Revealing the combined effects of lactulose and probiotic enterococci on the swine faecal microbiota using 454 pyrosequencing

Impact of Long-Term Supplementation with Probiotics on Gut Microbiota and Growth Performance in Post-Weaned Piglets

This study aimed to investigate effects of long-term probiotic supplementation on gut microbiota and growth performance in health weaned piglets. The non-probiotic group (N-PrB) was fed only a basal diet, while the probiotic group (PrB) was fed a basal diet + probiotic combination (E. faecium 1.6 × 108 CFU/g, B. subtilis 2.0 × 108 CFU/g, S. cerevisiae 3.0 × 108 CFU/g). The probiotics combination was provided to the PrB, mixing with the basal diet in 5 kg/ton. As a result, the PrB exhibited significantly improved weight gain compared to the N-PrB (p = 0.00991). In the gut microbiome analysis, the PrB exhibited a significant increasing tendency of α-diversity compared to those of the N-PrB (p < 0.01). In the bacterial relative abundance changes in bacteria comprising the gut microbiota, Ruminococcaceae (p = 0.00281) and Prevotella (p = 0.00687) tended to significantly increase in the PrB, but decreased in the N-PrB. The Eubaterium coprostanoligenes group exhibited an increasing tendency in both groups, but tended to increase more significantly in the PrB compared to the N-PrB (p = 0.00681). Muribaculaceae tended to significantly increase in the N-PrB, but decreased in the PrB (p = 0.002779). In this study, significant differences on the gut microbiome were found according to the probiotics supplementation in the weaned piglets and these gut microbiome changes appeared to improve the growth performance.

Impact of Intestinal Microbiota on Growth Performance of Suckling and Weaned Piglets

Small-scale studies investigating the relationship between pigs' intestinal microbiota and growth performance have generated inconsistent results. We hypothesized that on farms under favorable environmental conditions (e.g., promoting sow nest-building behavior, high colostrum production, low incidence of diseases and minimal use of antimicrobials), the piglet gut microbiota may develop toward a population that promotes growth and reduces pathogenic bacteria. Using 16S rRNA gene amplicon sequencing, we sampled and profiled the fecal microbiota from 170 individual piglets throughout suckling and postweaning periods (in total 670 samples) to track gut microbiota development and its potential association with growth. During the suckling period, the dominant genera were Lactobacillus and Bacteroides, the latter being gradually replaced by Clostridium sensu scricto 1 as piglets aged. The gut microbiota during the nursery stage, not the suckling period, predicted the average daily growth (ADG) of piglets. The relative abundances of SCFA-producing genera, in particular Faecalibacterium, Megasphaera, Mitsuokella, and Subdoligranulum, significantly correlated with high ADG of weaned piglets. In addition, the succession of the gut microbiota in high-ADG piglets occurred faster and stabilized sooner upon weaning, whereas the gut microbiota of low-ADG piglets continued to mature after weaning. Overall, our findings suggest that weaning is the major driver of gut microbiota variation in piglets with different levels of overall growth performance. This calls for further research to verify if promotion of specific gut microbiota, identified here at weaning transition, is beneficial for piglet growth. IMPORTANCE The relationship between pigs' intestinal microbiota and growth performance is of great importance for improving piglets' health and reducing antimicrobial use. We found that gut microbiota variation is significantly associated with growth during weaning and the early nursery period. Importantly, transitions toward a mature gut microbiota enriched with fiber-degrading bacteria mostly complete upon weaning in piglets with better growth. Postponing the weaning age may therefore favor the development of fiber degrading gut bacteria, conferring the necessary capacity to digest and harvest solid postweaning feed. The bacterial taxa associated with piglet growth identified herein hold potential to improve piglet growth and health.

Effects of Lacticaseibacillus casei (Lactobacillus casei) and Saccharomyces cerevisiae mixture on growth performance, hematological parameters, immunological responses, and intestinal microbiome in weaned pigs

Introduction

This study was conducted to evaluate the effects of Lacticaseibacillus casei (Lactobacillus casei) and Saccharomyces cerevisiae mixture on growth performance, hematological parameters, immunological responses, and gut microbiome in weaned pigs.

Methods

A total of 300 crossbred pigs [(Landrace × Yorkshire] × Duroc; 8.87 ± 0.34  kg of average initial body weight [BW]; 4  weeks of age) were divided into two dietary treatments (15 pigs/pen, 10 replicates/treatment) using a randomized complete block design (block = BW): control (CON) and the effective microorganism (MEM). The CON was not treated, while the MEM was treated with the mixture of L. casei (1 × 10⁷ CFU/mL) and S. cerevisiae (1 × 10⁷ CFU/mL) at 3 mL/pig/day for 4  weeks via the drinking water supply. Two feces and one blood sample from the randomly selected pigs in each pen were collected on D1 and D28 after weaning. Pigs were individually weighed, and pen feed intakes were recorded to evaluate pig growth performance. For the gut microbiome analysis, 16S rRNA gene hypervariable regions (V5 to V6) were sequenced using the Illumina MiSeq platform, and Quantitative Insight into Microbial Ecology (QIIME) and Microbiome Helper pipeline were used for 16S rRNA gene sequence analysis.

Results and Discussion

The daily weight gain and feed efficiency of MEM were significantly higher than those of CON (p < 0.001). There were no significant differences in hematological parameters and immune responses between CON and MEM. However, MEM had significantly lower Treponema genus, whereas significantly higher Lactobacillus and Roseburia genera compared to CON. Overall, our data showed that L. casei and S. cerevisiae mixture could promote growth performance through the modulation of gut microbiota in pigs. This study will help to understand the correlation between the growth performance and the gut microbiome.

