Effect of Bacillus subtilis CGMCC 1.1086 on the growth performance and intestinal microbiota of broilers

Effects of Bacillus subtilis and coccidial vaccination on cecal microbial diversity and composition of Eimeria-challenged male broilers

In a companion study, the effects of dietary antibiotic alternative and coccidial vaccination on the growth performance of male broilers have been reported. In this paper, the effects of dietary probiotics and coccidial vaccination on diversity and composition of cecal microbiota were investigated using a 3 (diets) × 2 (vaccinated or non-vaccinated) factorial setting of treatments. Three diets, including a corn and soybean-meal control diet, an antibiotic diet (a control diet supplemented with bacitracin and salinomycin), and a probiotic diet (a control diet supplemented with Bacillus subtilis) were provided to broiler chicken from day 0 to 42. To simulate an Eimeria challenge in the field, all chicks were gavaged with a 20× dose of commercial coccidial vaccine containing live Eimeria oocysts on day 14. Cecal contents were collected on day 42. High-throughput sequencing of the 16S rRNA gene was used to determine microbial diversity and composition. Coccidial vaccination to broilers reduced bacterial diversity (Shannon index) of the cecal microbiota. There was a significant interaction between the dietary additive and coccidial vaccination on the observed bacterial species number. Diets supplemented with B. subtilis increased bacterial species of non-vaccinated broilers but decreased bacterial species of vaccinated broilers. In contrast, diets supplemented with antibiotics reduced bacterial species of broilers from both groups. Interactions between dietary additive and coccidial vaccination were also observed on microbial composition. Vaccinated broilers fed the B. subtilis diet exhibited the lowest Firmicutes percentage and highest Bacteroidetes percentage within the microbial community. In addition, vaccinated broilers fed the B. subtilis diet exhibited the highest Rikenella microfusus percentage. From this study, the coccidial vaccination on the day of hatch reduced the microbial diversity of broilers at a later age. The inclusion of B. subtilis-probiotics in the feed of vaccinated broilers may reduce microbial diversity in cecal content by increasing the proportion of a predominant bacterial species, R. microfusus, in the microbial community.

Growth performance, apparent retention of components, and excreta dry matter content in Shaver White pullets (5 to 16 week of age) in response to dietary supplementation of graded levels of a single strain Bacillus subtilis probiotic

Administered in adequate amounts, probiotics can be an alternative to antibiotic growth promoters in poultry production. This study evaluated dose response of a single strain of Bacillus subtilis (SSB, DSM29784) on growth performance, apparent retention (AR) of components, and excreta DM content in pullets. A basal corn-soybean meal diet was formulated to meet the specifications for grower (week 5 to 10) and developer (week 11 to 16) phases. In each phase, SSB was added to the basal diet to create 4 test diets: 0 (control, CON), 1.1E+08 (low; LSSB), 2.2E+08 (medium; MSSB), or 1.1E+09 (high; HSSB) CFU of SSB/kg of feed. All diets had TiO2 (0.5%) as a digestibility marker. A total of 720 day-old Shaver White chicks were placed in 48 cages (15 pullets per cage) and reared on a commercial antibiotic free diet for a 4-wk period. At the beginning of week 5, treatments were allocated based on cage BW (n = 12). Birds had free access to feed and water throughout. The BW, BW uniformity, feed intake (FI) and FCR were obtained weekly. Excreta was collected at the end of each phase for AR of DM, organic matter, CP, neutral detergent fiber, minerals, and AME, as well as excreta DM content. In response to SSB inclusion, BW improved in a linear (P < 0.005) and quadratic (P < 0.0001) manner in grower. FI decreased in a linear and quadratic pattern (P < 0.05, week 8 to 10) in grower, and linearly (P < 0.05) across the developer phase. Overall FCR improved in linear and quadratic pattern (P < 0.01) in the grower phase. In both the phases, AME improved in a quadratic pattern (P < 0.05). Inclusion of SSB had a linear reduction (P < 0.0001) in excreta moisture content in the grower phase. In summary, these results demonstrate that B. subtilis probiotic improved performance through enhanced nutrient utilization and reduced excreta moisture content indicating improved pullet gut health.

Effects of multi-strain probiotic supplementation on intestinal microbiota, tight junctions, and inflammation in young broiler chickens challenged with Salmonella enterica subsp. enterica

Objective

This study assessed the effects of probiotics on cecal microbiota, gene expression of intestinal tight junction proteins, and immune response in the cecal tonsil of broiler chickens challenged with Salmonella enterica subsp. enterica.

Methods

One-day-old broiler chickens (n = 240) were randomly allocated to four treatments: negative control (Cont), multi-strain probiotic-treated group (Pro), Salmonella-infected group (Sal), and multi-strain probiotic-treated and Salmonella-infected group (ProSal). All chickens except those in the Cont and Pro groups were gavaged with 1×10⁸ cfu/mL of S. enterica subsp. enterica 4 days after hatching.

Results

Our results indicated that body weight, weight gain, and feed conversion ratio of birds were significantly reduced (p<0.05) by Salmonella challenge. Chickens challenged with Salmonella decreased cecal microbial diversity. Chickens in the Sal group exhibited abundant Proteobacteria than those in the Cont, Pro, and ProSal groups. Salmonella infection downregulated gene expression of Occludin, zonula occludens-1 (ZO1), and Mucin 2 in the jejunum and Occludin and Claudin in the ileum. Moreover, the Sal group increased gene expression of interferon-γ (IFN-γ), interleukin-6 (IL-6), IL-1β, and lipopolysaccharide-induced tumor necrosis factor-alpha factor (LITAF) and reduced levels of transforming growth factor-β4 and IL-10 compared with the other groups (p<0.05). However, chickens receiving probiotic diets increased Lactobacillaceae abundance and reduced Enterobacteriaceae abundance in the ceca. Moreover, supplementation with probiotics increased the mRNA expression of Occludin, ZO1, and Mucin 2 in the ileum (p<0.05). In addition, probiotic supplementation downregulated the mRNA levels of IFN-γ (p<0.05) and LITAF (p = 0.075) and upregulated IL-10 (p = 0.084) expression in the cecal tonsil.

