Evaluation and Selection of Bacillus Species Based on Enzyme Production, Antimicrobial Activity, and Biofilm Synthesis as Direct-Fed Microbial Candidates for Poultry

Effect of a Multi-Species Direct-Fed Microbial on Growth Performance, Nutrient Digestibility, Intestinal Morphology and Colonic Volatile Fatty Acids in Weanling Pigs

The potentials of ABO replacer of ENZ and DFM on growth performance, AID, colonic VFAs, gut morphology, fecal score and diarrhea incidence were evaluated. We randomly assigned 120 piglets to four experimental diets that included: (1) control diet (CON), fed the basal ration; (2) ABO was added at 250 ppm of in-feed ABO; (3) ENZ was added at a rate of 3 kg/ton feed; (4) DFM was added with 50 × 106 cfu/g of Bacillus subtilis and 2 × 106 cfu/g of Lactobacillus spp. at a rate of 1.2 kg/ton feed. A complete randomized design used six pens per treatment with five pigs per pen. Pigs had ad libitum access to feed and water throughout the 6-week trial. Feed intake and BW were recorded on weeks 0, 2, 4 and 6, as well as fecal scores and diarrhea incidences (visually recorded and calculated). At weeks 2 and 4, a sub-sample of pigs (n = 6) was sacrificed for intestinal morphology, enzyme activity and VFAs. The results of the study demonstrated that DFM piglets showed increased final BW (3 kg) (p < 0.001) vs. CON. Likewise, ADG was positively affected by the incorporation of ABO, ENZ and DFM in the diets, with an average increase of 8 to 17% on ADG compared with CON (p < 0.001). The AID of gross energy, organic matter, CP and EAAs in piglets fed ENZ and DFM were significantly higher (p < 0.05) than those of CON and ABO at weeks 2 and 4. Inclusion of DFM increased intestinal morphology, enzymatic activities and propionic and butyric acid more than in pigs fed CON, ABO and ENZ (p < 0.05). The fecal score and diarrhea incidence generally decreased over time in pigs fed DFM (p < 0.05). These findings indicate that dietary supplementation with DFM has better effects at any period on growth performance, CP and AA digestibility and beneficially altered the intestinal health in weanling piglets.

Identification of differentially expressed genes and metabolism signaling pathway in the spleen of broilers supplemented with probiotic Bacillus spp

Probiotics are essential in the body's nutrients, improving the ratio of meat to meat, immune response, and preventing diseases. In this study, RNA-sequencing (RNA-seq) was used to identify the differentially expressed genes (DEGs), enriched related pathways, and Gene Ontology (GO) terms among blank negative control (NC), supplemented with Bacillus spp. (BS) and commercial probiotic (PC) groups after a 42-day fed supplementation. The results showed that 2005, 1356, and 2189 DEGs were significantly altered in BS vs. NC, PC vs NC, and BS vs PC groups, respectively. On the other hand, 9 DEGs were further validated by qRT-PCR, indicating that the qRT-PCR and RNA-Seq results were more consistent. Therefore, the GO and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of DEGs showed that the DEGs were mainly enriched to metabolism signalling pathways (alpha-linolenic acid metabolism, linoleic acid metabolism, tryptophan metabolism, tyrosine metabolism, ether lipid metabolism, and metabolic pathway, etc) and immune response pathways (cytokine-cytokine receptor interaction, MAPK signalling pathway, and intestinal immune network for IgA production, neuroactive ligand-receptor interaction etc). These results will provide a better understanding of the role of probiotics in chicken development and provide basic information on the genetic development of chickens.

A New Bacillus velezensis Strain CML532 Improves Chicken Growth Performance and Reduces Intestinal Clostridium perfringens Colonization

Bacillus velezensis has gained increasing recognition as a probiotic for improving animal growth performance and gut health. We identified six B. velezensis strains from sixty Bacillus isolates that were isolated from the cecal samples of fifteen different chicken breeds. We characterized the probiotic properties of these six B. velezensis strains. The effect of a selected strain (B. velezensis CML532) on chicken growth performance under normal feeding and Clostridium perfringens challenge conditions was also evaluated. The results revealed that the six B. velezensis strains differed in their probiotic properties, with strain CML532 exhibiting the highest bile salt and acid tolerance and high-yield enzyme and antibacterial activities. Genomic analyses showed that genes related to amino acid and carbohydrate metabolism, as well as genes related to starch and cellulose hydrolysis, were abundant in strain CML532. Dietary supplementation with strain CML532 promoted chicken growth, improved the gut barrier and absorption function, and modulated the gut microbiota. Under the C. perfringens challenge condition, strain CML532 alleviated intestinal damage, reduced ileal colonization of C. perfringens, and also improved chicken growth performance. Collectively, this study demonstrated that the newly isolated B. velezensis strain is a promising probiotic with beneficial effects on chicken growth performance and gut health.