Early-Life Intervention of Lactoferrin and Probiotic in Suckling Piglets: Effects on Immunoglobulins, Intestinal Integrity, and Neonatal Mortality

The aim of this study was to determine the effects of early-life bovine lactoferrin and host specific probiotic interventions on growth performance, mortality, and concentrations of immunoglobulin A and immunoglobulin G and transforming growth factor beta 1 (a marker of intestinal integrity) in serum of neonatal piglets. A total of eight piglet litters from parity matched sows were randomly divided into four groups and assigned to one of the four interventions: control (sterile normal saline), bovine lactoferrin (100 mg bovine lactoferrin), probiotic (1 × 109 colony forming unit (cfu) of swine origin Pediococcus acidilactici FT28 probiotic), and bovine lactoferrin + probiotic (100 mg bovine lactoferrin and 1 × 109 CFU of P. acidilactici FT28 probiotic). All the interventions were given once daily through oral route for first 7 days of life. The average daily gain (p = 0.0004) and weaning weight (p < 0.0001) were significantly improved in the probiotic group. The piglet survivability was significantly higher in bovine lactoferrin and probiotic groups than control group in Log-rank (Mantel-Cox) test. The concentrations of immunoglobulin A on day 21 in bovine lactoferrin, probiotic, and bovine lactoferrin + probiotic groups increased significantly (p < 0.05). Immunoglobulin G concentrations on day 7 and 15 in bovine lactoferrin and bovine lactoferrin + probiotic groups and on day 15 in probiotic group were significantly (p < 0.05) elevated, whereas, the concentration of transforming growth factor-β1 was significantly (p < 0.05) increased from day 7 to 21 in all the supplemented groups. In conclusion, the early-life bovine lactoferrin and P. acidilactici FT28 probiotic interventions reduced the mortality in the suckling piglets by promoting the systemic immunity and enhancing the intestinal integrity.

Gut microbial shifts by synbiotic combination of Pediococcus acidilactici and lactulose in weaned piglets challenged with Shiga toxin-producing Escherichia coli

Development of alternatives to in-feed antibiotics in the swine industry have been the focused of many pig gut microbiota studies to improve animal health. In this study, we evaluated the effects of probiotic Pediococcus acidilactici (PRO), prebiotic lactulose (PRE), and their synbiotic combination (SYN) on gut microbiota using 16S rRNA gene sequencing in weaned piglets challenged with Shiga-toxin producing Escherichia coli (STEC). Our data showed that prebiotics, probiotics and synbiotics improved the intestinal health in weaned piglets. No significant differences were observed in species richness and species diversity in weaned piglets fed prebiotics, probiotics and their synbiotic combination. However, beta diversity analysis revealed distinct clustering of the microbiota of according to dietary treatment and by oral challenge of STEC. At the phylum level, Firmicutes to Bacteroidetes ratio was lower in the dietary treatment groups than the control group. Oral supplementation of prebiotics, probiotics and synbiotics enriched the abundance of Prevotella and Roseburia. Succinivibrio was elevated in PRO group; however, Phascolarctobacterium was depleted with STEC challenge regardless of dietary treatment. Overall, our data showed that administration of synbiotics in piglets improved intestinal health through gut microbiota modulation. Our data indicated that prebiotics, probiotics and their synbiotic combination could promote intestinal health through gut microbiota modulation in weaned piglets.

Pretreatment with probiotics Enterococcus faecium NCIMB 11181 attenuated Salmonella Typhimurium-induced gut injury through modulating intestinal microbiome and immune responses with barrier function in broiler chickens

Background

Preventing Salmonella infection and colonization in young birds is key to improving poultry gut health and reducing Salmonella contamination of poultry products and decreasing salmonellosis for human consumption (poultry meat and eggs). Probiotics can improve poultry health. The present study was conducted to investigate the impact of a probiotics, Enterococcus faecium NCIMB 11181 (E. faecium NCIMB 11181) on the intestinal mucosal immune responses, microbiome and barrier function in the presence or absence of Salmonella Typhimurium (S. Typhimurium, ST) infection.

Methods

Two hundred and forty 1-day-old Salmonella-free male broiler chickens (Arbor Acres AA⁺) were randomly allocated to four groups with 6 replicate cages of 10 birds each. The four experimental groups were follows: (1) negative control (NC), (2) S. Typhimurium, challenged positive control (PC), (3) the E. faecium NCIMB 11181-treated group (EF), (4) the E. faecium NCIMB 11181-treated and S. Typhimurium-challenged group (PEF).

Results

Results indicated that, although continuous feeding E. faecium NCIMB 11181 did not obviously alleviate growth depression caused by S. Typhimurium challenge (P > 0.05), E. faecium NCIMB 11181 addition significantly blocked Salmonella intestinal colonization and translocation (P < 0.05). Moreover, supplemental E. faecium NCIMB 11181 to the infected chickens remarkably attenuated gut morphological structure damage and intestinal cell apoptosis induced by S. Typhimurium infection, as evidenced by increasing gut villous height and reducing intestinal TUNEL-positive cell numbers (P < 0.05). Also, E. faecium NCIMB 11181 administration notably promoting the production of anti-Salmonella antibodies in intestinal mucosa and serum of the infected birds (P < 0.05). Additionally, 16S rRNA sequencing analysis revealed that E. faecium NCIMB 11181 supplementation ameliorated S. Typhimurium infection-induced gut microbial dysbiosis by enriching Lachnospiracease and Alistipes levels, and suppressing Barnesiella abundance. Predicted function analysis indicated that the functional genes of cecal microbiome involved in C5-branched dibasic acid metabolism; valine, leucine and isoleucine biosynthesis; glycerolipid metabolism and lysine biosynthesis were enriched in the infected chickens given E. faecium NCIMB 11181. While alanine, asparate and glutamate metabolism; MAPK signal pathway-yeast; ubiquine and other terpenoid-quinore biosynthesis, protein processing in endoplasmic reticulum; as well as glutathione metabolism were suppressed by E. faecium NCIMB 11181 addition.

Conclusion

Collectively, our data suggested that dietary E. faecium NCIBM 11181 supplementation could ameliorate S. Typhimurium infection-induced gut injury in broiler chickens. Our findings also suggest that E. faecium NCIMB 11181 may serve as an effective non-antibiotic feed additive for improving gut health and controlling Salmonella infection in broiler chickens.