Conclusion

The administration of multi-strain probiotics modulated intestinal microbiota, gene expression of tight junction proteins, and immunomodulatory activity in broiler chickens.

Effects of peanut meal extracts fermented by Bacillus natto on the growth performance, learning and memory skills and gut microbiota modulation in mice

Recent studies have demonstrated that the nutritional properties of peanut meal (PM) can be improved after being fermented. The assessment of fermented PM has been reported to be limited to various physical and chemical evaluations in vitro. In the present study, PM was fermented by Bacillus natto to explore the effects of fermented PM extract (FE) on growth performance, learning and memory ability and intestinal microflora in mice. Ninety newly weaned male Kunming (KM) mice were randomly divided into seven groups: normal group (n 20), low-dose FE group (n 10), middle-dose FE group (MFE) (n 10), high-dose FE group (HFE) (n 20), unfermented extraction group (n 10), model group (10) and natural recovery group (10). Learning and memory skills were performed by the Morris water maze (MWM) test, and the variation in gut microbiota (GM) composition was assessed by 16S rDNA amplicon sequencing. The results show that HFE remarkably improved the growth performance in mice. In the MWM test, escape latency was shortened in both MFE and HFE groups, while the percentage of time, distance in target quadrant and the number crossing over the platform were significantly increased in the HFE group. Moreover, the FE played a preventive role in the dysbacteriosis of mice induced by antibiotic and increased the richness and species evenness of GM in mice.

The Positive Effects of Grifola frondosa Heteropolysaccharide on NAFLD and Regulation of the Gut Microbiota

Non-alcoholic fatty liver disease (NAFLD) is a major public health problem in many countries. In this study, the ability of Grifola frondosa heteropolysaccharide (GFP) to ameliorate NAFLD was investigated in rats fed a high-fat diet (HFD). The molecular mechanisms modulating the expression of specific gene members related to lipid synthesis and conversion, cholesterol metabolism, and inflammation pathways were determined. The components of the intestinal microflora in rats were analyzed by high-throughput next-generation 16S rRNA gene sequencing. Supplementation with GFP significantly increased the proportions of Allobaculum, Bacteroides, and Bifidobacterium and decreased the proportions of Acetatifactor, Alistipes, Flavonifractor, Paraprevotella, and Oscillibacter. In addition, Alistipes, Flavonifractor, and Oscillibacter were shown to be significant cecal microbiota according to the Spearman’s correlation test between the gut microbiota and biomedical assays (|r| > 0.7). Histological analysis and biomedical assays showed that GFP treatments could significantly protect against NAFLD. In addition, Alistipes, Flavonifractor, and Oscillibacter may play vital roles in the prevention of NAFLD. These results suggest that GFP could be used as a functional material to regulate the gut microbiota of NAFLD individuals.

The Microbial Pecking Order: Utilization of Intestinal Microbiota for Poultry Health

The loss of antibiotics as a tool to improve feed efficiency in poultry production has increased the urgency to understand how the microbiota interacts with animals to impact productivity and health. Modulating and harnessing microbiota-host interactions is a promising way to promote poultry health and production efficiencies without antibiotics. In poultry, the microbiome is influenced by many host and external factors including host species, age, gut compartment, diet, and environmental exposure to microbes. Because so many factors contribute to the microbiota composition, specific knowledge is needed to predict how the microbiome will respond to interventions. The effects of antibiotics on microbiomes have been well documented, with different classes of antibiotics having distinctive, specific outcomes on bacterial functions and membership. Non-antibiotic interventions, such as probiotics and prebiotics, target specific bacterial taxa or function to enhance beneficial properties of microbes in the gut. Beneficial bacteria provide a benefit by displacing pathogens and/or producing metabolites (e.g., short chain fatty acids or tryptophan metabolites) that promote poultry health by improving mucosal barrier function or immune function. Microbiota modulation has been used as a tool to reduce pathogen carriage, improve growth, and modulate the immune system. An increased understanding of how the microbiota interacts with animal hosts will improve microbiome intervention strategies to mitigate production losses without the need for antibiotics.

Effect of dietary supplementation of Bacillus subtilis spores on growth performance, oxidative status, and digestive enzyme activities in Japanese quail birds

The present trial investigated the feeding effect of B. subtilis spores on growth performance, blood metabolites, antioxidative status, and digestive enzyme activities in growing quails. A total of 750 1-day-old Japanese quail chicks were randomly allotted equally into five experimental groups: control (BS0) fed a maize-soybean basal diet with no additives, the others were supplemented with: B. subtilis spores with the levels of 1 × 10³ (BS3), 1 × 10⁵ (BS5), 1 × 10⁷ (BS7), and 1 × 10⁹ (BS9)/kg diet. Quails fed on B. subtilis diets exhibited linearly increasing live body weight and body weight gain and decreased feed-to-gain ratio compared with the control group. Daily feed intake was not significantly altered. Increasing levels of B. subtilis led to a linear increase in serum total protein and albumin levels, and a linear decrease in concentrations of glucose, creatinine, urea-N, aspartate aminotransferase, and alanine aminotransferase. Hypolipidemic impact of feeding B. subtilis spores was greatly observed and enhanced by increasing its dietary inclusion level. Triiodothyronine and thyroxine activities were significantly elevated in treated groups. Glutathione content and catalase activities were linearly increased in groups BS7, BS9, and BS5, while lipid peroxidation was decreased in all treatment groups. Duodenal proteolytic, lipolytic, and amylolytic activities as well as nutrient digestibility were linearly increased in treated groups. In conclusion, dietary supplementation of B. subtilis spores almost at all studied levels was able to promote the antioxidative status and digestive enzymes activities, while only the high concentrations (BS7 and BS9) could improve the nutrient digestion and growth performance of growing Japanese quail.

