Mucosa-associated bacterial microbiome of the gastrointestinal tract of weaned pigs and dynamics linked to dietary calcium-phosphorus

Calcium deposition in chicken eggshells: role of host genetics and gut microbiota

Eggshell is predominantly composed of calcium carbonate, making up about 95% of its composition. Eggshell quality is closely related to the amount of calcium deposition in the shell, which requires chickens to maintain a robust state of calcium metabolism. In this study, we introduced a novel parameter, Total Eggshell Weight (TESW), which measures the total weight of eggshells produced by chickens over a period of 10 consecutive d, providing valuable information on the intensity of calcium metabolism in chickens. Genome-wide association study (GWAS) was conducted to explore the genetic determinants of eggshell calcification in a population of 570 Rhode Island Red laying hens at 90 wk of age. This study revealed a significant association between a specific SNP (rs14249431) and TESW. Additionally, using random forest modeling and 2-tailed testing, we identified 3 genera, Lactobacillus in the jejunum, Lactobacillus, and Fournierella in the cecum, that exhibited a significant association with TESW. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis of claudin-1 and occludin genes in individuals with low TESW and high abundance of jejunal Lactobacillus confirmed that the inhibitory effect of jejunal Lactobacillus on calcium uptake was achieved through the up-regulation of tight junctions in intestinal epithelial cells. Notably, both host and microbial factors influence TESW, displaying a mutually influential relationship between them. The microbiome-wide Genome-Wide Association Study (mb-GWAS) identified significant associations between these 3 genera and specific genomic variants, such as rs316115020 and rs316420452 on chromosome 5, rs313198529 on chromosome 11, linked to Lactobacillus in the cecum. Moreover, rs312552529 on chromosome 1 exhibited potential association with Fournierella in the cecum. This study highlights the influence of host genetics and gut microbiota on calcium deposition in eggshells during the late laying phase, providing a foundational reference for studying calcium metabolism in hens.

Effects of supplemental bacteriophage on the gut microbiota and nutrient digestibility of ileal-cannulated pigs

This study measured the potential changes of the microbiota in the gastrointestinal tract and energy and nutrient digestibility by supplemental bacteriophages in pigs. Twelve castrated male pigs (initial mean body weight = 29.5 ± 2.3 kg) were surgically cannulated using T-cannula. The animals were housed individually in pens equipped with a feeder and a nipple waterer. The pigs were allotted to 1 of 3 experimental diets in a quadruplicated 3 × 2 Latin square design with 3 experimental diets, 2 periods, and 12 pigs resulting in 8 replicates per diet. The 3 diets were a control mainly based on corn and soybean meal with no antibiotics or bacteriophages, a diet containing 0.1% antibiotics, and a diet containing 0.2% bacteriophages. On day 5 of the experimental period, feces were collected and on days 6 and 7, ileal digesta were collected. Genomic DNA for bacteria were extracted from the ileal digesta and feces and the V4 region of the 16S rRNA gene was amplified. The ileal and fecal digestibility of energy, dry matter, organic matter, crude protein, and fiber was unaffected by dietary antibiotics or bacteriophages. At the phylum level, the supplemental antibiotic or bacteriophage tended to result in a higher proportion of Firmicutes (p = 0.059) and a lower proportion of Bacteroidetes (p = 0.099) in the ileal digesta samples compared with the control group with no difference between the antibiotic and bacteriophage groups. At the genus level, the supplemental antibiotic or bacteriophage tended to result in a higher proportion of Lactobacillus (p = 0.062) and a lower proportion of Bacteroides (p = 0.074) and Streptococcus (p = 0.088) in the ileal digesta compared with the control group with no difference between the antibiotic and bacteriophage groups. In the feces, supplemental antibiotics or bacteriophages reduced the proportion of Bifidobacterium compared with the control group (p = 0.029) with no difference between the antibiotic and bacteriophage groups. Overall, supplemental antibiotics and bacteriophages showed positive effect on the microbiota of in the ileal digesta without largely affecting energy or nutrient digestibility, with no differences between the antibiotic and bacteriophage groups in growing pigs.

An insight into the temporal dynamics in the gut microbiome, metabolite signaling, immune response, and barrier function in suckling and weaned piglets under production conditions

Little information is available on age- and creep-feeding-related microbial and immune development in neonatal piglets. Therefore, we explored age- and gut-site-specific alterations in the microbiome, metabolites, histo-morphology, and expression of genes for microbial signaling, as well as immune and barrier function in suckling and newly weaned piglets that were receiving sow milk only or were additionally offered creep feed from day of life (DoL) 10. The experiment was conducted in two replicate batches. Creep feed intake was estimated at the litter level. Piglets were weaned on day 28 of life. Gastric and cecal digesta and jejunal and cecal tissue were collected on DoL 7, 14, 21, 28, 31, and 35 for microbial and metabolite composition, histomorphology, and gene expression. In total, results for 10 piglets (n = 5/sex) per dietary group (sow milk only versus additional creep feed) were obtained for each DoL. The creep feed intake was low at the beginning and only increased in the fourth week of life. Piglets that were fed creep feed had less lactate and acetate in gastric digesta on DoL 28 compared to piglets fed sow milk only (p < 0.05). Age mainly influenced the gastric and cecal bacteriome and cecal mycobiome composition during the suckling phase, whereas the effect of creep feeding was small. Weaning largely altered the microbial communities. For instance, it reduced gastric Lactobacillaceae and cecal Bacteroidaceae abundances and lowered lactate and short-chain fatty acid concentrations on DoL 31 (p < 0.05). Jejunal and cecal expression of genes related to microbial and metabolite signaling, and innate immunity showed age-related patterns that were highest on DoL 7 and declined until DoL 35 (p < 0.05). Weaning impaired barrier function and enhanced antimicrobial secretion by lowering the expression of tight junction proteins and stimulating goblet cell recruitment in the jejunum and cecum (p < 0.05). Results indicated that age-dependent alterations, programmed genetically and by the continuously changing gut microbiome, had a strong impact on the expression of genes for gut barrier function, integrity, innate immunity, and SCFA signaling, whereas creep feeding had little influence on the microbial and host response dynamics at the investigated gut sites.

Composition of mucus- and digesta-associated bacteria in growing pigs with and without diarrhea differed according to the presence of colonic inflammation

BACKGROUND

In the pig production, diarrhea can occur during different growth stages including the period 4-16 weeks post weaning, during which a diarrheal outbreak also termed as colitis-complex diarrhea (CCD) can occur and it is distinct from post-weaning diarrhea (1-2 weeks post weaning). We hypothesized that CCD in growing pigs is associated with changes in colonic microbiota composition and fermentation patterns, and the aim of the present observational study was to identify changes in digesta-associated bacteria (DAB) and mucus-associated bacteria (MAB) in the colon of growing pigs with and without diarrhea. A total number of 30 pigs (8, 11, and 12 weeks of age) were selected; 20 showed clinical signs of diarrhea and 10 appeared healthy. Based on histopathological examination of colonic tissues, 21 pigs were selected for further studies and classified as follows: without diarrhea, no colon inflammation (NoDiar; n = 5), with diarrhea, without colonic inflammation (DiarNoInfl; n = 4), and with diarrhea, with colonic inflammation (DiarInfl; n = 12). Composition (based on 16S rRNA gene amplicon sequencing) and fermentation pattern (short-chain fatty acids; SCFA profile) of the DAB and MAB communities were characterized.

RESULTS

The DAB showed higher alpha diversity compared to MAB in all pigs, and both DAB and MAB showed lowest alpha diversity in the DiarNoInfl group. Beta diversity was significantly different between DAB and MAB as well as between diarrheal groups in both DAB and MAB. Compared to NoDiar, DiarInfl showed increased abundance of various taxa, incl. certain pathogens, in both digesta and mucus, as well as decreased digesta butyrate concentration. However, DiarNoInfl showed reduced abundance of different genera (mainly Firmicutes) compared to NoDiar, but still lower butyrate concentration.

CONCLUSION

Diversity and composition of MAB and DAB changed in diarrheal groups depending on presence/absence of colonic inflammation. We also suggest that DiarNoInfl group was at the earlier stage of diarrhea compared with DiarInfl, with a link to dysbiosis of colonic bacterial composition as well as reduced butyrate concentration, which plays a pivotal role in gut health. This could have led to diarrhea with inflammation due to a dysbiosis, associated with an increase in e.g., Escherichia-Shigella (Proteobacteria), Helicobacter (Campylobacterota), and Bifidobacterium (Actinobacteriota), which may tolerate or utilize oxygen and cause epithelial hypoxia and inflammation. The increased consumption of oxygen in epithelial mucosal layer by infiltrated neutrophils may also have added up to this hypoxia. Overall, the results confirmed that changes in DAB and MAB were associated with CCD and reduced butyrate concentration in digesta. Moreover, DAB might suffice for future community-based studies of CCD.

Lactic acid bacteria biofilms and their antimicrobial potential against pathogenic microorganisms

The continuous growth of pathogenic microorganisms and associated biofilms poses severe public health challenges, particularly in food and clinical environments. However, these difficulties have enabled scientists to develop novel and safe methods for combating pathogens. The use of biofilms produced by lactic acid bacteria (LAB) against pathogenic bacteria has recently gained popularity. This review provides an in-depth look at LAB biofilms, their distribution, and mechanisms of action against pathogenic bacteria. More importantly, the bioactive substances produced by LAB-forming biofilm may be active against undesirable microorganisms and their products, which is of great interest in improving human health. Therefore, this review implies that a combination of LAB biofilms and other LAB products like bacteriocins could provide viable alternatives to traditional methods of combating pathogenic microorganisms and their biofilms.