Probiotics or synbiotics addition to sows’ diets alters colonic microbiome composition and metabolome profiles of offspring pigs

Little information exists about the effects of maternal probiotics and synbiotics addition on the gut microbiome and metabolome of offspring. The present study evaluated the effects of probiotics or synbiotics addition to sows’ diets on colonic microbiota and their metabolites in offspring using 16S rRNA gene sequencing and metabolome strategy. A total of 64 pregnant Bama mini-pigs were randomly divided into control, antibiotic, probiotics, and synbiotics groups and fed the corresponding experimental diets during pregnancy and lactation. After weaning, two piglets per litter and eight piglets per group were selected and fed a basal diet. The β-diversity analysis showed that the colonic microbiota of offspring had a clear distinction among the four groups at 65 days of age. Maternal probiotics addition increased the Actinobacteria abundance at 65 days of age and Tenericutes and Firmicutes abundances at 95 days of age of offspring compared with the other three groups, whereas maternal antibiotic addition increased Spirochaetes and Proteobacteria abundances at 95 days of age of offspring compared with the other three groups. Metabolomic analysis showed that colonic metabolites were different between the groups, regardless of the days of age. Furthermore, both PICRUSt2 and enrichment analysis of metabolic pathways showed that maternal probiotics and synbiotics addition affected metabolism of carbohydrate, amino acid, cofactors and vitamins in the colonic microbiota. Compared with the control group, the colonic concentration of indole decreased and skatole increased in the probiotics group, whereas indole increased and skatole decreased in the synbiotics group. Maternal probiotics addition increased the colonic concentrations of acetate and butyrate at 65 and 125 days of age, whereas probiotics and synbiotics addition decreased short-chain fatty acids concentrations at 95 days of age. In addition, the colonic concentrations of putrescine, cadaverine, 1,7-heptanediamine, and spermidine were increased in the antibiotic, probiotics, and synbiotics groups compared with the control group at 95 days of age. The correlation analysis showed that Gemmiger, Roseburia, and Faecalibacterium abundances were positively correlated with acetate, propionate, and butyrate concentrations; Gemmiger, Blautia, and Faecalibacterium were positively correlated with putrescine and spermidine; and Faecalibacterium, Blautia, Clostridium, and Streptococcus were positively correlated with (R)-3-hydroxybutyric acid. Collectively, these findings suggest that probiotics and synbiotics addition to sows’ diets exerts effects on offspring pigs by altering gut microbiota composition and their metabolites. The potential beneficial effect on gut health is discussed.

Administration of probiotic lactic acid bacteria to modulate fecal microbiome in feedlot cattle

Modulation of animal gut microbiota is a prominent function of probiotics to improve the health and performance of livestock. In this study, a large-scale survey to evaluate the effect of lactic acid bacteria probiotics on shaping the fecal bacterial community structure of feedlot cattle during three experimental periods of the fattening cycle (163 days) was performed. A commercial feedlot located in northwestern Argentina was enrolled with cattle fed mixed rations (forage and increasing grain diet) and a convenience-experimental design was conducted. A pen (n = 21 animals) was assigned to each experimental group that received probiotics during three different periods. Groups of n = 7 animals were sampled at 40, 104 and 163 days and these samples were then pooled to one, thus giving a total of 34 samples that were subjected to high-throughput sequencing. The microbial diversity of fecal samples was significantly affected (p < 0.05) by the administration period compared with probiotic group supplementation. Even though, the three experimental periods of probiotic administration induced changes in the relative abundance of the most representative bacterial communities, the fecal microbiome of samples was dominated by the Firmicutes (72–98%) and Actinobacteria (0.8–27%) phyla, while a lower abundance of Bacteroidetes (0.08–4.2%) was present. Probiotics were able to modulate the fecal microbiota with a convergence of Clostridiaceae, Lachnospiraceae, Ruminococcaceae and Bifidobacteriaceae associated with health and growth benefits as core microbiome members. Metabolic functional prediction comparing three experimental administration periods (40, 104 and 163 days) showed an enrichment of metabolic pathways related to complex plant-derived polysaccharide digestion as well as amino acids and derivatives during the first 40 days of probiotic supplementation. Genomic-based knowledge on the benefits of autochthonous probiotics on cattle gastrointestinal tract (GIT) microbiota composition and functions will contribute to their selection as antibiotic alternatives for commercial feedlot.

Phylogenetic diversity analysis of shotgun metagenomic reads describes gut microbiome development and treatment effects in the post-weaned pig

Intensive farming practices can increase exposure of animals to infectious agents against which antibiotics are used. Orally administered antibiotics are well known to cause dysbiosis. To counteract dysbiotic effects, numerous studies in the past two decades sought to understand whether probiotics are a valid tool to help re-establish a healthy gut microbial community after antibiotic treatment. Although dysbiotic effects of antibiotics are well investigated, little is known about the effects of intramuscular antibiotic treatment on the gut microbiome and a few studies attempted to study treatment effects using phylogenetic diversity analysis techniques. In this study we sought to determine the effects of two probiotic- and one intramuscularly administered antibiotic treatment on the developing gut microbiome of post-weaning piglets between their 3^rd and 9^th week of life. Shotgun metagenomic sequences from over 800 faecal time-series samples derived from 126 post-weaning piglets and 42 sows were analysed in a phylogenetic framework. Differences between individual hosts such as breed, litter, and age, were found to be important contributors to variation in the community composition. Host age was the dominant factor in shaping the gut microbiota of piglets after weaning. The post-weaning pig gut microbiome appeared to follow a highly structured developmental program with characteristic post-weaning changes that can distinguish hosts that were born as little as two days apart in the second month of life. Treatment effects of the antibiotic and probiotic treatments were found but were subtle and included a higher representation of Mollicutes associated with intramuscular antibiotic treatment, and an increase of Lactobacillus associated with probiotic treatment. The discovery of correlations between experimental factors and microbial community composition is more commonly addressed with OTU-based methods and rarely analysed via phylogenetic diversity measures. The latter method, although less intuitive than the former, suffers less from library size normalization biases, and it proved to be instrumental in this study for the discovery of correlations between microbiome composition and host-, and treatment factors.

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.

Synbiotics: a New Route of Self-production and Applications to Human and Animal Health

Synbiotics are preparations in which prebiotics are added to probiotics to achieve superior performance and benefits on the host. A new route of their formation is to induce the prebiotic biosynthesis within the probiotic for synbiotic self-production or autologous synbiotics. The aim of this review paper is first to overview the basic concept and (updated) definitions of synergistic synbiotics, and then to focus particularly on the prebiotic properties of probiotic wall components while describing the environmental factors/stresses that stimulate autologous synbiotics, that is, the biosynthesis of prebiotic-forming microcapsule by probiotic bacteria, and finally to present some of their applications to human and animal health.