Use of 16S rRNA gene sequencing for prediction of new opportunistic pathogens in chicken ileal and cecal microbiota

In this study, we addressed differences in the development of gut microbiota in 4 successive batches of commercially hatched broiler parent chickens. When planning this study, we expected to find a batch with compromised performance which would allow identification of microbiota of suboptimal composition. Microbiota composition was determined only by sequencing the V3/V4 region of 16S rRNA genes in samples collected from chickens 5 to 18 wk of age. In a total, 100 and 160 samples originating from the ileum or cecum were processed, respectively. In one of the flocks with suboptimal performance we identified an increased abundance of Helicobacter brantae forming over 80% of ileal microbiota in individual chickens. Moreover, we also tested samples of 53-wk-old hens from the same genetic line in which egg production decreased. In this case, cecal microbiota was enriched for Fusobacterium mortiferum forming over 30% of total cecal microbiota. Although none of the identified unusual microbiota members have been well recognized as pathogenic, they may represent new opportunistic pathogens of chickens worth of further investigation. Analysis of gut microbiota composition by next generation sequencing thus proved as a useful and unbiased alternative to bacterial culture, especially in the cases of unspecific symptoms like decrease in flock performance.

Characteristics of the intestinal flora of specific pathogen free chickens with age

Specific pathogen-free (SPF) experimental animals are recognized as standard laboratory animals in the fields of biomedical, animal husbandry and veterinary research and production. Intestinal flora plays a critical role in nutrient absorption, improving health and protecting the host from pathogens. We therefore explored the variation and maintenance of intestinal flora in SPF chicks in order to better understand the composition of intestinal microflorain SPF chickens, and provide reference for the study of intestinal flora of SPF experimental animals. Five chicks were randomly selected at each of 14, 28, and 42 days, and ceca were removed for DNA extraction. The Illumina Miseq platform was used for microbiome analysis of the V3-V4 region of the 16S rRNA gene. During the course of chick gut microbiome development, we observed major changes in diversity, especially between day 14 and day 28. Firmicutes, Proteobacteria, and Bacteroidetes were the main bacterial taxa, and Firmicutes increased significantly with age. The genus with the highest relative abundance was Lactobacillus, followed by Faecalibacterium. In addition, while abundance of Ruminococcaceae spp., Ruminococcus, and Blautia increased with age, Lactobacillus, Enterobacteriaceae spp., and Oscillospira decreased with age. Interestingly, the abundance of Faecalibacterium first increased and then decreased over time. The characteristics of SPF chicken gut flora at different ages establish a basis for the regulation of intestinal flora in the early stage of brooding, and also provide a theoretical foundation for controlling and preventing infections and poultry diseases in newborn chickens.

Gut Microbiota and Mucin Composition in Female Broiler Chickens Fed Diets including Yellow Mealworm (Tenebrio molitor, L.)

A total of 160 female broiler chickens were divided into four dietary treatments (control feed [C] and 5, 10 and 15% TM meal inclusion, respectively, with five replicate pens/treatment and eight birds/pen) to investigate the effects of Tenebrio molitor (TM) meal utilization on poultry gut microbiota and mucin composition. The cecal microbiota assessment displayed a shift in the beta diversity in chickens fed TM-based diets. The TM10 and TM15 birds showed a significant decrease in the relative abundance of Firmicutes phylum and lower Firmicutes:Bacteroidetes ratios (False Discovery Rate [FDR] < 0.05), respectively, than the TM5 group. The relative abundance of Clostridium, Alistipes and Sutterella genera significantly increased in TM chickens (FDR < 0.05), while birds fed TM-based diets displayed a significant decrease in the relative abundance of Ruminococcus genus in comparison with the C group (FDR < 0.05). Gut mucin composition evaluation revealed higher mucin staining intensity in the intestinal villi of TM5 birds than the other TM groups, as well as mucin reduction in the intestinal villi of TM10 birds when compared to the C group (p < 0.05). In conclusion, dietary TM meal utilization (especially the 10-15% inclusion levels) may negatively influence either the cecal microbiota or the intestinal mucin dynamics of broiler chickens.

Different incubation patterns affect selective antimicrobial properties of the egg interior: experimental evidence from eggs of precocial and altricial birds

Avian eggs contend with omnipresent microorganisms entering the egg interior, where they affect embryo viability and hatchling phenotype. The incubation behaviour and deposition of egg white antimicrobial proteins (AMPs) vary highly across the avian altricial-precocial spectrum. Experimental evidence of how these alterations in avian reproductive strategies affect the antimicrobial properties of the precocial and altricial egg interior is lacking, however. Here, we tested the egg white antimicrobial activity in eggs of two representative model species, from each end of the avian altricial-precocial spectrum, against potentially pathogenic and beneficial probiotic microorganisms. Eggs were experimentally treated to mimic un-incubated eggs in the nest, partial incubation during the egg-laying period, the onset of full incubation and the increased deposition of two main egg white AMPs, lysozyme and ovotransferrin. We moreover assessed to what extent egg antimicrobial components, egg white pH and AMP concentrations varied as a result of different incubation patterns. Fully incubated precocial and altricial eggs decreased their antimicrobial activity against a potentially pathogenic microorganism, whereas partial incubation significantly enhanced the persistence of a beneficial probiotic microorganism in precocial eggs. These effects were most probably conditioned by temperature-dependent alterations in egg white pH and AMP concentrations. While lysozyme concentration and pH decreased in fully incubated precocial but not altricial eggs, egg white ovotransferrin increased along with the intensity of incubation in both precocial and altricial eggs. This study is the first to experimentally demonstrate that different incubation patterns may have selective antimicrobial potential mediated by species-specific effects on antimicrobial components in the egg white.