Efficacy of a bacterial 6-phytase supplemented beyond traditional dose levels on jejunal mucosa-associated microbiota, ileal nutrient digestibility, bone parameters, and intestinal health, and growth performance of nursery pigs

This study aimed to determine the efficacy of a bacterial 6-phytase (Buttiauxella spp.) supplemented beyond traditional dose levels based on jejunal mucosa-associated microbiota, apparent ileal digestibility (AID), intestinal health and bone parameters, and growth performance of nursery pigs. Seventy-two weaned pigs (36 barrows and 36 gilts at 21 d of age with 5.8 ± 0.5 kg BW) were allotted to six treatments based on randomized complete block design with sex and initial BW as blocks and fed in three dietary phases (phase 1 for 14 d, phase 2 for 10 d, and phase 3 for 14 d). The treatments included a negative control (NC) diet without phytase formulated meeting nutrient requirements by NRC and the other five treatments were deficient in calcium (Ca) and phosphorus (P) by 0.12% with increasing levels of a bacterial 6-phytase (0, 500, 1,000, 2,000, and 5,000 FTU/kg feed). Titanium dioxide (0.4%) was added to phase 3 diets as an indigestible marker to measure AID of nutrients. On day 45, all pigs were euthanized to collect ileal digesta to measure AID, the third metacarpus to measure bone parameters, and jejunal mucosa to evaluate intestinal health and microbiota. Data were analyzed using the MIXED procedure for polynomial contrasts and the NLMIXED procedure for broken line analysis using the SAS 9.4. Broken line analysis demonstrated that 948 FTU/kg feed increased (P < 0.05) the ADG and the bone P content. Increasing phytase supplementation increased (linear, P < 0.05) AID of CP, bone P, and ash content. Increasing phytase supplementation reduced (P < 0.05) the fecal score during phases 2 and 3. Broken line analysis demonstrated that 1,889 FTU/kg feed increased (P < 0.05) bone breaking strength. Increasing phytase supplementation (PC vs. Phy) increased (P < 0.05) AID of ether extract (EE) and P. The supplementation of phytase at 2,000 FTU/kg feed tended (P = 0.087) to reduce the relative abundance of Prevotellaceae. In conclusion, the supplementation of a bacterial 6-phytase beyond traditional dose levels improved bone breaking strength, bone ash, and P content, AID of CP, EE, and P, and growth performance of nursery pigs with reduced relative abundance of Bacteroidetes specifically Prevotellaceae in the jejunal mucosa. Supplementation of a bacterial 6-phytase between 1,000 and 2,000 FTU/kg feed provided benefits associated with growth performance and bone parameters of nursery pigs.

Soluble corn fiber, resistant corn starch, and protected butyrate effects on performance, gastrointestinal volatile fatty acids, and apparent total-tract digestibility of calcium and phosphorus in nursery pigs

An experiment was conducted to determine how feeding calcium (Ca)-deficient diet would affect gastrointestinal pH and volatile fatty acids (VFAs), Ca digestibility, bone mineral density (BMD), and performance in nursery pigs; and if supplementation of nondigestible oligosaccharides would affect these same parameters. In total, 240 weaned pigs (BW = 7.1 kg) were placed into 80 pens with 3 pigs/pen. The eight dietary treatments consisted of: 1) positive control (PC, 0.83% total Ca), 2) negative control (NC, 0.50% total Ca), 3 and 4) NC + 5% or 7.5% soluble corn fiber (SCF), 5 and 6) NC + 5% or 7.5% resistant corn starch (rCS), 7 and 8) NC + 0.25% or 0.50% fat-protected butyrate (pBRT). Pigs were ad libitum fed the dietary treatments for 21 d to determine average daily gain (ADG), average daily feed intake (ADFI) and gain:feed ratio (GF) with a fecal sample collected from each pen to determine Ca digestibility using acid insoluble ash as the dietary marker, with 1 pig/pen euthanized on d 21 for collection of ileal and colon contents and the left humerus. Pigs fed the NC diet had a lower colonic pH compared with pigs fed the PC (P = 0.06) but no effect on total VFA was observed (P > 0.10). Pigs fed diets containing SCF and rCS had lower colonic pH and total VFA compared to pigs fed the NC diet (P ≤ 0.05). Pigs fed diets containing pBRT had greater colonic total VFA compared to pigs fed the NC diet (P ≤ 0.07), but no difference in colonic pH was observed (P > 0.10). Pigs fed the NC diet had a greater Ca digestibility compared to pigs fed the PC (P ≤ 0.01), with no treatment to the NC having any effect on Ca digestibility compared to pigs fed the NC (P > 0.10). There was no effect of dietary Ca level on BMD and no overall addition of feeding SCF, rCS, or pBRT on BMD compared to pigs fed the NC (P > 0.10). There was no impact on pig ADG, ADFI, or GF by reducing dietary Ca by 40% (i.e., pigs fed the NC) compared to pigs fed the PC (P > 0.10). Relative to pigs fed the NC, there was no overall effect of SCF, rCS, or pBRT on ADG, ADFI, or GF (P > 0.10). In conclusion, feeding young pigs a Ca-deficient diet reduced colonic pH, increased digestibility of Ca, but had no impact on bone mineralization or overall pig performance. Supplementation of nondigestible oligosaccharides pr protected butyrate had either no effect or an inconsistent effect on colonic pH, Ca, or PHOS digestibility, bone mineralization, or overall pig performance.

Gut Microbiome Studies in Livestock: Achievements, Challenges, and Perspectives

The variety and makeup of the gut microbiome are frequently regarded as the primary determinants of health and production performances in domestic animals. High-throughput DNA/RNA sequencing techniques (NGS) have recently gained popularity and permitted previously unheard-of advancements in the study of gut microbiota, particularly for determining the taxonomic composition of such complex communities. Here, we summarize the existing body of knowledge on livestock gut microbiome, discuss the state-of-the-art in sequencing techniques, and offer predictions for next research. We found that the enormous volumes of available data are biased toward a small number of globally distributed and carefully chosen varieties, while local breeds (or populations) are frequently overlooked despite their demonstrated resistance to harsh environmental circumstances. Furthermore, the bulk of this research has mostly focused on bacteria, whereas other microbial components such as protists, fungi, and viruses have received far less attention. The majority of these data were gathered utilizing traditional metabarcoding techniques that taxonomically identify the gut microbiota by analyzing small portions of their genome (less than 1000 base pairs). However, to extend the coverage of microbial genomes for a more precise and thorough characterization of microbial communities, a variety of increasingly practical and economical shotgun techniques are currently available.

Linkages of Various Calcium Sources on Immune Performance, Diarrhea Rate, Intestinal Barrier, and Post-gut Microbial Structure and Function in Piglets

The purpose of this experiment was to investigate the effects of different sources of calcium on immune performance, diarrhea rate, intestinal barrier, and post-intestinal flora structure and function in weaned piglets. A total of 1,000 weaned piglets were randomly assigned to five groups 10 replicate pens per treatment, 20 piglets per pen and fed calcium carbonate, calcium citrate, multiple calcium, and organic trace minerals of different concentrations of acidifier diets. The results of the study showed that the replacement of calcium carbonate with calcium citrate and multiple calcium had almost no significant effect on immune indexes (IL-1β, IL-6, IL-10, TNF-α) of piglets compared with the control group (p > 0.05). The five groups did not show a change in the diarrhea rate and diarrhea index (p > 0.05). The diet containing multiple calcium dramatically decreased the TP compared to the C and L diet (p < 0.05). No significant difference in HDL was noted in the five groups (p > 0.05). However, the concentration of LDL in blood in the multiple calcium group was significantly higher than that in groups L and D (p < 0.05). Moreover, the concentration of Glu in blood in the multiple calcium group was significantly higher than that in group C (p < 0.05). Compared with the control group, calcium citrate plus organic trace minerals diet markedly increased UCG-005 abundance in the colon (p < 0.05). In addition, the relative abundance of Prevotellaceae_NK3B31_group had an upward trend in the colon of the M group compared to the D group (p = 0.070). Meanwhile, calcium citrate plus organic trace minerals diet markedly increased Clostridium_sensu_stricto_1 abundance in the colon (p < 0.05). Metagenomic predictions by PICRUSt suggested that the colonic and fecal microbiota was mainly involved in carbohydrate metabolism, amino acid metabolism, energy metabolism, and metabolism of cofactors and vitamins.

Effects of Different Sources of Calcium in the Diet on Growth Performance, Blood Metabolic Parameters, and Intestinal Bacterial Community and Function of Weaned Piglets

Despite a well-documented effect of calcium on the piglet's intestinal microbiota composition, it is less known about changes in microbial function or the effect of different sources of calcium. The experiment was designed to study the effects of dietary calcium from different sources on production, immune indexes, antioxidant capacity, serum biochemical indexes, and intestinal microflora of weaning piglets. A total of 1,000 piglets were randomly assigned to five groups (10 replicate pens per treatment with 20 pigs per pen) and fed diets supplemented with calcium carbonate, calcium citrate, multiple calcium, organic trace minerals, and different concentrations of acidifier. The results showed that the replacement of calcium carbonate with calcium citrate and multiple calcium had almost no significant difference in the growth performance of pigs compared with the control group, and only the diet of multiple calcium dramatically decreased the average daily feed intake (ADFI) compared to the calcium citrate diet on days 15-28 (p < 0.05). The five groups did not change the content of MDA, SOD, and GSH-Px (p > 0.10). A similar situation occurs in the immune function of the blood. There was no significant effect in immune indexes (IgA, IgG, and IgM) among different treatments after weaning at 6 weeks for piglets (p > 0.10). The 16S rRNA sequencing of ileal and cecal microbiota revealed that only the relative abundance of Actinobacteriota at the phyla level was significantly greater in the ileum of the A group compared to the other treatments (p < 0.05). There was a clear effect on seven bacteria in the top 30 genera of ileum and cecum for five groups (p < 0.05). The result of PICRUSt predicted that the intestinal microbe was mainly involved in carbohydrate and amino acid metabolism, membrane transport, and metabolism of cofactors and vitamins. Besides, adding calcium citrate to a weaned piglet diet is better than other choices from the third week to the fourth week. In conclusion, diets with different calcium sources changed ADFI and some intestinal microbial composition of weaned piglets but had little effect on intestinal microbial function.