Dietary ε-Polylysine Affects on Gut Microbiota and Plasma Metabolites Profiling in Mice

Given the antibacterial effects of ε-polylysine acting on cell membranes, and that glycerol phospholipids are important components of the cell membrane, we hypothesized that ε-polylysine may regulate glycerophospholipid metabolism by modifying the gut microbiota. To test this hypothesis, we treated post-weaning C57 mice with different levels of ε-polylysine (0, 300, 600, and 1,200 ppm) in their basic diet. The growth performance and morphology of intestine were then determined. Modification of the gut microbiota and their function were analyzed using 16S rDNA sequencing. Metabolite identification was performed using the LC-MS method. The results showed that body weight decreased with an increasing supplemental level of ε-polylysine from 5 to 7 weeks (P < 0.05), but no significant difference was observed after 8 weeks (P > 0.05). Supplementation with 1,200 ppm ε-polylysine changed the morphology of the jejunum and ileum, increased the villus length, decreased the crypt depth of the jejunum, and decreased the villus length and crypt depth of the ileum (P < 0.05). ε-Polylysine shifted the intestine microbiota by changing alpha diversity (Chao 1, observed species, Shannon, and Simpson indices) and varied at different times. ε-polylysine decreased Firmicutes and increased Bacteroidetes at 4 week, but increased Firmicutes and decreased Bacteroidetes at 10 week. ε-Polylysine regulated genera associated with lipid metabolism such as Parabacteroides, Odoribacter, Akkermansia, Alistipes, Lachnospiraceae UCG-001, Collinsella, Ruminococcaceae, and Intestinimonas. During the adult period, the genera Alistipes, Lachnospiraceae UCG-001, and Streptomyces were positively associated with PC, PE, LysoPC, LysoPE, 1-Arachidonoylglycerophosphoinositol and OHOHA-PS (R > 0.6, P < 0.001), but changes in Blautia, Christensenellaceae R-7 group, Odoribacter, Allobaculum, Ruminococcaceae UCG-004, Ruminococcaceae UCG-005, and Lachnospiraceae UCG-010 were negatively correlated with glycerophospholipid metabolites (R < −0.6, P < 0.001). The abundance of glycerophospholipid metabolites, including PC, PE, lysoPC, and lysoPE, were decreased by ε-polylysine. Furthermore, ε-polylysine reduced the incidence of the genera including Ruminococcus, Prevotella, Prevotellaceae, Butyricimonas, and Escherichia-Shigella and reduced the abundance of Faecalibaculum, Christensenellaceae R-7 group, Coriobacteriaceae UCG-002. In conclusion, ε-polylysine modified gut microbiota composition and function while also restraining pathogenic bacteria. The glycerophospholipid metabolism pathway and associated metabolites may be regulated by intestinal bacteria.

Multi-omics reveals host metabolism associated with the gut microbiota composition in mice with dietary ε-polylysine

This study aimed to assess the influence of dietary supplementation of ε-polylysine on the gut microbiota and host nutrient metabolism, which is not systematically discussed by multi-omics analysis. A total of 40 mice were randomly divided into two groups exposed to either a basal diet (AIN-76A) or a basal diet with 150 ppm ε-polylysine. Fecal samples were collected for gut bacteria identification. Liver and plasma samples were collected for metabolomic and proteomic analyses. The results showed that ε-polylysine decreased the body weight of mice and affected the presence of certain types of intestinal microorganisms. The richness of the microbiota and number of phyla increased with age. ε-Polylysine affected the presence of genera and species, and either regulated or took part in the metabolism of energy, nitrogen, amino acids, lipids, carbohydrates, glycans, cofactors, and vitamins. The metabolite profiling showed that lipid and lipid-like molecules metabolites occupied the majority percent of plasma and liver metabolites. Additionally, ε-polylysine regulated the key role of metabolites and related metabolic enzymes in the metabolic pathways, especially phospholipid metabolism. In conclusion, dietary ε-polylysine improved the immunity of growing mice, and had a greater effect on the anabolism of nutrients in adult mice.

In vitro and in vivo activity of new strains of Bacillus subtilis against ESBL-producing Escherichia coli: an experimental study

AIMS

The gastro-intestinal tract is a major reservoir of extended-spectrum beta-lactamase (ESBL) producing Escherichia coli. Bacillus spores may be used as probiotics to decrease digestive colonization by ESBL-E. coli. Our aim was to assess the in vitro and in vivo activity of new Bacillus strains against ESBL-E. coli.

METHODS AND RESULTS

We screened the in vitro activity of 50 Bacillus strains against clinical isolates of ESBL-E. coli and selected B. subtilis strains CH311 and S3B. Both strains decreased ESBL-E. coli titers by 4 log₁₀ CFU L^-1 in an in vitro model of gut content, whereas the B. subtilis CU1 strain did not. In a murine model of intestinal colonization by ESBL-E. coli, CH311 and S3B did not decrease fecal titers of ESBL-E. coli. Ten sequences of putative antimicrobial peptides were identified in the genomes of CH311 and S3B, but not in CU1.

CONCLUSIONS

Two new B. subtilis strains showed strong in vitro activity against ESBL-E. coli.

SIGNIFICANCE AND IMPACT OF STUDY

Despite strong in vitro activities of new B. subtilis strains against ESBL-E. coli, intestinal colonisation was not altered by curative Bacillus treatment even if their spores proved to germinate in the gut. Thus, this work underlines the importance of in vivo experiments to identify efficient probiotics. The use of potential antimicrobial compounds identified by genome sequencing remains an attractive alternative to explore.

The microbiota in cirrhosis and its role in hepatic decompensation

Cirrhosis - the common end-stage of chronic liver disease - is associated with a cascade of events, of which intestinal bacterial overgrowth and dysbiosis are central. Bacterial toxins entering the portal or systemic circulation can directly cause hepatocyte death, while dysbiosis also affects gut barrier function and increases bacterial translocation, leading to infections, systemic inflammation and vasodilation, which contribute to acute decompensation and organ failure. Acute decompensation and its severe forms, pre-acute-on-chronic liver failure (ACLF) and ACLF, are characterised by sudden organ dysfunction (and failure) and high short-term mortality. Patients with pre-ACLF and ACLF present with high-grade systemic inflammation, usually precipitated by proven bacterial infection and/or severe alcoholic hepatitis. However, no precipitant is identified in 30% of these patients, in whom bacterial translocation from the gut microbiota is assumed to be responsible for systemic inflammation and decompensation. Different microbiota profiles may influence the rate of decompensation and thereby outcome in these patients. Thus, targeting the microbiota is a promising strategy for the prevention and treatment of acute decompensation, pre-ACLF and ACLF. Approaches include the use of antibiotics such as rifaximin, faecal microbial transplantation and enterosorbents (e.g. Yaq-001), which bind microbial factors without exerting a direct effect on bacterial growth kinetics. This review focuses on the role of microbiota in decompensation and strategies targeting microbiota to prevent acute decompensation.