Offspring Microbiomes Differ Across Breeding Sites in a Panmictic Species

High dispersal rates are known to homogenize host’s population genetic structure in panmictic species and to disrupt host local adaptation to the environment. Long-distance dispersal might also spread micro-organisms across large geographical areas. However, so far, to which extent selection mechanisms that shape host’s population genetics are mirrored in the population structure of the enteric microbiome remains unclear. High dispersal rates and horizontal parental transfer may homogenize bacterial communities between breeding sites (homogeneous hypothesis). Alternatively, strong selection from the local environment may differentiate bacterial communities between breeding sites (heterogeneous hypothesis). Furthermore, selection from age-specific environmental or physiological factors may differentiate the microbiome between juveniles and adults. Here, we analyzed the cloacal bacterial 16S rRNA gene of fledgling greater flamingos, Phoenicopterus roseus, across nine western Mediterranean breeding sites and four breeding seasons (n = 731) and adult birds (n = 27) from a single site. We found that fledgling cloacal microbiome, as measured by alpha diversity, beta diversity, the relative abundance of assigned sequence variants (ASVs) belonging to a phylum and genus composition within phylum, varied significantly between sampling sites and across time within site despite high adult dispersal rates. The spatio-temporal effects were stronger on individual ASV absence/presence than on ASV abundance (i.e., than on core microbiome composition). Spatial effects had a stronger effect than temporal effects, particularly on ASV abundance. Our study supports the heterogeneous hypothesis whereby local environmental conditions select and differentiate bacterial communities, thus countering the homogenizing effects of high-dispersing host species. In addition, differences in core microbiome between adult vs. fledgling samples suggests that differences in age-specific environmental and/or physiological factors result in differential selection pressure of core enteric microbiome between age classes, even within the same environment. In particular, the genus Corynebacterium, associated with both seasonal fat uptake and migration in previous studies, was much more abundant in high-dispersing fledglings than in more resident adults. To conclude, selection mechanisms that shape the host’s genetic structure cannot be extended to the genetic structure of the enteric microbiome, which has important implications regarding our understanding of both host local adaptation mechanisms and enteric microbiome population genetics.

Intestinal Morphologic and Microbiota Responses to Dietary Bacillus spp. in a Broiler Chicken Model

Dietary inclusion of probiotic Bacillus spp. beneficially affect the broiler chickens by balancing the properties of the indigenous microbiota causing better growth performance. The effects of three Bacillus spp. on the growth performance, intestinal morphology and the compositions of jejunal microflora were investigated in broiler chickens. A total of 480 1-day-old male Arbor Acres broilers were randomly divided into four groups. All groups had six replicates and 20 birds were included in each replicate. The control birds were fed with a corn-soybean basal diet, while three treatment diets were supplemented with Bacillus coagulans TBC169, B. subtilis PB6, and B. subtilis DSM32315 with a dosage of 1 × 109 cfu/kg, respectively. The experiment lasted for 42 days. The compositions and diversity of jejunal microflora were analyzed by MiSeq high-throughput sequencing. The B. coagulans TBC169 group showed marked improvements of growth performance, nutrient digestibility and intestinal morphology compared with the other B. subtilis treatments. B. coagulans TBC169 supplementation improved the average body weight (BW), average daily weight gain (ADG), total tract apparent digestibility of crude protein and gross energy (GE), and reduced feed conversion rate (FCR) compared with the control group (P < 0.05). The villus height to crypt depth ratio (VH/CD) of jejunum and duodenum was increased in the birds fed with B. coagulans TBC169 compared with the control group (P < 0.05). However, two B. subtilis treatments presented more positive variation of the jejunum microflora of chickens than that in the B. coagulans TBC169 group. B. subtilis PB6 and B. subtilis DSM32315 treatments improved the diversity of jejunal microbiota on day 21 compared with the control (P < 0.05), while which were decreased on day 42 (P < 0.05). The supplementation with B. coagulans TBC169 significantly improved the proportion of Firmicutes, otherwise two B. subtilis significantly improved the proportion of Proteobacteria, Bacteroidetes, Actinobacteria, and Acidobacteria at the phylum level during starter phase and decreased the proportion of Bacteroidetes during growing phase compared with the control. The supplementation with B.subtilis DSM32315 significantly improved the proportion of Clostridiales during starter phase, whereas two B. subtilis significantly improved the proportion of Pseudomonas, Burkholderia, Prevotella, DA101 during growing phase at the genus level compared with the control. In conclusion, the dietary supplementation with probiotic Bacillus spp. strains improved body weight and intestinal morphology in broiler chickens, which might be associated with the gut microbiota.

Protective effect of Bacillus amyloliquefaciens against Salmonella via polarizing macrophages to M1 phenotype directly and to M2 depended on microbiota

Bacillus amyloliquefaciens SC06 (BaSC06), a potential probiotic, plays a positive role in animal growth performance and immune function.

Modulation of intestinal microbiota, morphology and mucin composition by dietary insect meal inclusion in free-range chickens

Background

Gut health in poultry depends on the balance between the host, intestinal microbiota, intestinal microscopic features and diet. The effects of insect meal (a promising alternative protein source for poultry feed) on chicken gut morphology have recently been reported, but no data about intestinal microbiota and mucin composition modulation are available. The present study evaluated the effects of dietary Tenebrio molitor (TM) meal inclusion on gut health of free-range chickens by intestinal microbiota, morphology and mucin composition characterization.

Results

One hundred forty female medium-growing hybrids were divided into 2 dietary treatments (control feed [C] and 7.5% TM inclusion, with 5 replicate pens/treatment and 14 birds/pen) and slaughtered at 97 days of age (2 birds/pen for a total of 10 chickens/diet). The gut microbiota assessment on cecal content samples by 16S rRNA amplicon based sequencing showed higher alpha (Shannon, P < 0.05) and beta (Adonis and ANOSIM, P < 0.001) diversity in birds fed TM diet than C. In comparison with C group, TM birds displayed significant increase and decrease, respectively, of the relative abundances of Firmicutes and Bacteroidetes phyla, with higher Firmicutes:Bacteroidetes ratios (False Discovery Rate [FDR] < 0.05). The relative abundance of Clostridium, Oscillospira, Ruminococcus, Coprococcus and Sutterella genera was higher in TM chickens than C (FDR < 0.05). On the contrary, TM birds displayed significant decrease of the relative abundance of Bacteroides genus compared to the C group (FDR < 0.05). Gut morphology evaluation by morphometric analysis on small intestine revealed similar villus height, crypt depth and villus height to crypt depth ratio between C and TM birds. Characterization of gut mucin composition by periodic-acid Schiff, Alcian Blue pH 2.5 and high iron diamine staining on small and large intestine showed unaffected mucin staining intensity in TM chickens when compared to C group.

