates from enrichment of pig feces on complex polysaccharides

One of the fascinating functions of mammalian intestinal microbiota is fermentation of plant cell wall components. Eight-week continuous culture enrichments of pig feces with cellulose and xylan/pectin were used to isolate bacteria from this community. A total of 575 bacterial isolates were classified phylogenetically using 16S rRNA gene sequencing. Six phyla were represented in the bacterial isolates: Firmicutes (242), Bacteroidetes (185), Proteobacteria (65), Fusobacteria (55), Actinobacteria (23), and Synergistetes (5). The majority of the bacterial isolates had ≥ 97 % similarity to cultured bacteria with sequences in the RDP, but 179 isolates represent new species and/or genera. Within the Firmicutes isolates, most were classified in the families of Lachnospiraceae, Enterococcaceae, Staphylococcaceae, and Clostridiaceae I. The majority of the Bacteroidetes were most closely related to Bacteroides thetaiotaomicron, Bacteroides ovatus, and B. xylanisolvens. Many of the Firmicutes and Bacteroidetes isolates were identified as species that possess enzymes that ferment plant cell wall components, and the rest likely support these bacteria. The microbial communities that arose in these enrichment cultures had broad bacterial diversity. With over 30 % of the isolates not represented in culture, there are new opportunities to study genomic and metabolic capacities of these members of the complex intestinal microbiota.

Changes in intestinal morphology and microbiota caused by dietary administration of inulin and Bacillus subtilis in gilthead sea bream (Sparus aurata L.) specimens

Changes produced in gilthead sea bream (Sparus aurata L.) intestinal morphology and microbiota caused by dietary administration of inulin and Bacillus subtilis have been studied. Gilthead sea bream specimens were fed diets containing 0 (control), inulin (10 g kg(-1)), B. subtilis (10(7) cfu g(-1)), or B. subtilis + inulin (10(7) cfu g(-1) + 10 g kg(-1)) for four weeks. Curiously, fish fed the experimental diets (inulin, B. subtilis, or B. subtilis + inulin) showed the same morphological alterations when studied by light and electron microscopy, while significant differences in the signs of intestinal damage were detected by the morphometric study. All of the observed alterations were present only in the gut mucosa, and intestinal morphometric study revealed no effect of inulin or B. subtilis on the intestinal absorptive area. Furthermore, experimental diets cause important alterations in the intestinal microbiota by significantly decreasing bacterial diversity, as demonstrated by the specific richness, Shannon, and range-weighted richness indices. The observed alterations demonstrate that fish fed experimental diets had different signs of gut oedema and inflammation that could compromise their body homeostasis, which is mainly maintained by the epithelial lining of the gastrointestinal tract. To our knowledge, this is the first in vivo study regarding the implications of the use of synbiotics (conjunction of probiotics and prebiotics) on fish gut morphology and microbiota.

Effect of Phytogenic Feed Additives in Soybean Meal on In vitro Swine Fermentation for Odor Reduction and Bacterial Community Comparison

The effect of different phytogenic feed additives on reducing odorous compounds in swine was investigated using in vitro fermentation and analyzed their microbial communities. Soybean meal (1%) added with 0.1% different phytogenic feed additives (FA) were in vitro fermented using swine fecal slurries and anaerobically incubated for 12 and 24 h. The phytogenic FAs used were red ginseng barn powder (Panax ginseng C. A. Meyer, FA1), persimmon leaf powder (Diospyros virginiana L., FA2), ginkgo leaf powder (Ginkgo biloba L., FA3), and oregano lippia seed oil extract (Lippia graveolens Kunth, OL, FA4). Total gas production, pH, ammonia-nitrogen (NH₃-N), hydrogen sulfide (H₂S), nitrite-nitrogen (NO₂⁻-N), nitrate-nitrogen (NO₃⁻-N), sulfate (SO₄⁻⁻), volatile fatty acids (VFA) and other metabolites concentration were determined. Microbial communities were also analyzed using 16S rRNA DGGE. Results showed that the pH values on all treatments increased as incubation time became longer except for FA4 where it decreased. Moreover, FA4 incubated for 12 and 24 h was not detected in NH₃-N and H₂S. Addition of FAs decreased (p<0.05) propionate production but increased (p<0.05) the total VFA production. Ten 16S rRNA DGGE bands were identified which ranged from 96 to 100% identity which were mostly isolated from the intestine. Similarity index showed three clearly different clusters: I (FA2 and FA3), II (Con and FA1), and III (FA4). Dominant bands which were identified closest to Eubacterium limosum (ATCC 8486T), Uncultured bacterium clone PF6641 and Streptococcus lutetiensis (CIP 106849T) were present only in the FA4 treatment group and were not found in other groups. FA4 had a different bacterial diversity compared to control and other treatments and thus explains having lowest odorous compounds. Addition of FA4 to an enriched protein feed source for growing swine may effectively reduce odorous compounds which are typically associated with swine production.