Response of Growth Performance, Blood Biochemistry Indices, and Rumen Bacterial Diversity in Lambs to Diets Containing Supplemental Probiotics and Chinese Medicine Polysaccharides

This study aims to investigate the effects of probiotics and Chinese medicine polysaccharides (CMPs) on growth performance, blood indices, rumen fermentation, and bacteria composition in lambs. Forty female lambs were randomly divided into four groups as follows: control, probiotics, CMP, and compound (probiotics + CMP) groups. The results showed that probiotics treatment increased the concentrations of blood glucose (GLU) and immunoglobulin G (IgG) and enhanced rumen microbial protein contents but declined the value of pH in rumen fluid compared with the control (P < 0.05). Furthermore, supplementation with CMP enhanced the average daily gain (ADG) and the contents of IgA, IgG, and IgM in the serum but decreased the F:G ratio compared with the control (P < 0.05). Besides, both CMP and compound (probiotics + CMP) treatments decreased the ratio of acetic acid and propionic acid compared with the control (P < 0.05). High-throughput sequencing data showed that at the genus level, the relative abundance of Veillonellaceae_UCG-001 in the probiotics group was increased, the relative abundance of Succiniclasticum and norank_f__Muribaculaceae in the CMP group were enhanced, and the relative abundance of Ruminococcaceae_UCG-002 in the compound group was raised compared with the control (P < 0.05). In summary, supplementation with probiotics can promote rumen protein fermentation but decrease the diversity of bacteria in rumen fluid; however, CMP treatment increased the relative abundance of Fibrobacteria, changed rumen microbial fermentation mode, increased the immune function, and ultimately improved the growth performance.

Olive Fruit Extracts Supplement Improve Antioxidant Capacity via Altering Colonic Microbiota Composition in Mice

Oxidative stress, one of the most common biological dysfunctions, is usually associated with pathological conditions and multiple diseases in humans and animals. Chinese olive fruit (Canarium album L.) extracts (OE) are natural plant extracts rich in polyphenols (such as hydroxytyrosol, HT) and with antioxidant, anti-hyperlipidemia, and anti-inflammatory potentials. This study was conducted to investigate the antioxidant capacity of OE supplementation and its related molecular mechanism in mice. Mice (25.46 ± 1.65 g) were treated with 100 mg/kg body weight (BW) OE or saline solution for 4 weeks, and then the antioxidant and anti-inflammatory capacities of mice were examined. The results showed that OE supplement significantly increased the serum antioxidative enzyme activities of total antioxidant activity (T-AOC), superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), and catalase and decreased the serum malondialdehyde (MDA) level, indicating that OE treatment enhanced the antioxidant capacity in mice. qPCR results showed that the transcriptional expression of antioxidant SOD1, CAT, Gpx1, and Gpx2 were significantly down-regulated in the small intestine (jejunum and ileum) after OE administration. Meanwhile, OE treatment significantly decreased the T-AOC and increased the MDA level in the small intestine. Furthermore, OE administration dramatically reduced the mRNA expression of pro-inflammatory cytokines (TNF-α and IL-1β), which confirmed its antioxidant and anti-inflammatory capacities with OE administration. Using amplicon sequencing technology, 16S rRNA sequencing results showed that OE supplement significantly increased the colonic Firmicutes/Bacteroidetes ratio, which also had a negative correlation with the serum MDA level and positively correlated with serum GSH-Px activity through Pearson correlation analysis. Besides that, Alloprevotella was negatively correlated with serum T-AOC. Colidextribacter was positively correlated with serum MDA and negatively correlated with serum T-AOC, SOD, and GSH-Px levels. In summary, this study showed that treatment with 100 mg/kg BW polyphenol-rich OE could alter colonic microbiota community, which was strongly associated with improved antioxidant capacity in mice.

Probiotics mediated gut microbiota diversity shifts are associated with reduction in histopathology and shedding of Lawsonia intracellularis

BACKGROUND

Clinical intervention during bacterial infections in farm animals such as pigs commonly includes the use of antimicrobials. With the rise of antimicrobial resistance and the attempts to reduce the use of antibiotics in food animals, effective alternatives are urgently needed to reduce or even remove pathogens and disease risks. Improving clinical outcomes and overall pig health by using probiotics appears attractive. However, reliable data sets on the efficacy of probiotics are scarce. The obligate intracellular bacterium Lawsonia intracellularis is widespread in pigs and associated with severe enteropathy, mainly in the ileum, commonly resulting in substantial reduction in weight gain. The impact of three in-feed probiotics and a commercial live L. intracellularis vaccine was compared in a pig challenge model. Probiotic treatment was associated with reduced L. intracellularis fecal shedding and reduced gut lesions. Here, the bacterial microbiota of the ileum of these pigs was characterized with 16S rRNA gene sequencing and was subsequently analyzed with bioinformatics tools.

RESULTS

The greatest microbial richness was observed in the probiotic treated group T03-LAW, which accounted for 87% of richness observed in the study. Treatment had a significant impact on both the microbiota structure and taxonomic profile in the ileum, explaining between 26 and 36% of the structural variation, with the strongest association in the T03-LAW group. Overall, the largest changes were observed for the pigs treated with in-feed Bacillus pumilus; the microbiota of these pigs had the greatest diversity and highest richness. We also observed depleted and enriched core microbiota amongst the groups; however, there was no correlation with clinical characteristics. The results suggest that an increased diversity of the ileal microbiota is associated with a reduction in shedding, i.e. a unit increase in Shannon diversity index resulted in 2.8 log reduction in shedding.

CONCLUSIONS

Probiotic supplementation of a base feed ration increased ileum microbiota diversity leading to a mitigation of the effects of a pathogenic L. intracellularis challenge. An even and diverse microbiota community benefits pigs infected with L. intracellularis, however, investigations are needed to determine if this is also true for other pathogens. The study unambiguously demonstrates the usefulness of probiotic supplementation in reducing the impact of enteric pathogens and pathogen shedding rates in food animals without the use of antimicrobials.