Growth performance, bone mineralization, nutrient digestibility, and fecal microbial composition of multi-enzyme-supplemented low-nutrient diets for growing-finishing pigs

A study evaluated the effects of adding multi-enzyme mixture to diets deficient in net energy (NE), standardized ileal digestible (SID) amino acids (AA), standardized total tract digestible (STTD) P, and Ca on growth performance, bone mineralization, nutrient digestibility, and fecal microbial composition of grow-finish pigs. A total of 300 pigs (initial body weight [BW] = 29.2 kg) were housed by sex and BW in 45 pens of 7 or 6 pigs and fed 5 diets in a randomized complete block design. Diets were positive control (PC), and negative control 1 (NC1) or negative control 2 (NC2) without or with multi-enzyme mixture. The multi-enzyme mixture supplied at least 1,800, 1,244, 6,600, and 1,000 units of xylanase, β -glucanase, arabinofuranosidase, and phytase per kilogram of diet, respectively. The PC was adequate in all nutrients. The NC1 diet had lower content NE, SID AA, STTD P, and Ca than PC diet by about 7%, 7%, 32%, and 13%, respectively. The NC2 diet had lower NE, SID AA, STTD P, and Ca than PC diet by 7%, 7%, 50%, and 22%, respectively. The diets were fed in four phases based on BW: Phase 1: 29-45 kg, Phase 2: 45-70 kg, Phase 3: 70-90 kg, and Phase 4: 90-120 kg. Nutrient digestibility, bone mineralization, and fecal microbial composition were determined at the end of Phase 1. Pigs fed PC diet had greater (P < 0.05) overall G:F than those fed NC1 diet or NC2 diet. Multi-enzyme mixture increased (P < 0.05) overall G:F, but the G:F of the multi-enzyme mixture-supplemented diets did not reach (P < 0.05) that of PC diet. Multi-enzyme mixture tended to increase (P = 0.08) femur breaking strength. Multi-enzyme mixture increased (P < 0.05) the ATTD of GE for the NC2 diet, but unaffected the ATTD of GE for the NC1 diet. Multi-enzyme mixture decreased (P < 0.05) the relative abundance of the Cyanobacteria and increased (P < 0.05) relative abundance of Butyricicoccus in feces. Thus, the NE, SID AA, STTD P, and Ca could be lowered by about 7%, 7%, 49%, and 22%, respectively, in multi-enzyme mixture-supplemented diets without negative effects on bone mineralization of grow-finish pigs. However, multi-enzyme mixture supplementation may not fully restore G:F of the grow-finish pigs fed diets that have lower NE and SID AA contents than recommended by 7%. Since an increase in content of Butyricicoccus in intestine is associated with improved gut health, addition of the multi-enzyme mixture in diets for pigs can additionally improve their gut health.

Assessing the Impact of Diet on the Mucosa-Adhered Microbiome in Piglets Using Comparative Analysis of Rectal Swabs and Colon Content

Previously, we demonstrated that rectal swabs provide a legitimate alternative to faecal sampling for the assessment of the intestinal microbiota in young piglets. However, we also reported that mucosa-adhered microbial populations were more represented in rectal swabs compared to faecal samples, albeit to a degree that varied per swab-sample. Here, we explored the possibility to exploit this variable enrichment of adhered populations in the rectal swabs to assess the impact of diet on mucosa-adhered microbiota in pre-weaning piglets. Paired samples of rectal swabs and colon luminal contents were collected from piglets just before weaning during two independent but similarly designed animal experiments [n = 28 piglets (experiment 1); n = 16 piglets (experiment 2)], with an early feeding treatment (EF) group that had access to customised fibrous feed in addition to sow's milk and a control (CON) group exclusively reared on sow's milk. The intestinal microbiome composition in rectal swabs and colon samples collected at 29 days of age were subjected to metataxonomic analysis. The results identified the genera Escherichia-Shigella, Anaerococcus, Peptostreptococcus, Enterococcus, Trueperella, Actinomyces, and Peptoniphilus as discriminative taxa enriched in rectal swabs compared to colon. Apart from Escherichia-Shigella (10-11% average relative abundance), most of these mucosa-adhered microbial genera display relatively low abundance. Rectal swab microbiota was found to be more variable, which is likely due to variable enrichment of mucosa-adhered microbes. Although almost exclusively driven by one of the experiments, the post-weaning diarrhoea-associated taxa Escherichia-Shigella, was enriched in CON compared to the EF group, suggesting that early life feeding may suppress post-weaning-diarrhoea-related problems in piglets. Our findings demonstrate that rectal swabs allow the investigation of the mucosa-adhered microbial populations as a function of dietary treatment in piglets. This offers opportunities to further study dietary approaches that suppress the abundance of the post-weaning diarrhoea associated adherent microbes like Escherichia-Shigella. Furthermore, we demonstrate that the paired swab-colon microbiota information (obtained from a subset of animals) can predict the mucosa-adhered populations or "mucosity factor" in rectal swab samples, facilitating the analysis of the adhered microbiota in large animal cohort studies using readily obtainable rectal swabs.

Intestinal microbiota and its interaction to intestinal health in nursery pigs

The intestinal microbiota has gained increased attention from researchers within the swine industry due to its role in promoting intestinal maturation, immune system modulation, and consequently the enhancement of the health and growth performance of the host. This review aimed to provide updated scientific information on the interaction among intestinal microbiota, dietary components, and intestinal health of pigs. The small intestine is a key site to evaluate the interaction of the microbiota, diet, and host because it is the main site for digestion and absorption of nutrients and plays an important role within the immune system. The diet and its associated components such as feed additives are the main factors affecting the microbial composition and is central in stimulating a beneficial population of microbiota. The microbiota–host interaction modulates the immune system, and, concurrently, the immune system helps to modulate the microbiota composition. The direct interaction between the microbiota and the host is an indication that the mucosa-associated microbiota can be more effective in evaluating its effect on health parameters. It was demonstrated that the mucosa-associated microbiota should be evaluated when analyzing the interaction among diets, microbiota, and health. In addition, supplementation of feed additives aimed to promote the intestinal health of pigs should consider their roles in the modulation of mucosa-associated microbiota as biomarkers to predict the response of growth performance to dietary interventions.

Influenza A H1N1 Induced Disturbance of the Respiratory and Fecal Microbiome of German Landrace Pigs - a Multi-Omics Characterization

Seasonal influenza outbreaks represent a large burden for the health care system as well as the economy. While the role of the microbiome has been elucidated in the context of various diseases, the impact of respiratory viral infections on the human microbiome is largely unknown. In this study, swine was used as an animal model to characterize the temporal dynamics of the respiratory and gastrointestinal microbiome in response to an influenza A virus (IAV) infection. A multi-omics approach was applied on fecal samples to identify alterations in microbiome composition and function during IAV infection. We observed significantly altered microbial richness and diversity in the gastrointestinal microbiome after IAV infection. In particular, increased abundances of Prevotellaceae were detected, while Clostridiaceae and Lachnospiraceae decreased. Moreover, our metaproteomics data indicated that the functional composition of the microbiome was heavily affected by the influenza infection. For instance, we identified decreased amounts of flagellin, correlating with reduced abundances of Lachnospiraceae and Clostridiaceae, possibly indicating involvement of a direct immune response toward flagellated Clostridia during IAV infection. Furthermore, enzymes involved in short-chain fatty acid (SCFA) synthesis were identified in higher abundances, while metabolome analyses revealed rather stable concentrations of SCFAs. In addition, 16S rRNA gene sequencing was used to characterize effects on the composition and natural development of the upper respiratory tract microbiome. Our results showed that IAV infection resulted in significant changes in the abundance of Moraxellaceae and Pasteurellaceae in the upper respiratory tract. Surprisingly, temporal development of the respiratory microbiome structure was not affected. IMPORTANCE Here, we used swine as a biomedical model to elucidate the impact of influenza A H1N1 infection on structure and function of the respiratory and gastrointestinal tract microbiome by employing a multi-omics analytical approach. To our knowledge, this is the first study to investigate the temporal development of the porcine microbiome and to provide insights into the functional capacity of the gastrointestinal microbiome during influenza A virus infection.

The Role of Dietary and Microbial Fatty Acids in the Control of Inflammation in Neonatal Piglets

Simple Summary

The maturation of the gut is a specific and very dynamic process in new-born piglets. Consequently, piglet’s gut is very susceptible to disturbances, especially in stressful periods of life, such as weaning, when the gut lining often becomes inflamed and leaky. Dietary fatty acids (FA) do not only serve as source of energy and essential FA, but they are important precursors for bioactive lipid mediators, which modulate inflammatory signalling in the body. The current review summarizes results on dietary sources of FA for piglets, the signalling cascades, bioactivities, the necessity to consider the autoxidation potential of polyunsaturated FA and the area of microbially produced long-chain FA. That said, porcine milk is high in fat, whereby the milk FA composition partly depends on the dietary FA composition of the sow. Therefore, manipulation of the sow diet is an efficient tool to increase the piglet’s intake of specific FA, e.g., n-3 polyunsaturated FA which show anti-inflammatory activity and may support intestinal integrity and functioning in the growing animal.

