Bacillus licheniformis–fermented products and enramycin differentially modulate microbiota and antibiotic resistome in the cecal digesta of broilers

Intestinal Microbiome Profiles in Broiler Chickens Raised with Different Probiotic Strains

The composition of the intestinal microbiota can influence the metabolism and overall functioning of avian organisms. Therefore, the objective of this study was to evaluate the effect of three different probiotics and an antibiotic on the microbiomes of 1.400 male Cobb® broiler raised for 42 days. The experiment was conducted with the following treatments: positive control diet (basal diet + antibiotic); negative control diet (basal diet without antibiotic and without probiotic); basal diet + Normal Avian Gut Flora (NAGF); basal diet + multiple colonizing strain probiotics (MCSPs); and basal diet + non-colonizing single strain probiotics (NCSSPs). The antibiotic (enramycin-antibiotic growth promoter) and probiotics were administered orally during all experiment (1 to 42 days), mixed with broiler feed. To determine the composition of the microbiota, five samples of ileal digesta were collected from 42-day-old chickens of each experimental group. The alpha and beta diversity of the ileal microbiota showed differences between the groups. MCSPs presented greater richness and uniformity compared to the positive control, negative control, and NCSSPs treatments, while the negative control exhibited greater homogeneity among samples than NCSSPs. MCSPs also showed a higher abundance of the genus Enterococcus. There were differences between the groups for low-abundance taxa (<0.5%), with NAGF showing higher levels of Delftia, Brevibacterium, and Bulleidia. In contrast, NCSSPs had a higher abundance of Ochrobactrum, Rhodoplanes, and Nitrospira. It was concluded that the treatments analyzed in this study induced modulations in the ileal microbiota of the chickens examined.

Comprehensive Metagenomic Analysis of Veterinary Probiotics in Broiler Chickens

Probiotics are widely used in broiler chickens to support the gut microbiome, gut health, and to reduce the amount of antibiotics used. Despite their benefits, there is concern over their ability to carry and spread antimicrobial resistance genes (ARGs), posing a significant public health risk. This study utilized next-generation sequencing to investigate ARGs in probiotics approved for poultry, focusing on their potential to be transferred via mobile genetic elements such as plasmids and phages. We examined the gut microbiome and resistome changes in 60 broiler chickens over their rearing period, correlating these changes with different probiotic treatments. Specific resistance mechanisms against critically important antibiotics were identified, including genes related to fluoroquinolone resistance and peptide antibiotic resistance. We also found genes with significant relevance to public health (aadK, AAC(6')-Ii) and multiple drug-resistance genes (vmlR, ykkC, ykkD, msrC, clbA, eatAv). Only one phage-encoded gene (dfrA43) was detected, with no evidence of plasmid or mobile genetic element transmission. Additionally, metagenomic analysis of fecal samples showed no significant changes corresponding to time or diet across groups. Our findings highlight the potential risks associated with the use of probiotics in poultry, particularly regarding the carriage of ARGs. It is crucial to conduct further research into the molecular genetics of probiotics to develop strategies that mitigate the risk of resistance gene transfer in agriculture, ensuring the safe and effective use of probiotics in animal husbandry.

Impact of Bacillus licheniformis-Fermented Products on Growth and Productivity in Heat-Stressed Laying Ducks