Modern concept of probiotics and principles of development of new-generation symbiotic preparations

The purpose of this work is to review data on the biological effectiveness of probiotics, their mechanisms of action, and the prospects for the development of new-generation preparations. Scientific and practical justification of symbiotic drugs of a new generation – metabiotics as a continuation of the probiotic concept is given. The authors discuss the literature data and their own results, which allow them to propose new approaches to the creation of symbiotic drugs. The authors scientifically substantiate the main scientific provisions of the probiotic concept for the development of new-generation symbiotic drugs:

The Effect of Recently Developed Synbiotic Preparations on Dominant Fecal Microbiota and Organic Acids Concentrations in Feces of Piglets from Nursing to Fattening

Simple Summary

Widespread antibiotic resistance among microorganisms led to a prohibition or limitation of using antibiotic growth promoters in livestock breeding. In order to maintain the animal production on the level which could satisfy the demands, and to reduce the risk of infections occurrence among the livestock, alternative preparations are being searched for. Pro- and prebiotics are wildly studied; however, their combination, which are called synbiotics, are expected to impact animals’ health more considerably. There are a number of pro- and prebiotic preparations available on the market; nevertheless, synbiotics are rare, which is why this research was focused on their impact on pigs’ intestinal microbiota and organic acids synthesis. The results showed that newly developed synbiotics could have a more beneficial impact on piglets’ health rather than commercial probiotics.

Abstract

The study was conducted to determine the influence of newly elaborated synbiotic preparations on piglets’ intestinal microbiota and its metabolism. Animals were distributed among six experimental groups, in reference to used feed supplements, namely, synbiotics (A, B, or C) or commercially available probiotics (BioPlus 2B^®, Chr. Hansen A/S, Horsholm, Denmark or Cylactin^® LBC, DSM Nutritional Products Ltd., Kaiseraugst, Switzerland), or its absence (control group). Until the 29th day of life, piglets were breastfed by sows, whose feed was supplemented, and fecal samples were collected at the 7th and 28th day of piglets’ life. After weaning of the piglets, the research was continued until the 165th day of the pigs’ life. The area of this work included the analysis of the piglets’ dominant fecal microbiota by the plate count method. Moreover, high-performance liquid chromatography analysis (HPLC) was applied to establish variations in the concentrations of organic acids, namely, lactic acid, short-chain fatty acids (SCFAs), and branched-chain fatty acids (BCFAs). It was observed that synbiotics have a more significant beneficial effect on the intestinal microbiota of piglets and their metabolism, and therefore their health, in comparison to commercial probiotics used individually. Moreover, synbiotic preparations prevent the negative impact of weaning on piglets’ microbial population in the gastrointestinal tract, which could reduce the occurrence of diarrhea.

Comparative assessment of faecal microbial composition and metabonome of swine, farmers and human control

The gastrointestinal tract of humans and swine consist of a wide range of bacteria which interact with hosts metabolism. Due to the differences in co-evolution and co-adaptation, a large fraction of the gut microbiome is host-specific. In this study, we evaluated the effect of close human-animal interaction to the faecal metagenome and metabonome of swine, farmer and human control. Three distinct clusters were observed based on T-RFLP-derived faecal microbial composition. However, 16S-inferred faecal microbiota and metabolic profiles showed that only human control was significantly different from the swine (P < 0.05). The metabonome of farmers and human controls were highly similar. Notably, higher trimethylamine N-oxide (TMAO) and butyrate were detected in human control and swine, respectively. The relative abundance of TMAO was positively correlated with Prevotella copri. Overall, we compared and established the relationship between the metabolites and microbiota composition of swine, farmers and human control. Based on the data obtained, we deduced that long term occupational exposure to swine and farm environment had affected the gut bacterial composition of farmers. Nonetheless, the effect was less prominent in the metabolite profiles, suggesting the gut bacteria expressed high functional plasticity and are therefore resilience to the level of community shift detected.

Gut-derived Enterococcus faecium from ulcerative colitis patients promotes colitis in a genetically susceptible mouse host

Background

Recent metagenomic analyses have revealed dysbiosis of the gut microbiota of ulcerative colitis (UC) patients. However, the impacts of this dysbiosis are not fully understood, particularly at the strain level.

Results

We perform whole-genome shotgun sequencing of fecal DNA extracts from 13 healthy donors and 16 UC and 8 Crohn’s disease (CD) patients. The microbiota of UC and CD patients is taxonomically and functionally divergent from that of healthy donors, with E. faecium being the most differentially abundant species between the two microbial communities. Transplantation of feces from UC or CD patients into Il10^−/− mice promotes pathological inflammation and cytokine expression in the mouse colon, although distinct cytokine expression profiles are observed between UC and CD. Unlike isolates derived from healthy donors, E. faecium isolates from the feces of UC patients, along with E. faecium strain ATCC 19434, promotes colitis and colonic cytokine expression. Inflammatory E. faecium strains, including ATCC 19434 and a UC-derived strain, cluster separately from commercially available probiotic strains based on whole-genome shotgun sequencing analysis. The presence of E. faecium in fecal samples is associated with large disease extent and the need for multiple medications in UC patients.

Conclusions

E. faecium strains derived from UC patients display an inflammatory genotype that causes colitis.

Lactulose drives a reversible reduction and qualitative modulation of the faecal microbiota diversity in healthy dogs

Hepatic encephalopathy is a frequent and debilitating complication of liver disorders. Lactulose is an established and reasonably effective treatment, yet with incompletely understood mechanisms of action. The aims of this study were to examine how the faecal microbiota composition changed before, during and after lactulose treatment in a large animal model. Healthy, privately owned dogs (n = 18) completed a prospective cohort study. Faecal samples were collected weekly, while the subjects were either on their usual diet (week 1), or a standardised diet (weeks 2–9), with added oral lactulose in weeks 6–7. DNA extraction and 16S rRNA gene sequencing were undertaken. Faecal samples from week 7 had a significantly lower microbiota richness/diversity, based on observed operational taxonomic units, Shannon/Chao1 indexes and Pielou’s Evenness. Beta diversity based on UniFrac distances was significantly different in week 7 compared to weeks 1, 5 and 9. At the phylum level, week 7 was associated with a significant increase of Firmicutes and Actinobacteria, and a decrease of Bacteroidetes and Fusobacteria, when compared to weeks 5 and 9. In summary, we have shown that lactulose induces a reversible qualitative and quantitative change of the faecal microbiota, which may explain its clinical efficacy in the management of hepatic encephalopathy.