Abstract

Excessive inflammation and a reduced gut mucosal barrier are major causes for gut dysfunction in piglets. The fatty acid (FA) composition of the membrane lipids is crucial for mediating inflammatory signalling and is largely determined by their dietary intake. Porcine colostrum and milk are the major sources of fat in neonatal piglets. Both are rich in fat, demonstrating the dependence of the young metabolism from fat and providing the young organism with the optimum profile of lipids for growth and development. The manipulation of sow’s dietary polyunsaturated FA (PUFA) intake has been shown to be an efficient strategy to increase the transfer of specific FAs to the piglet for incorporation in enteric tissues and cell membranes. n-3 PUFAs, especially seems to be beneficial for the immune response and gut epithelial barrier function, supporting the piglet’s enteric defences in situations of increased stress such as weaning. Little is known about microbial lipid mediators and their role in gut barrier function and inhibition of inflammation in neonatal piglets. The present review summarizes the current knowledge of lipid nutrition in new-born piglets, comparing the FA ingestion from milk and plant-based lipid sources and touching the areas of host lipid signalling, inflammatory signalling and microbially derived FAs.

Galacto-oligosaccharides improve barrier function and relieve colonic inflammation via modulating mucosa-associated microbiota composition in lipopolysaccharides-challenged piglets

BACKGROUND

Galacto-oligosaccharides (GOS) have been shown to modulate the intestinal microbiota of suckling piglets to exert beneficial effects on intestinal function. However, the modulation of intestinal microbiota and intestinal function by GOS in intestinal inflammation injury models has rarely been reported. In this study, we investigated the effects of GOS on the colonic mucosal microbiota composition, barrier function and inflammatory response of lipopolysaccharides (LPS)-challenged suckling piglets.

METHODS

A total of 18 newborn suckling piglets were divided into three groups, the CON group, the LPS-CON group and the LPS-GOS group. Piglets in the LPS-GOS group were orally fed with 1 g/kg body weight of GOS solution every day. On the d 14, piglets in the LPS-CON and LPS-GOS group were challenged intraperitoneally with LPS solution. All piglets were slaughtered 2 h after intraperitoneal injection and sampled.

RESULTS

We found that the colonic mucosa of LPS-challenged piglets was significantly injured and shedding, while the colonic mucosa of the LPS-GOS group piglets maintained its structure. Moreover, GOS significantly reduced the concentration of malondialdehyde (MDA) and the activity of reactive oxygen species (ROS) in the LPS-challenged suckling piglets, and significantly increased the activity of total antioxidant capacity (T-AOC). GOS significantly increased the relative abundance of norank_f__Muribaculaceae and Romboutsia, and significantly decreased the relative abundance of Alloprevotella, Campylobacter and Helicobacter in the colonic mucosa of LPS-challenged suckling piglets. In addition, GOS increased the concentrations of acetate, butyrate and total short chain fatty acids (SCFAs) in the colonic digesta of LPS-challenged suckling piglets. GOS significantly reduced the concentrations of interleukin 1β (IL-1β), interleukin 6 (IL-6), tumor necrosis factor-α (TNF-α) and cluster of differentiation 14 (CD14), and the relative mRNA expression of Toll-like receptor 4 (TLR4) and myeloid differentiation primary response 88 (MyD88) in the LPS-challenged suckling piglets. In addition, GOS significantly reduced the relative mRNA expression of mucin2 (MUC2), and significantly increased the protein expression of Claudin-1 and zonula occluden-1 (ZO-1) in LPS-challenged suckling piglets.

CONCLUSIONS

These results suggested that GOS can modulate the colonic mucosa-associated microbiota composition and improve the intestinal function of LPS-challenged suckling piglets.

Comparative analysis of fecal microbiota composition diversity in Tibetan piglets suffering from diarrheagenic Escherichia coli (DEC)

This study was ascertained to investigate the adverse effects of pathogenic E. coli on gut microbiota of Tibetan piglets with history of yellow and white dysentery. For this purpose, a total of 18 fecal samples were collected from infected and healthy Tibetan piglets for 16S rRNA gene amplification and sequencing of V3-V4 region. Results showed that Firmicutes, Bacteroidia Fusobacteriota, Proteobacteria and Actinobacteriota were the predominant bacteria in Tibetan piglets at the level of phylum classification. Results on classification at family level showed that Lactobacillus, Bacteroidota, Fusobacteriota and Enterobacteriaceae were the dominant bacteria. Results on classification of bacteria at phylum level compared with normal piglets indicated that Bacteroidota, Actinobacteriota, Euryarchaota and Spirochaetota in fecal microbial community in Tibetan piglets showing yellow dysenteric and diarrhea group were significantly decreased (P ≤ 0.05). Compared with the feces of healthy Tibetan piglets, the abundance of Escherichia-Shigella, Lactobacillus and Enterococcus increased significantly in feces of Tibetan piglets having yellow dysentery and white dysentery. Moreover, results exhibited that the Proteobacteria and Fusobacteriota were significantly increased (P ≤ 0.05) suggesting dominant microbial community. Results revealed that E. coli induced different pathological alterations in intestine including damage to intestinal epithelial cells, infiltration of inflammatory cells, presence of red blood cells in spaces of tissues, hemorrhages and necrosis of intestinal villi in piglets with history of yellow dysentery. This study for the first time reported the composition, characteristics, and differences of the fecal microflora diversity of Tibetan piglets with yellow and white dysentery in Qinghai-Tibet Plateau, which can provide a suitable support for effective control of diarrhoeal disease in these animals.

Supplementation of a lacto-fermented rapeseed-seaweed blend promotes gut microbial- and gut immune-modulation in weaner piglets

BACKGROUND

The direct use of medical zinc oxide in feed will be abandoned after 2022 in Europe, leaving an urgent need for substitutes to prevent post-weaning disorders.

RESULTS

This study investigated the effect of using rapeseed-seaweed blend (rapeseed meal added two brown macroalgae species Ascophylum nodosum and Saccharina latissima) fermented by lactobacilli (FRS) as feed ingredients in piglet weaning. From d 28 of life to d 85, the piglets were fed one of three different feeding regimens (n = 230 each) with inclusion of 0%, 2.5% and 5% FRS. In this period, no significant difference of piglet performance was found among the three groups. From a subset of piglets (n = 10 from each treatment), blood samples for hematology, biochemistry and immunoglobulin analysis, colon digesta for microbiome analysis, and jejunum and colon tissues for histopathological analyses were collected. The piglets fed with 2.5% FRS manifested alleviated intraepithelial and stromal lymphocytes infiltration in the gut, enhanced colon mucosa barrier relative to the 0% FRS group. The colon microbiota composition was determined using V3 and V1-V8 region 16S rRNA gene amplicon sequencing by Illumina NextSeq and Oxford Nanopore MinION, respectively. The two amplicon sequencing strategies showed high consistency between the detected bacteria. Both sequencing strategies indicated that inclusion of FRS reshaped the colon microbiome of weaned piglets with increased Shannon diversity. Prevotella stercorea was verified by both methods to be more abundant in the piglets supplied with FRS feed, and its abundance was positively correlated with colonic mucosa thickness but negatively correlated with blood concentrations of leucocytes and IgG.

CONCLUSIONS

FRS supplementation relieved the gut lymphocyte infiltration of the weaned piglets, improved the colon mucosa barrier with altered microbiota composition. Increasing the dietary inclusion of FRS from 2.5% to 5% did not lead to further improvements.

Modeling microbe-host interaction in the pathogenesis of Crohn's disease

Alterations in the gut microbiota structure and function are thought to play an important role in the pathogenesis of Crohn's disease (CD). The rapid advancement of high-throughput sequencing technologies led to the identification of microbiome risk signatures associated with distinct disease phenotypes and progressing disease entities. Functional validation of the identified microbiome signatures is essential to understand the underlying mechanisms of microbe-host interactions. Germfree mouse models are available to study the functional role of disease-conditioning complex gut microbial ecosystems (dysbiosis) or pathobionts (single bacteria) in the pathogenesis of CD-like inflammation. Here, we discuss the clinical and mechanistic relevance and limitations of gnotobiotic mouse models in the context of CD. In addition, we will address the role of diet as an essential external factor modulating microbiome changes, potentially underlying disease initiation and development.

Dietary osteopontin-enriched algal protein as nutritional support in weaned pigs infected with F18-fimbriated enterotoxigenic Escherichia coli

This study investigated the effects of dietary osteopontin (OPN)-enriched algal protein on growth, immune status, and fecal fermentation profiles of weaned pigs challenged with a live infection of F18-fimbriated enterotoxigenic E. coli (ETEC). At 21 d of age, 54 pigs (5.95 ± 0.28 kg BW; blocked by BW) were allotted to 1 of 3 experimental groups combining dietary and health statuses. A control diet, containing 1% wild-type algal protein, was fed to both sham-inoculated (NC) and ETEC-inoculated (PC) pigs, while the test diet contained 1% OPN-enriched algal protein as fed only to ETEC-inoculated pigs (OA). All pigs received their assigned dietary treatment starting at study initiation to permit a 10-d acclimation period prior to inoculation. Growth performance, fecal dry matter, as well as hematological, histopathological, immune, and microbiota outcomes were analyzed by ANOVA, where treatment and time were considered as fixed effects and pig as a random effect; significance was accepted at P < 0.05. Overall, ETEC-inoculated pigs (PC and OA) exhibited decreased (P < 0.05) ADG and G:F, as well as increased (P < 0.05) peripheral blood helper T-cells and total leukocyte counts, compared with NC pigs during the postinoculation period. The OA treatment also elicited the highest (P < 0.05) concentrations of circulating tumor necrosis factor-α and volatile fatty acid concentrations in luminal contents at various postinoculation time-points, compared with other treatments. A principal coordinate analysis based on Unifrac weighted distances indicated that NC and OA groups had similar overall bacterial community structures, while PC pigs exhibited greater diversity, but infection status had no impact on α-diversity. Osteopontin-specific effects on microbial community structure included enrichment within Streptococcus and Blautia genera and decreased abundance of 12 other genera as compared with PC pigs. Overall, ETEC-infected pigs receiving 1% OPN-enriched algal protein exhibited changes immunity, inflammatory status, and colonic microbial community structure that may benefit weanling pigs experiencing F18 ETEC infection.