Conclusions

Dietary TM meal inclusion may positively modulate the gut microbiota of the free-range chickens without influencing the intestinal morphology and mucin composition. Since the rapid growth of chickens directly depends on morphological and functional integrity of the digestive tract, the gut health assessment by a post mortem multidisciplinary approach appears to be fundamental.

Electronic supplementary material

The online version of this article (10.1186/s12917-018-1690-y) contains supplementary material, which is available to authorized users.

Effects of pea extrusion and enzyme and probiotic supplementation on performance, microbiota activity and biofilm formation in the broiler gastrointestinal tract

1. The effects of supplementation of broiler chicken diets with pea meal, carbohydrase enzymes and a probiotic were investigated for potential performance improvement. 2. Raw or extruded pea meal (cv Model, grown in Poland) was included in a wheat-soybean meal-based diet at 250 g/kg. The diets were unsupplemented (control) or supplemented with either carbohydrase enzymes (200 U/kg xylanase and 10 U/kg β-glucanase in feed) or a probiotic (Bacillus subtilis), or both. The diets were fed to Ross 308 broilers aged 9-28 days. 3. After two additional days, chick gastrointestinal tracts were excised and analysed for the presence of Bacillus subtilis biofilm; and the ileal and caecal digesta were analysed for bacterial enzyme activities and to determine the concentration of short-chain fatty acids (SCFAs). 4. Feeding the pea-based diet supplemented with the probiotic compromised feed utilisation, due to higher feed intake. The addition of enzymes to the raw, but not the extruded, pea containing diet partially ameliorated this effect (pea form × additives; P < 0.002). 5. In the ileal digesta, interactions between the dietary treatments were observed for the activities of all bacterial glycolytic enzymes and for SCFA concentrations. β-glucosidase, α-galactosidase and β-glucuronidase were highest in birds fed the diet containing extruded pea supplemented with the probiotic and enzymes (pea form x additives; P = 0.018 to P < 0.006). In the caecal digesta, interactions were observed for bacterial enzyme activities, but not for total SCFA concentration. Biofilm formation in the caecum indicated that the probiotic strain was metabolically active in the broiler gut. 6. In conclusion, supplementation of diets containing raw or extruded pea meal with enzymes and a Bacillus subtilis spore-based probiotic modulated microbiota activity but had no clear effects on broiler performance. Probiotic administration did not cause excessive fermentation in the ileum and caecum but enhanced Bacillus subtilis spp. biofilm formation in the caecum, which may be indicative of a beneficial effect on gut health.

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.

High-throughput sequencing reveals the effect of Bacillus subtilis CGMCC 1.921 on the cecal microbiota and gene expression in ileum mucosa of laying hens

This study evaluated the effects of Bacillus subtilis CGMCC 1.921 supplementation on the production performance, cecal microbiota and mucosal transcriptome of laying hens by 16s rRNA gene sequencing and RNA-seq. A total of 144 27-week-old Hy-Line Brown laying hens were allocated into two treatments, namely, a basal diet without additions (T0) and the basal diet supplemented with 1.0 × 108 cfu/g (T1) B. subtilis CGMCC 1.921, with six replicates of 12 birds in each for 24 weeks. The results showed that T1 significantly decreased feed:egg ratio compared with T0 (P < 0.05). Dietary supplementation with B. subtilis CGMCC 1.921 increased the Shannon index (P < 0.05) which indicated enhanced diversity of cecal microflora. An increasing trend in Observed species index (P = 0.072) was observed in hens fed with diets supplemented with B. subtilis CGMCC 1.921 that showed a higher species richness. And T1 modulated cecal microbiota by increasing the relative proportion of Alistipes, Subdoligranulum, Ruminococcaceae UCG-014, Anaerotruncus, Ruminiclostridium 5, Ruminococcaceae UCG-010, Erysipelatoclostridium, Ruminococcaceae UCG-009, Family XIII AD3011 group, Bacillus, Faecalicoccus, Firmicutes bacterium CAG822, Oxalobacter, and Dielma at genus level (P < 0.05). In addition, there was a tendency of increase in the relative abundance of Lactobacillus (P = 0.055), Anaerobiospirillum (P = 0.059) and Family XIII UCG-001 (P = 0.054), Peptococcus (P = 0.078), and Ruminococcaceae UCG-004 (P = 0.078). Moreover, heatmap analysis indicated that the abundance of Campylobacter and Clostridium sensu stricto 1 was lower than T0. A total of 942 genes were identified by differential expression analysis, among which 400 genes were upregulated and 542 genes were downregulated. Bioinformatics analysis suggested that the upregulated genes were involved in Peroxisome Proliferator Activated Receptor (PPAR) signaling pathway, starch and sucrose metabolism, glycine/serine/threonine metabolism, and galactose metabolism, which may promote nutrient absorption. This study provided novel insights into the probiotic mechanisms of B. subtilis on laying hens.

Simultaneous Supplementation of Bacillus subtilis and Antibiotic Growth Promoters by Stages Improved Intestinal Function of Pullets by Altering Gut Microbiota