Synbiotics impact on dominant faecal microbiota and short-chain fatty acids production in sows

The aim of this study was to estimate the influence of synbiotics on intestinal microbiota and its metabolism in sows. Three different synbiotics were administered with feed to animals from three experimental groups. Two groups of sows were given commercially available probiotics (BioPlus 2B®, Cylactin® LBC) as forage additives for comparison. The control group of sows was given unmodified fodder. The study was conducted for 48 days (10 days before farrowing, and continued 38 days after) and faeces samples were collected four times. The scope of this work was to designate the dominant microbiota in sows' faeces. Therefore, the total number of anaerobic bacteria, Bifidobacterium sp., Lactobacillus sp., Bacteroides sp., Clostridium sp., Enterococcus sp., Enterobacteriaceae, Escherichia coli and yeast was determined, using the plate method. Changes in the concentration of lactic acid, short-chain fatty acids (SCFAs) and branched-chain fatty acids (BCFAs) were also determined in correlation with the feed additives administered to the sows using high-performance liquid chromatography analysis (HPLC). Our results allowed us to conclude that synbiotics have a beneficial effect on intestinal microbiota of sows and its metabolism. We observed that the impact of the synbiotics on the microbiota was more significant than the one induced by probiotics.

Effects of phycocyanin in modulating the intestinal microbiota of mice

The health‐promoting effects of phycocyanin (PC) have become widely accepted over the last two decades. In this study, we investigated the effects of different doses of PC in modulating the intestinal microbiota and the intestinal barrier in mice. Six‐week‐old male C57BL/6 mice were treated with PC for 28 days. Fecal samples were collected before and after PC intervention, and the microbiota were analyzed by 16S rRNA high‐throughput sequencing. Bacterial abundance and diversity increased after PC intervention. Saccharolytic bacteria of the families Lachnospiraceae and Ruminococcaceae, which can produce butyric acid, increased after PC treatment. The family Rikenellaceae, which contains hydrogen‐producing bacteria, also increased after PC intervention. The PC treatment reduced intestinal permeability and increased the intestinal barrier function, as demonstrated by hematoxylin–eosin staining and reduced serum lipopolysaccharide levels. The modulating effects on the intestinal microbiota were more favorable in the low‐dose PC group.

Effects of Dietary Supplementation With Enterococcus faecium and Clostridium butyricum, Either Alone or in Combination, on Growth and Fecal Microbiota Composition of Post-weaning Pigs at a Commercial Farm

Lactic acid bacteria (LAB) and butyric acid bacteria (BAB) are commonly used as probiotics in swine production. However, their combined effect on post-weaning pigs has not been assessed. Therefore, here we investigated the individual and combined efficacy of dietary Enterococcus faecium and Clostridium butyricum on the growth and gut microbiota of post-weaning pigs at a commercial farm. Four independent trials were conducted, in each of which five pens containing 10 pigs were assigned to one of five treatments: C, basal diet; L, basal diet + live E. faecium; D, basal diet + heat-killed E. faecium; M, basal diet + C. butyricum; or L+M, basal diet + live E. faecium + C. butyricum. Each trial was conducted over a 90-day period that was divided into two phases (Phase 1, days 0–40 post-weaning; and Phase 2, days 40–90 post-weaning), with the probiotics being supplemented only during Phase 1. Ten pigs in each pen were used for body weight (BW) analysis and fecal samples were collected from five or six of these pigs. In addition, the fecal samples from one randomly selected trial were used for gut microbiota analysis. We found that pigs in the L, D, and L+M treatment groups had a significantly higher BW than those in C (p < 0.05) but pigs in the L+M treatment group had a similar BW to those in the L and M groups. Furthermore, there were no significant differences in alpha diversity among the treatments but the beta diversity (weighted UniFrac distances) showed distinct clustering patterns, with pigs in C having discrete microbiota from those in all of the probiotics treatment groups except D (C vs. L, q = 0.04; C vs. M, q = 0.06; C vs. L+M, q = 0.06). These findings indicate that dietary supplementation with live or heat-killed E. faecium enhances growth performance in pigs but there is no synergistic effect when E. faecium is used in combination with C. butyricum. Furthermore, the addition of live E. faecium and C. butyricum to the diet of pigs may change the structure of the gut microbiota.

Piglet gut microbial shifts early in life: causes and effects

The gut microbiome has long been known to play fundamentally important roles in the animal health and the well-being of its host. As such, the establishment and maintenance of a beneficial gut microbiota early in life is crucial in pigs, since early gut colonizers are pivotal in the establishment of permanent microbial community structures affecting the health and growth performance of pigs later in life. Emphasizing this importance of early gut colonizers, it is critical to understand the factors impacting the establishment of the piglet gut microbiome at weaning. Factors include, among others, diet, in-feed antibiotics, probiotics and prebiotic administration. The impact of these factors on establishment of the gut microbiome of piglets at weaning includes effects on piglet gut microbial diversity, structure, and succession. In this review, we thoroughly reviewed the most recent findings on the piglet gut microbiome shifts as influenced by weaning, and how these microbiome changes brought about by various factors that have been shown to affect the development of microbiota in piglets. This review will provide a general overview of recent studies that can help to facilitate the design of new strategies to modulate the gut microbiome in order to enhance gastrointestinal health, growth performance and well-being of piglets.

Effects of Clostridium butyricum and Enterococcus faecalis on growth performance, immune function, intestinal morphology, volatile fatty acids, and intestinal flora in a piglet model

We investigated the effects of Clostridium butyricum and Enterococcus faecalis (probiotics) in a piglet model.

Dissect the mode of action of probiotics in affecting host-microbial interactions and immunity in food producing animals

Prophylactic antimicrobials have been widely used in food animal production with the aim to prevent infectious diseases, enhance feed efficiency, and promote growth. However, the extensive use of antimicrobials in food animal production systems has led to the emergence of antimicrobial resistant pathogens, which are potential threats to human and animal health. Probiotics have been proposed to be a promising alternative of prophylactic antimicrobials, with potential beneficial effects on the host animal by improving the balance of intestinal microbiota and host immunity. Although an increasing body of evidence shows that probiotics could directly or indirectly affect gut microbiota and host immune functions, the lack of the understanding of how probiotics influence host-microbial interaction and immunity is one of the reasons for controversial findings from many animal trials, especially in food production animals. Therefore, in this review we focused on the most recent (last ten years) studies on how gut microbiota and host immune function changes in response to probiotics in food production animals (swine, poultry, and ruminant). In addition, the relationship between microbial changes and host immune function was illustrated, and how such relationship differs among animal species was further compared. Moreover, the future directions concerning the mechanisms of how probiotics modulate host-microbial interactions and host immunity were highlighted, which may assist in the optimal supplementation strategy to maximize the efficacy of probiotics to improve animal gut health and productivity.