Prevotella in Pigs: The Positive and Negative Associations with Production and Health

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

Microbiability of meat quality and carcass composition traits in swine

The impact of gut microbiome composition was investigated at different stages of production (weaning, Mid‐test and Off‐test) on meat quality and carcass composition traits of 1,123 three‐way crossbred pigs. Data were analysed using linear mixed models which included the fixed effects of dam line, contemporary group and gender as well as the random effects of pen, animal and microbiome information at different stages. The contribution of the microbiome to all traits was prominent although it varied over time, increasing from weaning to Off‐test for most traits. Microbiability estimates of carcass composition traits were greater than that of meat quality traits. Among all of the traits analysed, belly weight (BEL) had a higher microbiability estimate (0.29 ± 0.04). Adding microbiome information did not affect the estimates of genomic heritability of meat quality traits but affected the estimates of carcass composition traits. Fat depth had a greater decrease (10%) in genomic heritability at Off‐test. High microbial correlations were found among different traits, particularly with traits related to fat deposition with a decrease in the genomic correlation up to 20% for loin weight and BEL. This suggested that genomic correlation was partially contributed by genetic similarity of microbiome composition. The results indicated that better understanding of microbial composition could aid the improvement of complex traits, particularly the carcass composition traits in swine by inclusion of microbiome information in the genetic evaluation process.

Modeling host-microbiome interactions for the prediction of meat quality and carcass composition traits in swine

BACKGROUND

The objectives of this study were to evaluate genomic and microbial predictions of phenotypes for meat quality and carcass traits in swine, and to evaluate the contribution of host-microbiome interactions to the prediction. Data were collected from Duroc-sired three-way crossbred individuals (n = 1123) that were genotyped with a 60 k SNP chip. Phenotypic information and fecal 16S rRNA microbial sequences at three stages of growth (Wean, Mid-test, and Off-test) were available for all these individuals. We used fourfold cross-validation with animals grouped based on sire relatedness. Five models with three sets of predictors (full, informatively reduced, and randomly reduced) were evaluated. 'Full' included information from all genetic markers and all operational taxonomic units (OTU), while 'informatively reduced' and 'randomly reduced' represented a reduced number of markers and OTU based on significance preselection and random sampling, respectively. The baseline model included the fixed effects of dam line, sex and contemporary group and the random effect of pen. The other four models were constructed by including only genomic information, only microbiome information, both genomic and microbiome information, and microbiome and genomic information and their interaction.

RESULTS

Inclusion of microbiome information increased predictive ability of phenotype for most traits, in particular when microbiome information collected at a later growth stage was used. Inclusion of microbiome information resulted in higher accuracies and lower mean squared errors for fat-related traits (fat depth, belly weight, intramuscular fat and subjective marbling), objective color measures (Minolta a*, Minolta b* and Minolta L*) and carcass daily gain. Informative selection of markers increased predictive ability but decreasing the number of informatively reduced OTU did not improve model performance. The proportion of variation explained by the host-genome-by-microbiome interaction was highest for fat depth (~ 20% at Mid-test and Off-test) and shearing force (~ 20% consistently at Wean, Mid-test and Off-test), although the inclusion of the interaction term did not increase the accuracy of predictions significantly.

CONCLUSIONS

This study provides novel insight on the use of microbiome information for the phenotypic prediction of meat quality and carcass traits in swine. Inclusion of microbiome information in the model improved predictive ability of phenotypes for fat deposition and color traits whereas including a genome-by-microbiome term did not improve prediction accuracy significantly.

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.

Evaluating the association between feed efficiency and the fecal microbiota of early-life Duroc pigs using 16S rRNA sequencing

Improving the predication efficiency of porcine production performance at early stage will contribute to reducing the breeding and production costs. The intestinal microbiota had received plenty of attention in recent years due to their influence on host health and performance. The purpose of this study was to investigate the relationship between the fecal microbiota at early growth period and porcine feed efficiency (FE) under a commercial feeding environment. Ninety-one pigs were reordered according to the residual feed intake (RFI) values between day 90 on test and day 160 off test, 9 lowest RFI pigs and 9 highest RFI pigs were selected as the LRFI group and the HRFI group, respectively. Fecal samples from pigs in the early grower phase (day 80) were performed for microbial diversity, composition, and predicted functionality by using 16S rRNA sequencing. The results showed that no significant differences in microbial alpha diversity were observed between two RFI groups, whereas, some RFI-associated compositional differences were revealed. In particular, the microbiota of the LRFI group (more feed-efficient) had significantly higher levels of some members of Clostridiales and Bacteroidales (e.g., g_1_68 and g_norank_f_p_2534_18B5), which may promoted FE through protecting gut barrier function, compared with those of the HRFI pigs. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis found that the LRFI pigs were likely have microbiota with higher levels of amino acid metabolism. Moreover, redundancy analysis (RDA) showed that litter size, parity, and date of birth had significant effects on the bacterial community structure. These results improved our knowledge of the porcine early-life fecal microbiota and its potential link underlying RFI, which would be useful for future development of microbial biomarkers for predicting and improving porcine FE as well as investigation of targets for dietary strategies.

The role of gut microbiota in bone homeostasis

The gut microbiota (GM) is referred to as the second gene pool of the human body and a commensal, symbiotic, and pathogenic microorganism living in our intestines. The knowledge of the complex interaction between intestinal microbiota and health outcomes is a novel and rapidly expanding the field. Earlier studies have reported that the microbial communities affect the cellular responses and shape many aspects of physiology and pathophysiology within the body, including muscle and bone metabolism (formation and resorption). GM influences the skeletal homeostasis via affecting the host metabolism, immune function, hormone secretion, and the gut-brain axis. The premise of this review is to discuss the role of GM on bone homeostasis and skeletal muscle mass function. This review also opens up new perspectives for pathophysiological studies by establishing the presence of a 'microbiota-skeletal' axis and raising the possibility of innovative new treatments for skeletal development.

Correlation and association analyses in microbiome study integrating multiomics in health and disease

Correlation and association analyses are one of the most widely used statistical methods in research fields, including microbiome and integrative multiomics studies. Correlation and association have two implications: dependence and co-occurrence. Microbiome data are structured as phylogenetic tree and have several unique characteristics, including high dimensionality, compositionality, sparsity with excess zeros, and heterogeneity. These unique characteristics cause several statistical issues when analyzing microbiome data and integrating multiomics data, such as large p and small n, dependency, overdispersion, and zero-inflation. In microbiome research, on the one hand, classic correlation and association methods are still applied in real studies and used for the development of new methods; on the other hand, new methods have been developed to target statistical issues arising from unique characteristics of microbiome data. Here, we first provide a comprehensive view of classic and newly developed univariate correlation and association-based methods. We discuss the appropriateness and limitations of using classic methods and demonstrate how the newly developed methods mitigate the issues of microbiome data. Second, we emphasize that concepts of correlation and association analyses have been shifted by introducing network analysis, microbe-metabolite interactions, functional analysis, etc. Third, we introduce multivariate correlation and association-based methods, which are organized by the categories of exploratory, interpretive, and discriminatory analyses and classification methods. Fourth, we focus on the hypothesis testing of univariate and multivariate regression-based association methods, including alpha and beta diversities-based, count-based, and relative abundance (or compositional)-based association analyses. We demonstrate the characteristics and limitations of each approaches. Fifth, we introduce two specific microbiome-based methods: phylogenetic tree-based association analysis and testing for survival outcomes. Sixth, we provide an overall view of longitudinal methods in analysis of microbiome and omics data, which cover standard, static, regression-based time series methods, principal trend analysis, and newly developed univariate overdispersed and zero-inflated as well as multivariate distance/kernel-based longitudinal models. Finally, we comment on current association analysis and future direction of association analysis in microbiome and multiomics studies.

Interactions between host and gut microbiota in domestic pigs: a review

It is well established that pig gut microbiota plays a critical role in maintaining metabolic homeostasis as well as in a myriad of physiological, neurological and immunological functions; including protection from pathogens and digestion of food materials - some of which would be otherwise indigestible by the pig. A rich and diverse gut microbial ecosystem (balanced microbiota) is the hallmark of good health; while qualitative and quantitative perturbations in the microbial composition can lead to development of various diseases. Alternatively, diseases caused by stressors or other factors have been shown to negatively impact the microbiota. This review focuses primarily on how commensal microorganisms in the gastrointestinal tract of pigs influence biochemical, physiological, immunological, and metabolic processes within the host animal.

Fate of Thymol and Its Monoglucosides in the Gastrointestinal Tract of Piglets

The monoterpene thymol has been proposed as a valuable alternative to in-feed antibiotics in animal production. However, the effectiveness of the antimicrobial is comprised by its fast absorption in the upper gastrointestinal tract. In this work, two glucoconjugates, thymol α-d-glucopyranoside (TαG) and thymol β-d-glucopyranoside (TβG), were compared with free thymol for their potential to deliver higher concentrations of the active compound to the distal small intestine of supplemented piglets. Additionally, an analytical method was developed and validated for the simultaneous quantification of thymol and its glucoconjugates in different matrices. In stomach contents of pigs fed with 3333 μmol kg^-1 thymol, TαG, or TβG, total thymol concentrations amounted to 3048, 2357, and 1820 μmol kg^-1 dry matter, respectively. In glucoconjugate-fed pigs, over 30% of this concentration was present in the unconjugated form, suggesting partial hydrolysis in the stomach. No quantifiable levels of thymol or glucoconjugates were detected in the small intestine or cecum for any treatment, indicating that conjugation with one glucose unit did not sufficiently protect thymol from early absorption.