The purpose of this study was to assess the impact of various concentrations of Bacillus licheniformis-fermented products (BLFP) on the growth and productivity of laying ducks (Anas platyrhynchos) subjected to heat stress during eight weeks of a feeding trial. A total of 150 one-day-old Brown Tsaiya ducks of both sexes were divided into five groups, with each group having three replicates and 10 ducks each for evaluation of growth performance. The treatment groups received dietary supplements of BLFP at levels of 0.1%, 0.2%, and 0.3%, along with a group receiving flavomycin (F) at 5 ppm, all over a 24-week period. The fermentation process in this study utilized a B. licheniformis strain (ATCC 12713) for the production of the spores through solid-state fermentation. The control group was given a basal diet consisting of yellow corn and soybean meal. The results showed that as compared to the flavomycin group, ducks in the 0.3% BLFP group had significantly higher body weights and better feed conversion rates. In addition, during the three weeks, the BLFP group showed higher feed consumption as compared to the control group. The jejunum villi length was significantly increased in the 0.2% BLPF group as compared to the control and flavomycin groups. This study also found that the flavomycin group had a significantly higher egg conversion rate, while the 0.1-0.3% BLFP groups had improved feed intake and the 0.3% group had significantly enhanced egg yolk color. Additionally, the 0.2% BLFP group showed substantial decreases in IL-1β, TNF-α, IL-6, and IL-10 levels in the liver as well as an uptick in the tight junction protein Occludin gene expression in the colon when compared to the control group. Furthermore, the expression of the heat shock protein 70 in the gut upregulated in the 0.1% and 0.2% BLFP groups. In conclusion, these observations demonstrate that dietary supplementation of 0.2% BLFP is an ideal concentration to increase gut morphology, alleviate inflammatory response, and promote gut integrity in heat-stressed laying ducks.

Draft genome sequences of Bacillus licheniformis strains MEZBL63 and MEZBL64 harboring the lichenysin toxin operon isolated from livestock in South Africa

Here, we report the draft genome sequences of two Bacillus licheniformis strains harboring the lichenysin operon that were isolated from healthy goat and horse in South Africa. The genomes were sequenced using Illumina MiSeq and had a length of 4,152,826 and 4,110,075 bp, respectively, with a G + C content of 46%.

Intervention effects of fructooligosaccharide and astragalus polysaccharide, as typical antibiotic alternatives, on antibiotic resistance genes in feces of layer breeding: advantages and defects

Although antibiotic alternatives are widely used in livestock and poultry breeding industry after in-feed antibiotics ban, their intervention effects on antibiotic resistance genes (ARGs) in these food animals' feces remain poorly understood. Here effects of fructooligosaccharide (FOS) and astragalus polysaccharide (APS), as typical antibiotic alternatives in China, on ARGs in layer feces were estimated by performing metagenomic sequencings and fluorescence quantitative PCR. Fructooligosaccharide significantly reduced sum abundance of ARGs and mobile genetic elements (MGEs) by increasing Lactobacillus clones and reducing Escherichia clones which had relatively higher abundances of ARG subtypes and MGE subtypes in layer feces. However, at least parts of core ARGs and MGEs categories were not reduced by FOS, such as aminoglycosides- and tetracyclines-resistant genes, Tn916, Integrase, and so on. MGEs and microbiome, especially Escherichia genus and Lactobacillus genus, were the key factors affecting ARGs' sum abundance. MGEs had a higher correlation coefficient with ARGs' sum abundance than Escherichia genus and Lactobacillus genus. These findings firstly reveal the defects of antibiotic alternatives in controlling bacterial resistance in livestock and poultry breeding after in-feed antibiotics ban, and more strategies are needed to control pollutions and risks of core ARGs and MGEs in food animals' feces under a special environment.

Effects of cyclic antimicrobial lipopeptides from Bacillus subtilis on growth performance, intestinal morphology, and cecal gene expression and microbiota community in broilers

This study investigated the effects of cyclic antimicrobial lipopeptides (CLPs) from Bacillus subtilis on the growth performance, gut morphology, and cecal gene expression and microbiota in broilers; 120 1-day-old unsexed Arbor Acres chicks were randomly divided into four groups, with six replicates in each group and five broilers per cage. These groups were fed a basal diet (C), basal diet plus 10-mg enramycin/kg (E), and basal diet plus 51-mg CLPs/kg (L) or 102-mg CLPs/kg (H). The results indicated that CLP supplementation linearly increased the body weight compared with the C group at 35 days of age. Between 15 and 35 days and 1 and 35 days of age, CLP supplementation linearly increased the average daily gain compared with the C group. The duodenal villus height was significantly increased in the H group compared with the C and E groups. In the cecum, CLP supplementation linearly increased SOD and ZO-1 mRNA expression compared with the C group. β diversity of microbiota indicated distinct clusters between the groups. CLP supplementation linearly increased the abundance of the genus Lactobacillus in the cecal digesta compared with the C group. These results demonstrate that B. subtilis-produced CLPs dose-dependently increase broilers' growth performance, improve their gut morphology, and modulate their gut microbiota.