Camellia Oil ( Camellia oleifera Abel.) Modifies the Composition of Gut Microbiota and Alleviates Acetic Acid-Induced Colitis in Rats

Ulcerative colitis (UC), one type of chronic inflammatory bowel disease (IBD), is a chronic and recurrent disorder of the gastrointestinal (GI) tract. As camellia oil (CO) is traditionally used to treat GI disorders, this study investigated the role of CO on acetic acid-induced colitis in the rat. The composition of the gut microbial community is related to many diseases; thus, this study also investigated the effects of CO on the composition of the gut microbiota. The rats were fed a dose of 2 mL/kg body weight CO, olive oil (OO), or soybean oil (SO) once a day for 20 days, and the gut microbiota was analyzed using 16S rRNA gene sequencing. Results of the gut microbiota examination showed significant clustering of feces after treatment with CO and OO; however, individual differences with OO varied considerably. Compared to SO and OO, the intake of CO increased the ratio of Firmicutes/Bacteroidetes, the α-diversity, relative abundance of the Bifidobacterium, and reduced Prevotella of the gut microbiota. On day 21, colitis was induced by a single transrectal administration of 2 mL of 4% acetic acid. However, pretreatment of rats with CO or OO for 24 days slightly enhanced antioxidant and antioxidant enzyme activities and significantly reduced inflammatory damage and lipid peroxidation, thus ameliorating acetic acid-induced colitis. These results indicated that CO was better able to ameliorate impairment of the antioxidant system induced by acetic acid compared to OO and SO, which may have been due to CO modifying the composition of the gut microbiota or CO being a rich source of phytochemicals.

Effect of lactulose intervention on gut microbiota and short chain fatty acid composition of C57BL/6J mice

Gut microbiota have strong connections with health. Lactulose has been shown to regulate gut microbiota and benefit host health. In this study, the effect of short‐term (3 week) intervention of lactulose on gut microbiota was investigated. Gut microbiota were detected from mouse feces by 16S rRNA high‐throughput sequencing, and short chain fatty acids (SCFAs) were detected by gas chromatography‐mass spectrometry (GC‐MS). Lactulose intervention enhanced the α‐diversity of the gut microbiota; increased the abundance of hydrogen‐producing bacteria Prevotellaceae and Rikenellaceae, probiotics Bifidobacteriaceae and Lactobacillaceae, and mucin‐degrading bacteria Akkermansia and Helicobacter; decreased the abundance of harmful bacteria Desulfovibrionaceae and branched‐chain SCFAs (BCFAs). These results suggest that lactulose intervention effectively increased the diversity and improved the structure of the intestinal microbiota, which may be beneficial for host health.

Probiotic roles of Lactobacillus sp. in swine: insights from gut microbiota

The use of lactobacilli as probiotics in swine has been gaining attention due to their ability to improve growth performance and carcass quality, prevent gastrointestinal infection and most importantly, their 'generally recognized as safe' status. Previous studies support the potential of lactobacilli to regulate host immune systems, enhance gut metabolic capacities and maintain balance in the gut microbiota. Research on swine gut microbiota has revealed complex gut microbial community structure and showed the importance of Lactobacillus to the host's health. However, the species- and strain-specific characteristics of lactobacilli that confer probiotic benefits are still not well understood. The diversity of probiotic traits in a complex gut ecosystem makes it challenging to infer the relationships between specific functions of Lactobacillus sp. and host health. In this review, we provide an overview of how lactobacilli play a pivotal role in the swine gut ecosystem and identify key characteristics that influence gut microbial community structure and the health of pigs. In addition, based on recent and ongoing meta-omics and omics research on the gut microbiota of pigs, we suggest a workflow combining culture-dependent and culture-independent approaches for more effective selection of probiotic lactobacilli.

Protective effects of Bacillus subtilis against Salmonella infection in the microbiome of Hy-Line Brown layers

Objective

This study investigated the effects of Bacillus subtilis CSL2 (B. subtilis CSL2) administration before Salmonella challenge on the fecal microbiota and microbial functionality of Hy-line Brown (HLB) laying hens.

Methods

Fecal samples were collected from control (CON), Salmonella-infected (SAL) and Salmonella-infected, probiotic-treated (PRO) groups before and after Salmonella challenge for microbiome analysis using 16S rRNA gene pyrosequencing.

Results

Infection with Salmonella led to decreased microbial diversity in hen feces; diversity was recovered with Bacillus administration. In addition, Salmonella infection triggered significant alterations in the composition of the fecal microbiota. The abundance of the phylum Firmicutes decreased while that of Proteobacteria, which includes a wide variety of pathogens, increased significantly. Bacillus administration resulted in normal levels of abundance of Firmicutes and Proteobacteria. Analysis of bacterial genera showed that Salmonella challenge decreased the population of Lactobacillus, the most abundant genus, and increased populations of Pseudomonas and Flavobacterium genera by a factor of 3 to 5. On the other hand, Bacillus administration caused the abundance of the Lactobacillus genus to recover to control levels and decreased the population of Pseudomonas significantly. Further analysis of operational taxonomic units revealed a high abundance of genes associated with two-component systems and secretion systems in the SAL group, whereas the PRO group had more genes associated with ribosomes.

Conclusion

The results of this study indicate that B. subtilis CSL2 administration can modulate the microbiota in HLB laying hens, potentially acting as a probiotic to protect against Salmonella Gallinarum infection.

Revealing the combined effects of lactulose and probiotic enterococci on the swine faecal microbiota using 454 pyrosequencing

Demand for the development of non‐antibiotic growth promoters in animal production has increased in recent years. This report compared the faecal microbiota of weaned piglets under the administration of a basal diet (CON) or that containing prebiotic lactulose (LAC), probiotic Enterococcus faecium NCIMB 11181 (PRO) or their synbiotic combination (SYN). At the phylum level, the Firmicutes to Bacteroidetes ratio increased in the treatment groups compared with the CON group, and the lowest proportion of Proteobacteria was observed in the LAC group. At the family level, Enterobacteriaceae decreased in all treatments; more than a 10‐fold reduction was observed in the LAC (0.99%) group compared with the CON group. At the genus level, the highest Oscillibacter proportion was detected in PRO, the highest Clostridium in LAC and the highest Lactobacillus in SYN; the abundance of Escherichia was lowest in the LAC group. Clustering in the discriminant analysis of principal components revealed distinct separation of the feeding groups (CON, LAC, PRO and SYN), showing different microbial compositions according to different feed additives or their combination. These results suggest that individual materials and their combination have unique actions and independent mechanisms for changes in the distal gut microbiota.