The gut microbiota response to helminth infection depends on host sex and genotype

Vertebrates' gut microbial communities can be altered by the hosts' parasites. Helminths inhabiting the gut lumen can interact directly with their host's microbiota via physical contact, chemical products, or competition for nutrients. Indirect interactions can also occur, for instance when helminths induce or suppress host immunity in ways that have collateral effects on the microbiota. If there is genetic variation in host immune responses to parasites, we would expect such indirect effects to be conditional on host genotype. To test for such genotype by infection interactions, we experimentally exposed Gasterosteus aculeatus to their naturally co-evolved parasite, Schistocephalus solidus. The host microbiota differed in response to parasite exposure, and between infected and uninfected fish. The magnitude and direction of microbial responses to infection differed between host sexes, and also differed between variants at autosomal quantitative trait loci. These results indicate that host genotype and sex regulate the effect of helminth infection on a vertebrate gut microbiota. If this result holds in other taxa, especially humans, then helminth-based therapeutics for dysbiosis might need to be tailored to host genotype and sex.

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.

Lactic Acid Treatment of Cereals and Dietary Phytase Modified Fecal Microbiome Composition Without Affecting Expression of Virulence Factor Genes in Growing Pigs

Besides the major nutrients, phosphorus (P) is an essential mineral for both the host animal and the porcine gut microbiota. Different strategies including phytase supplementation and more recently lactic acid (LA) are used to enhance the P availability from cereals in pig diets; however, their impact on the gut microbiota has been rarely related to fecal shedding of opportunistic pathogens. The present study investigated the effect of phytase supplementation and the treatment of dietary cereals with 2.5% LA on the fecal microbiome composition of metabolic active bacteria and expression of virulence factor genes of enterotoxigenic Escherichia coli and Clostridium perfringens in growing pigs. Phytase supplementation reduced the fecal abundance of the most abundant Lactobacillaceae family, whereas the LA-treatment of cereals had a stronger impact on the bacterial community, reducing amylolytic, pullulanolytic and hemicellulolytic Lactobacillaceae, Lachnospiraceae and Ruminococcaceae as well as the fecal bacterial species richness (Chao1) and diversity (Shannon index). Mainly the family Clostridiaceae benefited from the decline in the aforementioned families, being enriched by both dietary treatments. Multigroup data integration using sparse partial least squares-discriminant analysis showed that among the most discriminative operational taxonomic units (OTU) especially two unclassified Clostridiaceae-OTUs, one Prevotella copri-like OTU and one OTU within the vadinCA11 group were associated with calcium and P levels but were negatively linked with complex carbohydrates in feces. Heat-stable toxin A (Sta) of enterotoxigenic E. coli and Stx2e of Shiga-toxin producing E. coli were expressed in feces but were similar among feeding groups. Without modifying the total bacterial gene copies and virulence factor expression of E. coli, both dietary phytase supplementation and LA-treatment of cereals drastically altered the bacterial community composition in pig feces. Results thereby allowed for the characterization of bacterial nutrient dependencies, indicating a link between fecal P availability, complex carbohydrate composition and alterations in the predominant genera.

Low-calcium diet in mice leads to reduced gut colonization by Enterococcus faecium

The aim of this study was to determine whether dietary intervention influenced luminal Ca²⁺ levels and Enterococcus faecium gut colonization in mice. For this purpose, mice fed semi‐synthetic food AIN93 were compared to mice fed AIN93‐low calcium (LC). Administration of AIN93‐LC resulted in lower luminal Ca²⁺ levels independent of the presence of E. faecium. Furthermore, E. faecium gut colonization was reduced in mice fed AIN93‐LC based on culture, and which was in concordance with a reduction of Enterococcaceae in microbiota analysis. In conclusion, diet intervention might be a strategy for controlling gut colonization of E. faecium, an important opportunistic nosocomial pathogen.

Longitudinal development of the gut microbiota in healthy and diarrheic piglets induced by age-related dietary changes

Diarrhea is one of the most common enteric diseases in young piglets. Diverse factors such as an unstable gut microenvironment, immature intestinal immune system, early supplementary feeding, and weaning often induce dysfunction of gut microbiota, thus leading to a continuing high incidence of diarrhea in piglets. However, few studies have characterized the gut microbiota of diarrheic piglets following changes in diet and during the development of intestinal physiology. In this study, we used 16S rRNA gene sequencing to analyze the dynamic establishment of fecal microbiota in six healthy piglets in response to age‐related changes in the diet: sow‐reared, early supplementary creep‐feeding (sow‐reared + starter diet), and weaning (solid nursery diet). We compared the gut microbiota of these six healthy piglets with those of diarrheic piglets during each of the three dietary stages (n = 10 sow‐reared, n = 10 early supplementary creep‐feeding, and n = 5 weaning). We found that weaning (solid nursery feeding) was the primary factor leading to dynamic colonization by microbiota in healthy piglets, and diarrhea primarily affected the microbial communities of piglets before weaning. Healthy piglets showed a continuous decrease in Lactobacillus and Escherichia, as well as a gradual increase in Prevotella with the transition to solid food. An altered relationship between Prevotella and Escherichia may be the main cause of diarrhea in preweaned piglets, whereas reduced numbers of Bacteroides, Ruminococcus, Bulleidia, and Treponema that are responsible for the digestion and utilization of solid feeds may be related to the onset of postweaning piglet diarrhea. The Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) functional analysis indicated that a reduction in genes involved in carbohydrate metabolism induced by intestinal dysbacteriosis in diarrheic piglets was one of the major causes of diarrhea at the three dietary stages. These findings provide insights into developing an intervention strategy for better management of diarrhea in piglets.

Lactobacilli Isolated From Wild Boar (Sus scrofa) Antagonize Mycobacterium bovis Bacille Calmette-Guerin (BCG) in a Species-Dependent Manner

Background: Wildlife poses a significant burden for the complete eradication of bovine tuberculosis (bTB). In particular, wild boar (Sus scrofa) is one of the most important reservoirs of Mycobacterium bovis, the causal agent of bTB. Wild boar can display from mild TB lesions, usually found in head lymph nodes, to generalized TB lesions distributed in different anatomical regions; but rarely clinical signs, which complicates the diagnosis of Mycobacterium bovis infection and bTB control. Among the possibilities for this variability in lesion distribution is the influence of the host-beneficial commensal-primed immune barrier. In this respect, beneficial microbes may delay bTB dissemination as a consequence of an antagonistic competition for nutrients and phagocytes. In order to explore this possibility, we have tested whether typical commensals such as lactobacilli have the capacity to reduce the survival rate of the surrogate M. bovis strain Bacillus Calmette-Guerin (BCG); and to modulate its phagocyte intake.

Results: Three Lactobacillus species, L. casei, L. plantarum, and L. salivarius, isolated from wild boar feces displayed a pH-dependent inhibitory activity against BCG and influenced its intake by porcine blood phagocytes in a species-dependent manner. All lactobacilli showed a very significant bactericidal effect against BCG at low pH, but only isolates of L. plantarum and L. casei displayed such antimycobacterial activity at neutral pH. The genomes of these isolates revealed the presence of two-peptide bacteriocins whose precursor genes up-regulate in the presence of BCG cells. Furthermore, L. plantarum reduced significantly the BCG phagocytic intake, whereas L. casei had the opposite effect. L. salivarius had no significant influence on the phagocytic response to BCG.

Conclusions: Our in vitro results show that lactobacilli isolated from wild boar antagonize BCG as a consequence of their antimycobacterial activity and a competitive phagocytic response. These findings suggest that commensal bacteria could play a beneficial role in influencing the outcome of bTB dissemination. Further work with lactobacilli as a potential competitive pressure to control bTB will need to take into account the complex nature of the commensal microbiome, the specific immunity of the wild boar and the in vivo infection context with pathogenic strains of M. bovis.

Response of gastrointestinal fermentative activity and colonic microbiota to protected sodium butyrate and protected sodium heptanoate in weaned piglets challenged with ETEC F4. Arch Anim Nutr 2019;73:339-359. [PMID: 31342760 DOI: 10.1080/1745039x.2019.1641376]

This study aimed to evaluate the potential of two new fat-protected butyrate or heptanoate salts to improve gut health and control post-weaning colibacillosis in weaning piglets challenged with enterotoxigenic Escherichia coli (ETEC) F4⁺, particularly focusing on their impact on intestinal microbiota and fermentative activity along the gastrointestinal tract (GIT). Seventy-two 21-d-old pigs were fed a plain diet (CTR) or supplemented with sodium butyrate (BUT) or sodium heptanoate (HPT), both at 0.3%. After a week of adaptation, animals were orally challenged at days 8 and 9 with 5.8 · 10⁹ and 6.6 · 10¹⁰ cfu, respectively, and were euthanised on d 4 and d 8 post-inoculation (PI) (n = 8) to collect blood, digesta and tissue samples and characterise microbial groups, pathogen loads (qPCR), fermentation, ileal histomorphometry and immune markers. Colonic microbiota was analysed by 16S rRNA gene MiSeq sequencing. Supplementing both acid salts did not compensate clinical challenge effects nor performance impairments and neither histomorphometry nor serum biomarkers. Changes in the gastric fermentative activity were registered, BUT reducing lactic acid concentrations (day 8 PI), and with HPT fewer animals presenting detectable concentrations of propionic, butyric and valeric acids. At ileum BUT increased acetic acid concentration (day 8 PI), and both additives reduced short-chain fatty acids (SCFA) in the colon. Increases in enterobacteria and coliforms counts in ileal digesta (day 4 PI, p < 0.10) and mucosa scrapes (p < 0.05) were registered although E. coli F4 gene copies were unaffected. Regarding changes in the colonic microbiota (day 4 PI), Prevotellaceae and Prevotella were promoted with BUT supplementation whereas only minor groups were modified in HPT-treated animals. Summarising, although the pathogen loads or inflammatory mediators remained unresponsive, butyrate and heptanoate showed a significant impact on microbial fermentation along the whole GIT, being able to modify different bacterial groups at the colon. It could be hypothesised that these effects might be mediated by a carry-over effect of the changes observed in gastric fermentation, but possibly also to a better nutrient digestion in the foregut as a result of the reduced colonic SCFA concentrations.