Early nutrition of pullets could determine the overall development and the performance of laying hens. With the aim to reduce the use of antibiotic growth promoters (AGPs) and to maintain the growth and development of pullets, the effect of simultaneous short-termed supplementation of AGPs (bacitracin zinc 20 mg/kg and colistin sulfate 4 mg/kg) and Bacillus subtilis (B. subtilis) DSM17299 probiotic, as well as the effect of supplementation of AGPs (bacitracin zinc 20 mg/kg and colistin sulfate 4 mg/kg) during the whole period (0~16 weeks) on the overall growth and development, intestinal health, and caecal microbiota of pullets were evaluated. In the present study, a total of 630 one-day-old Hy-Line Brown layers were randomly distributed into five equal groups: including the AGPs group (supplemented with AGPs based on basal diets for 16 weeks), the BA3 group (supplemented with AGPs and B. subtilis based on basal diets for 3 weeks), the BA6 group (for 6 weeks), the BA12 group (for 12 weeks), and the BA16 group (for 16 weeks). When compared with the AGPs group, the supplementation of AGPs + B. subtilis for the first 3 weeks could maintain overall growth performance, including the average body weight, average feed intake, average daily weight gain, and feed conversion ratio of pullets at 3, 6, 12, and 16 weeks of age (P > 0.05). Meanwhile, the characteristic growth indexes in different periods were separately measured. At 3 weeks of age, the amylase activity in ileum was elevated (P = 0.028), and the length of tibia was up to the standard in the BA3 group. At 12 weeks of age, the increased villus height (P = 0.046) of jejunum, increased villus height (P = 0.023) and ratio of villus height to crypt depth (P = 0.012) of ileum, decreased crypt depth (P = 0.002) of ileum, and elevated mRNA levels of sucrase in jejunum (P < 0.05) were all identified in the BA3 group. At 16 weeks of age, the secreted immunoglobulin A (sIgA) content in the jejunum mucosa of the BA3 group was greater than the other groups (P < 0.001). Furthermore, altered intestinal microbiota was found in the BA3 group. Specifically, decreased amounts of Alistipes, Bacteroides, Odoribacter, Dehalobacterium, and Sutterella and increased amounts of Lactobacillus, Dorea, Ruminococcus, and Oscillospira were determined (P < 0.05) in the BA3 group at week 6. Meanwhile, decreased amounts of B. fragilis and C. leptum (P < 0.05) were identified in the BA3 group at week 12, which were found to be relevant for the improvement of intestinal morphology (P < 0.05) by Pearson analysis. In conclusion, simultaneous supplementation of AGP and B. subtilis for 0~3 weeks increased the relative abundance of beneficial microbiota in caecum in 0~6 weeks, then improved the intestinal morphology by elevating populations of B. fragilis and C. leptum in 7~16 weeks, and further upregulated sucrase expression and increased sIgA content in the intestinal mucosa in 13~16 weeks.

Effects of long-term Bacillus subtilis CGMCC 1.921 supplementation on performance, egg quality, and fecal and cecal microbiota of laying hens

This study evaluated the effects of long-term Bacillus subtilis CGMCC 1.921 supplementation on the performance, egg quality, and fecal/cecal microbiota of laying hens. A total of 360 28-week-old Hy-Line Brown laying hens were randomly allocated into 5 treatments with 6 replicates of 12 birds each for 24 weeks. The experimental treatments included a basal diet without additions (Con) and the basal diet supplemented with 1.0 × 105 (B1), 1.0 × 106 (B2), 1.0 × 107 (B3), and 1.0 × 108 (B4) cfu/g B. subtilis CGMCC 1.921. The results showed that feed:egg ratio significantly decreased (P < 0.05) in groups B1 (wk 13 to 16, 17 to 20, 21 to 24, and one to 24), B2 (wk 13 to 16, 17 to 20, and 21 to 24), B3 (wk 13 to 16, 17 to 20, 21 to 24, and one to 24), and B4 (wk 13 to 16, 17 to 20, 21 to 24, and one to 24). However, egg production, egg weight, and feed intake were not significantly different (P > 0.05) among treatments. Eggshell strength significantly improved (P < 0.05) in groups B1 (wk 8, 16, 20, and 24), B2 (wk 20 and 24), and B3 (wk 8, 16, 20, and 24). Fecal E. coli counts significantly decreased (P < 0.05) in groups B1 (wk 16), B2 (wk 12, 16, 20, and 24), B3 (wk 12, 20, and 24), and B4 (wk 16, 20, and 24). Lactobacillus in cecal digesta of groups B1, B3, and B4 increased significantly (P < 0.01). Bifidobacterium in cecal digesta of groups B1, B2, B3, and B4 increased significantly (P < 0.05). Bifidobacterium counts increased linearly (P = 0.015) and quadratically (P = 0.004) as B. subtilis CGMCC 1.921 supplementation increased. Compared with Con, E. coli in the cecal digesta of groups B2 and B4 decreased significantly (P < 0.01). C. perfringens in the cecal digesta of groups B3 and B4 decreased significantly (P < 0.05). E. coli:Lactobacillus ratio decreased in group B1 (P < 0.05) and B2, B3, and B4 (P < 0.01). Therefore, the probiotic B. subtilis CGMCC 1.921 effectively improved performance and egg quality via the reduction of fecal E. coli and beneficial modulation of cecal microbiota.

Gram-Positive Bacteria with Probiotic Potential for the Apis mellifera L. Honey Bee: The Experience in the Northwest of Argentina

Apis mellifera L. is one of the most important natural pollinators of significant crops and flowers around the world. It can be affected by different types of illnesses: american foulbrood, nosemosis, varroasis, viruses, among others. Such infections mainly cause a reduction in honey production and in extreme situations, the death of the colony. Argentina is the world's second largest honey exporter and the third largest honey producer, after China and Turkey. Given both the prominence of the honey bee in nature and the economic importance of apiculture in Argentina and the world, it is crucial to develop efficient and sustainable strategies to control honey bee diseases and to improve bee colony health. Gram-positive bacteria, such as lactic acid bacteria, mainly Lactobacillus, and Bacillus spp. are promising options. In the Northwest of Argentina, several Lactobacillus and Bacillus strains from the honey bee gut and honey were isolated by our research group and characterized by using in vitro tests. Two strains were selected because of their potential probiotic properties: Lactobacillus johnsonii CRL1647 and Bacillus subtilis subsp. subtilis Mori2. Under independent trials with both experimental and commercial hives, it was determined that each strain was able to elicit probiotic effects on bee colonies reared in the northwestern region of Argentina. One result was the increase in egg-laying by the queen which therefore produced an increase in bee number and, consequently, a higher honey yield. Moreover, the beneficial bacteria reduced the incidence of two important bee diseases: nosemosis and varroosis. These results are promising and extend the horizon of probiotic bacteria to the insect world, serving beekeepers worldwide as a natural tool that they can administer as is, or combine with other disease-controlling methods.