Differential effects of Bacillus subtilis- and Bacillus licheniformis-fermented products on growth performance, intestinal morphology, intestinal antioxidant and barrier function gene expression, cecal microbiota community, and microbial carbohydrate-active enzyme composition in broilers

This study investigated the differential effects of Bacillus subtilis-fermented products (SFPs) and Bacillus licheniformis-fermented products (LFPs) on the growth performance, intestinal morphology, intestinal gene expression, cecal microbiota community, and microbial carbohydrate-active enzyme composition of broilers. In total, 160 one-day-old unsexed Arbor Acres broiler chicks were randomly allocated to 4 treatment groups (with 8 replicates per group and 5 chicks per replicate): control (CON), enramycin (ENM), SFP, and LFP groups, which were fed a basal diet, basal diet supplemented with 10 mg/kg ENM, basal diet supplemented with 10⁸ colony-forming units (CFU) of B. subtilis spores per gram of feed, and basal diet supplemented with 10⁸ CFU of B. licheniformis spores per gram of feed, respectively. LFP treatment resulted in a higher (P < 0.01) body weight at the age of 35 d and higher average daily gain over 15 to 35 (P < 0.05) and 1 to 35 (P < 0.05) d of age than did the CON and SFP treatments. The average villus heights in the jejunum were longer (P < 0.05) in the LFP group than those in the SFP group. Moreover, the LFP group exhibited a higher jejunal barrier function gene expression (mucin 2, zonula occludens-1, and occludin) and cecal antioxidant gene expression (superoxide dismutase) than did the CON group (P < 0.05). A principal coordinate analysis of cecal microbiota and carbohydrate-active enzyme composition demonstrated distinct clustering among the groups. Lactobacillus crispatus abundance in the cecal digesta was higher (P < 0.01) in the SFP group than in the CON and LFP groups. Finally, microbial glycosyltransferase 2 gene expression in the cecal digesta was higher in the LFP group than in the CON and ENM groups. In conclusion, LFPs can improve the growth performance, increase intestinal barrier function and antioxidant gene expression, and modulate cecal microflora composition and carbohydrate-active enzyme composition of broilers. The overall effect of LFPs on growth promotion in broilers was superior to that of SFPs.

UPLC-TOF/MS-based metabolomics reveals the chemical changes and in vitro biological effects in fermentation of white ginseng by four probiotics

Microbial fermentation is a useful method for improving the biological activity of Chinese herbal medicine. Herein, we revealed the effects of solid-state fermentation by Lactiplantibacillus plantarum, Bacillus licheniformis, Saccharomyces cerevisiae, Eurotium cristatum and multiple strains on total flavonoid content, total phenol content, as well as antioxidants, α-amylase inhibitory activities and α-glucosidase inhibitory activities in white ginseng (WG). Metabolite differences between non-fermented and fermented WG by different probiotics were comprehensively investigated using ultra-performance liquid chromatography time-of-flight mass spectrometry (UPLC-TOF-MS). Results showed that the total flavonoid content, ferric reducing antioxidant power, scavenging activities of DPPH radical and ABTS radical, α-amylase inhibitory activities and α-glucosidase inhibitory activities of WG were considerably enhanced after processing by solid-state fermentation in all strains. The total phenol content was increased by E. cristatum and B. licheniformis fermentation, but decreased by L. plantarum, S. cerevisiae and multi-strain fermentation. Additionally, E. cristatum exhibited stronger biotransformation activity on WG compared to other strains. Significant differential metabolites were mainly annotated as prenol lipids, carboxylic acids and derivatives, flavonoids, polyphenols, coumarins and derivatives. Correlation analysis further showed that changes of these metabolites were closely related to antioxidant and hypoglycemic effects. Our results confirmed that fermentation of WG by different probiotics has distinct effects on biological activities and metabolite composition, and indicating fermentation as an important novel strategy to promote components and bioactivities of WG.