Characterization of the non-glandular gastric region microbiota in Helicobacter suis-infected versus non-infected pigs identifies a potential role for Fusobacterium gastrosuis in gastric ulceration

Helicobacter suis has been associated with development of gastric ulcers in the non-glandular part of the porcine stomach, possibly by affecting gastric acid secretion and altering the gastric microbiota. Fusobacterium gastrosuis is highly abundant in the gastric microbiota of H. suis-infected pigs and it was hypothesized that this micro-organism could play a role in the development of gastric ulceration. The aim of this study was to obtain further insights in the influence of a naturally acquired H. suis infection on the microbiota of the non-glandular part of the porcine stomach and in the pathogenic potential of F. gastrosuis. Infection with H. suis influenced the relative abundance of several taxa at phylum, family, genus and species level. H. suis-infected pigs showed a significantly higher colonization rate of F. gastrosuis in the non-glandular gastric region compared to non-infected pigs. In vitro, viable F. gastrosuis strains as well as their lysate induced death of both gastric and oesophageal epithelial cell lines. These gastric cell death inducing bacterial components were heat-labile. Genomic analysis revealed that genes are present in the F. gastrosuis genome with sequence similarity to genes described in other Fusobacterium spp. that encode factors involved in adhesion, invasion and induction of cell death as well as in immune evasion. We hypothesize that, in a gastric environment altered by H. suis, colonization and invasion of the non-glandular porcine stomach region and production of epithelial cell death inducing metabolites by F. gastrosuis, play a role in gastric ulceration.

Microbiota of the Gut-Lymph Node Axis: Depletion of Mucosa-Associated Segmented Filamentous Bacteria and Enrichment of Methanobrevibacter by Colistin Sulfate and Linco-Spectin in Pigs

Microorganisms are translocated from the gut to lymphatic tissues via immune cells, thereby challenging and training the mammalian immune system. Antibiotics alter the gut microbiome and consecutively might also affect the corresponding translocation processes, resulting in an imbalanced state between the intestinal microbiota and the host. Hence, understanding the variant effects of antibiotics on the microbiome of gut-associated tissues is of vital importance for maintaining metabolic homeostasis and animal health. In the present study, we analyzed the microbiome of (i) pig feces, ileum, and ileocecal lymph nodes under the influence of antibiotics (Linco-Spectin and Colistin sulfate) using 16S rRNA gene sequencing for high-resolution community profiling and (ii) ileocecal lymph nodes in more detail with two additional methodological approaches, i.e., cultivation of ileocecal lymph node samples and (iii) metatranscriptome sequencing of a single lymph node sample. Supplementation of medicated feed showed a local effect on feces and ileal mucosa-associated microbiomes. Pigs that received antibiotics harbored significantly reduced amounts of segmented filamentous bacteria (SFB) along the ileal mucosa (p = 0.048; 199.17-fold change) and increased amounts of Methanobrevibacter, a methanogenic Euryarchaeote in fecal samples (p = 0.005; 20.17-fold change) compared to the control group. Analysis of the porcine ileocecal lymph node microbiome exposed large differences between the viable and the dead fraction of microorganisms and the microbiome was altered to a lesser extent by antibiotics compared with feces and ileum. The core microbiome of lymph nodes was constituted mainly of Proteobacteria. RNA-sequencing of a single lymph node sample unveiled transcripts responsible for amino acid and carbohydrate metabolism as well as protein turnover, DNA replication and signal transduction. The study presented here is the first comparative study of microbial communities in feces, ileum, and its associated ileocecal lymph nodes. In each analyzed site, we identified specific phylotypes susceptible to antibiotic treatment that can have profound impacts on the host physiological and immunological state, or even on global biogeochemical cycles. Our results indicate that pathogenic bacteria, e.g., enteropathogenic Escherichia coli, could escape antibiotic treatment by translocating to lymph nodes. In general ileocecal lymph nodes harbor a more diverse and active community of microorganisms than previously assumed.

Phytate degradation, intestinal microbiota, microbial metabolites and immune values are changed in growing pigs fed diets with varying calcium-phosphorus concentration and fermentable substrates

The present study assessed effects of diets containing varying calcium-phosphorus (CaP) concentration and fermentable substrates on digestibility of diets, intestinal microbiota and immune system using 32 crossbred pigs (initial BW 54.7 kg). In a 2 × 2 factorial arrangement, pigs were fed either a corn-soybean meal (CSB) or corn-field pea (CFP) diet with either low [-] (4.4 g Ca/kg; 4.2 g total P/kg) or high [+] (8.3 g Ca/kg; 7.5 g total P/kg; supplemented with monocalcium phosphate) CaP content for a period of 9 weeks. In week 8, blood samples were taken, and at the end of the trial, all pigs were euthanized to collect digesta and mesenteric lymphoid tissue. Apparent total tract digestibility (ATTD) of P was greater (p < 0.05) for pigs fed the CaP+ and CFP diets than CaP- and CSB diets. The myo-inositol 1,2,3,4,5,6-hexakis (dihydrogen phosphate) (InsP₆ ) concentration in jejunal digesta was higher (p < 0.05) for CaP+ than in CaP- fed pigs. In addition, caecal and faecal InsP₅ isomer concentration were greater (p < 0.05) for CSB than CFP diets. In the caecum, gene copy numbers of saccharolytic bacteria, such as Eubacterium rectale and Roseburia spp., as well as SCFA concentration were higher (p < 0.05) for CaP+ than CaP- diets. In particular, innate immune cell numbers, such as natural killer cells, dendritic cells, monocytes and neutrophils, were greater (p < 0.05) for CaP+ than CaP- fed pigs. Diets high in CaP resulted in higher abundance of potential beneficial bacteria and might promote the first line of defence enhancing the activation of the cellular adaptive immune response, thereby possibly decreasing the risk for intestinal disturbances. These results strongly suggest that both, CaP supply and dietary ingredients differing in fermentability, may beneficially affect gut health through increase in SCFA-producing bacteria and/or bacteria with anti-inflammatory properties.

Insight Into Dynamics of Gut Microbial Community of Broilers Fed With Fructooligosaccharides Supplemented Low Calcium and Phosphorus Diets

We investigated how the microbiota in the ileum and cecum of broiler chickens fed a diet of low calcium (Ca) and available phosphorus (aP) and prebiotic fructooligosaccharides (FOS) supplements changed over a 3 weeks period. Three dietary treatments were randomly assigned to four replicate cages of five birds each, including: positive control (PC), a wheat-corn-soybean meal-based diet; negative control (NC), as PC with 0.2% reduced Ca and aP; and NC + FOS, as NC supplemented with 0.5% of FOS. Ileal and cecal digesta were sampled from each replicate (n = 4) on d21 and processed for 16S rRNA gene amplicon (V4 region) sequencing using Illumina platform. Statistical differences were observed in the microbiome by GI location as determined by 2-way ANOVA and Permutational MANOVA. On average, 24,216 sequence reads per sample were generated resulting in 800 and 1,280 operational taxonomic units in the ileal and cecal digesta, respectively. Difference (P < 0.0001) on alpha diversity and abundances of several phyla was observed between ileal and cecal digesta. ß-diversity was different (P < 0.05) between each treatment groups in the ileum but not in the cecum. In the cecum, species richness, phylogenetic diversity, and the number of observed species were higher in PC compared to NC + FOS (P < 0.05). Several phyla, including Cyanobacteria, Firmicutes, and Proteobacteria, had significantly different abundance in the ileal and cecal digesta (P < 0.05). In the ileal digesta, positive correlation were observed between Salinibacterium and Lysobacter and PC diet. Blautia, Faecalibacterium and Pseudomonas and the NC diet and Lactobacillus and Escherichia and the NC + FOS diet. In the cecal digesta, Butyrivibrio, and Allobaculum were positively correlated to PC. Although, Clostridium and Anaerotruncus were positively correlated to NC + FOS, they showed negative correlation to PC and NC. The study concludes that dietary Ca and aP level and FOS supplementation alters ileal microbiota of the broiler chickens.

Analysis of the Bacterial and Host Proteins along and across the Porcine Gastrointestinal Tract

Pigs are among the most important farm animals worldwide and research to optimize their feed efficiency and improve their welfare is still in progress. The porcine intestinal microbiome is so far mainly known from sequencing-based studies. Digesta and mucosa samples from five different porcine gastrointestinal tract sections were analyzed by metaproteomics to obtain a deeper insight into the functions of bacterial groups with concomitant analyses of host proteins. Firmicutes (Prevotellaceae) dominated mucosa and digesta samples, followed by Bacteroidetes. Actinobacteria and Proteobacteria were much higher in abundance in mucosa compared to digesta samples. Functional profiling reveals the presence of core functions shared between digesta and mucosa samples. Protein abundances of energy production and conversion were higher in mucosa samples, whereas in digesta samples more proteins were involved in lipid transport and metabolism; short-chain fatty acids production were detected. Differences were also highlighted between sections, with the small intestine appearing more involved in carbohydrate transport and metabolism than the large intestine. Thus, this study produced the first functional analyses of the porcine GIT biology, discussing the findings in relation to expected bacterial and host functions.