Sodium butyrate improved performance while modulating the cecal microbiota and regulating the expression of intestinal immune-related genes of broiler chickens

This study evaluated the effect of sodium butyrate (SB) on performance, expression of immune-related genes in the cecal tonsils, and cecal microbiota of broiler chickens when dietary energy and amino acids concentrations were reduced. Day-old male Ross 708 broiler chicks were fed dietary treatments in a 3 × 2 factorial design (8 pens per treatment) with 3 dietary formulations (control diet; reduction of 2.3% of amino acids and 60 kcal/kg; and reduction of 4.6% of amino acids and 120 kcal/kg) with or without the inclusion of 0.1% of SB. Feed intake (FI), body weight gain (BW gain), and feed conversion ratio (FCR) were recorded until 28 d of age. From 14 to 28 d, there was an interaction of nutrient density by SB (P = 0.003) wherein BW gain of birds fed SB was impaired less by the energy/amino acids reduction than unsupplemented birds. A similar result was obtained from 1 to 28 d (P = 0.004). No interaction (P < 0.05) between nutrient density by SB was observed for FCR. Nutritional density of the diets and SB modified the structure, composition, and predicted function of the cecal microbiota. The nutritionally reduced diet altered the imputed function performed by the microbiota and the SB supplementation reduced these variations, keeping the microbial function similar to that observed in chickens fed a control diet. The frequency of bacterial species presenting the butyryl-CoA: acetate CoA-transferase gene increased in the microbiota of chickens fed a nutritionally reduced diet without SB supplementation, and was not changed by nutrient density of the diet when supplemented with SB (interaction; P = 0.01). SB modulated the expression of immune related genes in the cecal tonsils; wherein SB upregulated the expression of A20 in broilers fed control diets (P < 0.05) and increased IL-6 expression (P < 0.05). These results show that SB had positive effects on the productive performance of broilers fed nutritionally reduced diets, partially by modulating the cecal microbiota and exerting immune-modulatory effects.

Effects of intranasal administration with Bacillus subtilis on immune cells in the nasal mucosa and tonsils of piglets

The nasal mucosa is the body's first barrier against pathogens entering through the respiratory tract. The respiratory immune system of pigs has more similarities with humans than the mouse respiratory system does, and so was selected as the animal model in the present study. To evaluate the effects of Bacillus subtilis as a potential probiotic to stimulate local immune responses, piglets were intranasally administered with Dylight 488-labeled B. subtilis (WB800-green fluorescent protein). The results revealed that B. subtilis was able to reach the lamina propria of the nasal mucosa, nasopharyngeal tonsils and soft palate tonsils. Piglets were subsequently administered intranasally with B. subtilis (WB800) at 3, 12 and 28 days. The results revealed that, following administration with B. subtilis, the number of dendritic cells, immunoglobulin A⁺ B cells and T cells in the nasal mucosa and tonsils significantly increased (P<0.05). No obvious differences were observed in the morphological structure following B. subtilis administration. There were no statistical differences were observed in the expression of interleukin (IL)-1β, tumor necrosis factor-α and IL-8 mRNA between the B. subtilis treated group and the control group in the nasal mucosa, nasopharyngeal tonsil or soft palate tonsil. Toll-like receptor (TLR)-2 and TLR-9 mRNA expression in the tonsils was significantly increased following B. subtilis administration compared with the control group (P<0.05). The results demonstrate that B. subtilis administration increases the number of immune cells in the nasal mucosa and tonsils of piglets and stimulates nasal mucosal and tonsillar immunity. The present study lays the foundation for further study into the intranasal administration of B. subtilis in humans to enhance the immunity of human nasal mucosa to respiratory diseases.

Host and Environmental Factors Affecting the Intestinal Microbiota in Chickens

The initial development of intestinal microbiota in poultry plays an important role in production performance, overall health and resistance against microbial infections. Multiplexed sequencing of 16S ribosomal RNA gene amplicons is often used in studies, such as feed intervention or antimicrobial drug trials, to determine corresponding effects on the composition of intestinal microbiota. However, considerable variation of intestinal microbiota composition has been observed both within and across studies. Such variation may in part be attributed to technical factors, such as sampling procedures, sample storage, DNA extraction, the choice of PCR primers and corresponding region to be sequenced, and the sequencing platforms used. Furthermore, part of this variation in microbiota composition may also be explained by different host characteristics and environmental factors. To facilitate the improvement of design, reproducibility and interpretation of poultry microbiota studies, we have reviewed the literature on confounding factors influencing the observed intestinal microbiota in chickens. First, it has been identified that host-related factors, such as age, sex, and breed, have a large effect on intestinal microbiota. The diversity of chicken intestinal microbiota tends to increase most during the first weeks of life, and corresponding colonization patterns seem to differ between layer- and meat-type chickens. Second, it has been found that environmental factors, such as biosecurity level, housing, litter, feed access and climate also have an effect on the composition of the intestinal microbiota. As microbiota studies have to deal with many of these unknown or hidden host and environmental variables, the choice of study designs can have a great impact on study outcomes and interpretation of the data. Providing details on a broad range of host and environmental factors in articles and sequence data repositories is highly recommended. This creates opportunities to combine data from different studies for meta-analysis, which will facilitate scientific breakthroughs toward nutritional and husbandry associated strategies to improve animal health and performance.

Draft Genome Sequences of Bacillus subtilis Strain DKU_NT_01 Isolated from Traditional Korean Food Containing Soybean (Chung-gook-jang)

Here, we report the whole-genome sequence of Bacillus subtilis strain DKU_NT_01 isolated from traditional Korean food containing soybean (chung-gook-jang). The de novo genome of Bacillus subtilis strain DKU_NT_01 has one contig and G+C content of 55.4%, is 4,954,264 bp in length, and contains 5,011 coding sequences (CDSs).