Stabilized rice bran improves weaning pig performance via a prebiotic mechanism

Stabilized rice bran (SRB) is classified as a "functional food" because of its prebiotic characteristics. With increasing grain prices and the pressure to remove antibiotics from swine diets because of concern over antibiotic resistance, SRB was investigated as a nursery diet ingredient with and without the addition of antibiotics (ANT). Two hundred pigs were weaned at 21 d of age, blocked by BW, and allotted to diets containing 0 or 10% SRB ± ANT according to a 2 × 2 factorial arrangement of treatments. Five animals were housed per pen throughout a 28-d growth period. At the end of the trial, 1 pig from each pen was euthanized for measurement of intestinal morphology. Antibiotic supplementation improved ADG by 6.4% during Phase 2 (d 14 to 28; P = 0.02), but other production variables were unaffected by ANT. During Phase 2 and cumulatively (d 0 to 28), the supplementation of SRB improved G:F by 10% in ANT-free pigs but not in pigs fed ANT (ANT × SRB, P < 0.03). Ileal histology revealed an increase in crypt depth of pigs fed the diet containing ANT plus SRB and corresponding decreases in villi:crypt associated with both ANT and SRB supplementation (P < 0.05). Intraepithelial lymphocytes were increased by 15% in pigs fed SRB without ANT, but were unaffected by SRB in pigs fed ANT (ANT x SRB, P = 0.003). Colonic bifidobacteria tended to increase with SRB supplementation (P < 0.10). Differences in ileal and cecal digesta short-chain fatty acid concentrations were not detected. In summary, SRB improved the efficiency of nutrient utilization in nursery diets lacking antibiotics and tended to increase intestinal bifidobacteria concentrations, indicating that SRB may exert beneficial prebiotic effects in weanling pigs.

Histological alterations and microbial ecology of the intestine in gilthead seabream (Sparus aurata L.) fed dietary probiotics and microalgae

The effects on histology and microbial ecology in gilthead seabream (Sparus aurata) intestine caused by dietary probiotic and microalgae were studied. Fish were fed non-supplemented (C, control) or supplemented diets with Tetraselmis chuii, Phaeodactylum tricornutum and Bacillus subtilis single or combined (diets T, P, B, BT and BP) for 4 weeks. Curiously, fish fed the experimental diets showed similar morphological alterations when studied by light and electron microscopy and significant signs of intestinal damage were detected. No effect of microalgae or B. subtilis on the intestinal absorptive area was observed, whereas the number of goblet cells and IELs were significantly lower in fish fed the T, P, B and BT diets and T, BT and BP diets, respectively. Interestingly, only the diets containing B. subtilis resulted in a significant reduction of microvilli height. Alterations such as wide intercellular spaces and large vacuoles in enterocytes were observed in fish fed T, B, BT, BT and P in lesser degrees. These observations demonstrate that fish fed experimental diets presented different signs of oedema and inflammation that could compromise their body homeostasis. Moreover, the experimental diets cause important alterations in the intestinal microbiota by a significant decrease in bacterial diversity, as demonstrated by the fall in specific richness, Shannon and range-weighted richness indices. To our knowledge, this is the first in vivo study regarding the implications of the use of probiotics in combination with immunostimulants on fish intestinal morphology and microbiota. More morphofunctional studies are needed in order to correlate the nutritional and immune aspects of fish gut.