Illumina MiSeq Sequencing Investigation of Microbiota in Bronchoalveolar Lavage Fluid and Cecum of the Swine Infected with PRRSV

Porcine reproductive and respiratory syndrome virus (PRRSV) causes significant animal morbidity and mortality and economic losses worldwide. In this study, we analyzed the microbiota in bronchoalveolar lavage fluid (BAL), mucosa, and feces in cecum of the PRRSV-challenged pigs using the Illumina MiSeq sequencing platform, to investigate the role of microbiota in the pathogenesis and development of porcine reproductive and respiratory syndrome (PRRS). Quantitative insights into microbial ecology analyses indicated that the dominant bacterial groups in the lung from the PRRSV-challenged pigs were Haemophilus parasuis and Mycoplasma hyorhinis, with a relative abundance of 35-48% and 27-41%, respectively. Our results were consistent with the clinical observation that the PRRSV-infected pigs are always co-infected with other bacteria, such as Haemophilus and Mycoplasma. On the other hand, Campylobacter and Clostridium became the two most abundant bacteria in the mucosal and luminal microbiota of the cecum of the PRRSV-challenged pigs, and the relative abundance was four times higher than that in the healthy pigs. This suggested that Campylobacter and Clostridium might be associated with the pathogenesis of diarrhea in PRRS. Linear discriminant analysis effect size reveals significant microbial dysbiosis of BAL, mucosa, and feces in cecum of the PRRSV-challenged pigs. We have identified a structural imbalance of the microbiota, characterized by a reduced diversity of microbiota and abundance alterations of certain bacteria in the PRRSV-challenged pigs. The observed microbiota dysbiosis in this study provides insight into the roles of the microbiota in the complications of the PRRSV infection.

Implications of Probiotics on the Maternal-Neonatal Interface: Gut Microbiota, Immunomodulation, and Autoimmunity

Probiotics are being investigated for the treatment of autoimmune disease by re-balancing dysbiosis induced changes in the immune system. Pregnancy is a health concern surrounding autoimmune disease, both for the mother and her child. Probiotics for maternity are emerging on the market and have gained significant momentum in the literature. Thus far, evidence supports that probiotics alter the structure of the normal microbiota and the microbiota changes significantly during pregnancy. The interaction between probiotics-induced changes and normal changes during pregnancy is poorly understood. Furthermore, there is emerging evidence that the maternal gut microbiota influences the microbiota of offspring, leading to questions on how maternal probiotics may influence the health of neonates. Underpinning the development and balance of the immune system, the microbiota, especially that of the gut, is significantly important, and dysbiosis is an agent of immune dysregulation and autoimmunity. However, few studies exist on the implications of maternal probiotics for the outcome of pregnancy in autoimmune disease. Is it helpful or harmful for mother with autoimmune disease to take probiotics, and would this be protective or pathogenic for her child? Controversy surrounds whether probiotics administered maternally or during infancy are healthful for allergic disease, and their use for autoimmunity is relatively unexplored. This review aims to discuss the use of maternal probiotics in health and autoimmune disease and to investigate their immunomodulatory properties.

Microbiome profiling of commercial pigs from farrow to finish

Balanced bacterial communities within the gastrointestinal (GI) tract of animals are a key component of gut health, resulting in optimal performance and the prevention of disease. The purpose of this study was to characterize the commercial pig's baseline bacterial microbiome over time and across anatomical site. Several anatomical sites (duodenum/jejunum, ileum, cecum, and colon) were examined across multiple ages (days 0, 10, 21, 33, 62, 84, and market) for bacterial microbiome structure using 16S rRNA V4 region sequencing with Illumina MiSeq. General trends in the succession of the bacterial microbiome were observed over age, such as increasing populations of Clostridia and decreasing populations of Gammaproteobacteria (P < 0.05). However, apparent disruptions in the microbiome were also observed that did not follow these trends, specifically at sampling 24 h post-weaning where Lactobacillaceae were drastically reduced in relative abundance (P < 0.05). The introduction of solid feed between days 21 and 33 had the greatest overall impact on bacterial community structure as compared with the effects of age, changes in solid feed type, and pig movement. A core bacterial microbiome was identified across all anatomical sites consisting of the dominant operational taxonomic units (OTUs); samples were only differentiated based upon anatomical site when considering less abundant OTUs and differences in relative abundance. When considering mucosal vs. digesta samples from the cecum and ileum, several taxa were of significantly higher relative abundance in the mucosa (P < 0.05), including Anaerovibrio, Bacteroides, Desulfovibrio, Helicobacter, Oscillospira, Phascolarctobacterium, and Prevotella. Correlations between several genus-level taxa and pig weight were observed. Overall, this study provides an expanded view of the dynamic pig GI microbiome from farrow to finish.

Effect of Dietary Non-phytate Phosphorus Levels on the Diversity and Structure of Cecal Microbiota in Meat Duck from 1 to 21 d of age

The study was conducted to distinguish the effect of dietary non-phytate phosphorus (NPP) levels on the community diversity and structure of the cecal microbiota in meat duck based on 16S rDNA high-throughput sequencing. In total, 525 1-d-old ducklings were fed diets (105 ducklings, 7 pens of 15 ducklings, on each diet) containing five levels of NPP (0.22, 0.34, 0.40, 0.46, and 0.58%) for 21 days. The results showed that dietary NPP levels linearly and quadratically increased (P < 0.05) 21 d body weight, 1 to 21 d feed intake and NPP intake, and contrarily, linearly decreased (P < 0.05) β-diversity of cecal microbial population in ducks. ß-diversity analyses showed that microbiota clustering based on dietary NPP levels occured, with 0.22% NPP groups distinctly different from the 0.46% and 0.58% NPP group samples. Moreover, dietary NPP levels could change the relative abundance of the phylum Proteobacteria (linear, P < 0.05), genera Eubacterium coprostanoligenes (quadratic, P < 0.05), Ruminococcaceae UCG-014 (quadratic, P < 0.05) and Subdoligrannulum (linear, P < 0.05), and Lachnospiraceae family (quadratic, P < 0.05) in cecal microbiota of ducks. Increasing the dietary NPP level influenced the cecal microbiota and positively affected the growth of meat ducks.

Fumonisin-Exposure Impairs Age-Related Ecological Succession of Bacterial Species in Weaned Pig Gut Microbiota

Pigs are highly affected by dietary mycotoxin contamination and particularly by fumonisin. The effects of fumonisin on pig intestinal health are well documented, but little is known regarding its impact on gut microbiota. We investigate the effects of the fumonisin (FB1, 12 mg/kg feed) on the fecal microbiota of piglets (n = 6) after 0, 8, 15, 22, and 29 days of exposure. A control group of six piglets received a diet free of FB1. Bacterial community diversity, structure and taxonomic composition were carried out by V3–V4 16S rRNA gene sequencing. Exposure to FB1 decreases the diversity index, and shifts and constrains the structure and the composition of the bacterial community. This takes place as early as after 15 days of exposure and is at a maximum after 22 days of exposure. Compared to control, FB1 alters the ecological succession of fecal microbiota species toward higher levels of Lactobacillus and lower levels of the Lachnospiraceae and Veillonellaceae families, and particularly OTUs (Operational Taxonomic Units) of the genera Mitsuokella, Faecalibacterium and Roseburia. In conclusion, FB1 shifts and constrains age-related evolution of microbiota. The direct or indirect contribution of FB1 microbiota alteration in the global host response to FB1 toxicity remains to be investigated.

Interactions between metabolically active bacteria and host gene expression at the cecal mucosa in pigs of diverging feed efficiency

Little is known about the role of the gut mucosal microbiota and microbe-host signaling in the variation of pig's feed efficiency (FE). This study therefore aimed to investigate the FE-related differences in the metabolically active mucosal bacterial microbiota and expression of genes for innate immune response, barrier function, nutrient uptake, and incretins in the cecum of finishing pigs. Pigs (n = 72) were ranked for their residual feed intake (RFI; metric for FE) between days 42 and 91 postweaning and were stratified within litter and sex into high (HRFI; n = 8) and low RFI (LRFI; n = 8). Cecal mucosa and digesta were collected on day 137-141 of life. After isolating total RNA from the mucosa, the RNA was transcribed into cDNA which was used for gene expression analysis, total bacterial quantification, and high-throughput sequencing (Illumina MiSeq) of the hypervariable V3-V4 region of the 16S rRNA gene. The RFI differed by 2.1 kg between low RFI (LRFI; good FE) and high RFI (HRFI; poor FE) pigs (P < 0.001). The cecal mucosa was mainly colonized by Helicobacteraceae, Campylobacteraceae, Veillonellaceae, Lachnospiraceae, and Prevotellaceae. Despite the lack of differences in microbial diversity and absolute abundance, RFI-associated compositional differences were found. The predominant genus Campylobacter tended (P < 0.10) to be 0.4-fold more abundant in LRFI pigs, whereas low abundant Escherichia/Shigella (P < 0.05), Ruminobacter (P < 0.05), and Veillonella (P < 0.10) were 3.4-, 6.6-, and 4.4-fold less abundant at the cecal mucosa of LRFI compared to HRFI pigs. Moreover, mucin 2 and zona occludens-1 were less expressed (P < 0.05) in the cecal mucosa of LRFI compared to HRFI pigs. Cecal mucosal expression of monocarboxylate transporter-1, glucagon-like peptide-1, and peptide YY further tended (P < 0.10) to be downregulated in LRFI compared to HRFI pigs, indicating an enhanced VFA uptake and signaling in HRFI pigs. Sparse partial least square regression and relevance networking support the hypothesis that certain mucosal bacteria and luminal microbial metabolites were more associated than others with differences in RFI and cecal gene expression. However, present results do not allow the determination of whether mucosal bacterial changes contributed to variation in FE or were rather a consequence of FE-related changes in the pig's physiology or feeding behavior.