A Bacillus subtilis strain as probiotic in poultry: selection based on in vitro functional properties and enzymatic potentialities

We have proposed and validate an in vitro probiotic selection, based on enzymatic potentialities associated to well-established probiotic functional properties. A new Bacillus subtilis HB2 isolate, selected based on its high extracellular enzyme production, was chosen as a probiotic candidate for application as animal feed supplement. The HB2 strain showed an excellent acid and bile salts tolerance, a strong adhesion to chick enterocytes and produced antimicrobials against pathogens. An in vivo trial in poultry farming was conducted to evaluate the HB2 probiotic performance. After 35 days, HB2 achieved the higher growth performance than the control groups. The mortality and the feed conversion ratio were significantly decreased. Finally, the HB2 treated group showed wet litter and less severe ammonia odor in the atmosphere. Our study provides new insights into the importance of enzymatic potentialities, associated with the common functional properties, as a novel approach for probiotic selection.

First complete genome sequence of Bacillus glycinifermentans B-27

The first complete genome sequence of Bacillus glycinifermentans B-27 was determined by SMRT sequencing generating a genome sequence with a total length of 4,607,442 bases. Based on this sequence 4738 protein-coding sequences were predicted and used to identify gene clusters that are related to the production of secondary metabolites such as Lichenysin, Bacillibactin and Bacitracin. This genomic potential combined with the ability of B. glycinifermentans B-27 to grown in bile containing media might contribute to a future application of this strain as probiotic in productive livestock potentially inhibiting competing and pathogenic organisms.

Bacillus subtilis biofilm extends Caenorhabditis elegans longevity through downregulation of the insulin-like signalling pathway

Beneficial bacteria have been shown to affect host longevity, but the molecular mechanisms mediating such effects remain largely unclear. Here we show that formation of Bacillus subtilis biofilms increases Caenorhabditis elegans lifespan. Biofilm-proficient B. subtilis colonizes the C. elegans gut and extends worm lifespan more than biofilm-deficient isogenic strains. Two molecules produced by B. subtilis — the quorum-sensing pentapeptide CSF and nitric oxide (NO) — are sufficient to extend C. elegans longevity. When B. subtilis is cultured under biofilm-supporting conditions, the synthesis of NO and CSF is increased in comparison with their production under planktonic growth conditions. We further show that the prolongevity effect of B. subtilis biofilms depends on the DAF-2/DAF-16/HSF-1 signalling axis and the downregulation of the insulin-like signalling (ILS) pathway.

Probiotic bacteria can improve host health, but the mechanisms underlying such beneficial effects are often unclear. Here, the authors show that biofilm formation of the probiotic bacterium B. subtilis extends the lifespan of its host, the nematode C. elegans, by reducing insulin-like signalling.

Dietary live yeast and mannan-oligosaccharide supplementation attenuate intestinal inflammation and barrier dysfunction induced by Escherichia coli in broilers

The effects of live yeast (LY) and mannan-oligosaccharide (MOS) supplementation on intestinal disruption induced by Escherichia coli in broilers were investigated. The experimental design was a 3×2 factorial arrangement with three dietary treatments (control, 0·5 g/kg LY (Saccharomyces cerevisiae, 1·0×1010 colony-forming units/g), 0·5 g/kg MOS) and two immune treatments (with or without E. coli challenge from 7 to 11 d of age). Samples were collected at 14 d of age. The results showed that E. coli challenge impaired (P<0·05) growth performance during the grower period (1–21 d) and the overall period (1–35 d) of broilers, increased (P<0·05) serum endotoxin and diamine oxidase levels coupled with ileal myeloperoxidase and lysozyme activities, whereas reduced (P<0·05) maltase activity, and compromised the morphological structure of the ileum. Besides, it increased (P<0·05) the mRNA expressions of several inflammatory genes and reduced occludin expression in the ileum. Dietary treatment with both LY and MOS reduced (P<0·05) serum diamine oxidase and ileal myeloperoxidase levels, but elevated villus height (P<0·10) and the ratio of villus height:crypt depth (P<0·05) of the ileum. It also alleviated (P<0·05) E. coli-induced increases (P<0·05) in ileal Toll-like receptor 4, NF-κB and IL-1β expressions. Moreover, LY supplementation reduced (P<0·05) feed conversion ratio of birds during the grower period and enhanced (P<0·05) the community diversity (Shannon and Simpson indices) of ileal microbiota, whereas MOS addition counteracted (P<0·05) the decreased ileal IL-10 and occludin expressions in challenged birds. In conclusion, both LY and MOS supplementation could attenuate E. coli-induced intestinal disruption by alleviating intestinal inflammation and barrier dysfunction in broilers. Moreover, LY addition could improve intestinal microbial community structure and feed efficiency of broilers.

A low dose of an organophosphate insecticide causes dysbiosis and sex-dependent responses in the intestinal microbiota of the Japanese quail (Coturnix japonica)

Organophosphate insecticides have been directly or indirectly implicated in avian populations declining worldwide. Birds in agricultural environments are commonly exposed to these insecticides, mainly through ingestion of invertebrates after insecticide application. Despite insecticide exposure in birds occurring mostly by ingestion, the impact of organophosphates on the avian digestive system has been poorly researched. In this work we used the Japanese quail (Coturnix japonica) as an avian model to study short-term microbial community responses to a single dose of trichlorfon at low concentration in three sample origins of the gastrointestinal tract (GIT): caecum, large intestine and faeces. Using next-generation sequencing of 16S rRNA gene amplicons as bacterial markers, the study showed that ingestion of insecticide caused significant changes in the GIT microbiome. Specifically, microbiota composition and diversity differed between treated and untreated quail. Insecticide-associated responses in the caecum showed differences between sexes which did not occur with the other sample types. In caecal microbiota, only treated females showed significant shifts in a number of genera within the Lachnospiraceae and the Enterobacteriaceae families. The major responses in the large intestine were a significant reduction in the genus Lactobacillus and increases in abundance of a number of Proteobacteria genera. All microbial shifts in faeces occurred in phylotypes that were represented at low relative abundances. In general, changes in microbiota possibly resulted from contrasting responses towards the insecticide, either positive (e.g., biodegrading bacteria) or negative (e.g., insecticide-susceptible bacteria). This study demonstrates the significant impact that organophosphate insecticides have on the avian gut microbiota; showing that a single small dose of trichlorfon caused dysbiosis in the GIT of the Japanese quail. Further research is necessary to understand the implications on birds’ health, especially in females.