Peeling back the many layers of competitive exclusion

Baby chicks administered a fecal transplant from adult chickens are resistant to Salmonella colonization by competitive exclusion. A two-pronged approach was used to investigate the mechanism of this process. First, Salmonella response to an exclusive (Salmonella competitive exclusion product, Aviguard®) or permissive microbial community (chicken cecal contents from colonized birds containing 7.85 Log10Salmonella genomes/gram) was assessed ex vivo using a S. typhimurium reporter strain with fluorescent YFP and CFP gene fusions to rrn and hilA operon, respectively. Second, cecal transcriptome analysis was used to assess the cecal communities' response to Salmonella in chickens with low (≤5.85 Log10 genomes/g) or high (≥6.00 Log10 genomes/g) Salmonella colonization. The ex vivo experiment revealed a reduction in Salmonella growth and hilA expression following co-culture with the exclusive community. The exclusive community also repressed Salmonella's SPI-1 virulence genes and LPS modification, while the anti-virulence/inflammatory gene avrA was upregulated. Salmonella transcriptome analysis revealed significant metabolic disparities in Salmonella grown with the two different communities. Propanediol utilization and vitamin B12 synthesis were central to Salmonella metabolism co-cultured with either community, and mutations in propanediol and vitamin B12 metabolism altered Salmonella growth in the exclusive community. There were significant differences in the cecal community's stress response to Salmonella colonization. Cecal community transcripts indicated that antimicrobials were central to the type of stress response detected in the low Salmonella abundance community, suggesting antagonism involved in Salmonella exclusion. This study indicates complex community interactions that modulate Salmonella metabolism and pathogenic behavior and reduce growth through antagonism may be key to exclusion.

Screening and characterization of thermostable enzyme-producing bacteria from selected hot springs of Ethiopia

Hot springs are potential sources of diverse arrays of microbes and their thermostable hydrolytic enzymes. Water and sediment samples were collected from three hot springs of Ethiopia and enriched on nutrient and thermus agar media to isolate pure cultures of potential microbes. A total of 252 bacterial isolates were screened and evaluated for the production of amylase, protease, cellulase, and lipase. About 95.23%, 84.12%, 76.58%, and 65.07% of the isolates displayed promising amylase, proteases, cellulase, and lipase activities, respectively. Based on the diameter of the clear zone formed, 45 isolates were further screened and identified to species level using matrix-assisted laser desorption/ionization time-of-flight-mass spectrometry analysis and 16S rRNA gene sequencing. Five of the 45 isolates showed significantly high (P < 0.05) clear zone ratios as compared to others. The identified isolates were categorized under five bacterial species, namely, Bacillus licheniformis, Bacillus cereus, Paenibacillus thiaminolyticus, Paenibacillus dendritiformis, and Brevibacillus borstelensis. The most dominant species (66.7%) was B. licheniformis. It could be concluded that hot springs of Ethiopia are potential sources of thermostable extracellular hydrolytic enzymes for various industrial applications. Further optimization of the growth conditions and evaluation for better productivity of the desired products is recommended before attempting for large-scale production of the hydrolytic enzymes.

IMPORTANCE

Thermostable microbial enzymes play an important role in industries due to their stability under harsh environmental conditions, including extreme temperatures. Despite their huge application in different industries, however, the thermostable enzymes of thermophilic microorganism origin have not yet been fully explored in Ethiopia. Here, we explored thermophilic bacteria and their enzymes from selected hot spring water and sediment samples. Accordingly, thermophilic bacteria were isolated and screened for the production of extracellular hydrolytic enzymes. Promising numbers of isolates were found as producers of the enzymes. The potent enzyme producers were further identified using matrix-assisted laser desorption/ionization time-of-flight-mass spectrometry analysis and 16S rRNA gene sequencing. The findings revealed the presence of potential hydrolytic enzyme-producing thermophilic bacteria in hot springs of Ethiopia and necessitate further comprehensive study involving other extreme environments. Our findings also revealed the potential of Ethiopian hot springs in the production of thermostable enzymes of significant application in different industries, including food industries.

Effects of a multistrain Bacillus-based direct-fed microbial on gastrointestinal permeability and biomarkers of inflammation during and following feed restriction in mid-lactation Holstein cows

Objectives were to evaluate the effects of a multistrain Bacillus-based (Bacillus subtilis and Bacillus pumilus blend) direct-fed microbial (DFM) on production, metabolism, inflammation biomarkers and gastrointestinal tract (GIT) permeability during and following feed restriction (FR) in mid-lactation Holstein cows. Multiparous cows (n = 36; 138 ± 53 DIM) were randomly assigned to 1 of 3 dietary treatments: 1) control (CON; 7.5 g/d rice hulls; n = 12), 2) DFM10 (10 g/d Bacillus DFM, 4.9 × 109 cfu/d; n = 12) or 3) DFM15 (15 g/d Bacillus DFM, 7.4 × 109 cfu/d; n = 12). Before study initiation, cows were fed their respective treatments for 32 d. Cows continued to receive treatments during the trial, which consisted of 3 experimental periods (P): P1 (5 d) served as baseline for P2 (5 d), during which all cows were restricted to 40% of P1 dry matter intake (DMI), and P3 (5 d), a "recovery" where cows were fed ad libitum. On d 4 of P1 and on d 2 and 5 of P2, GIT permeability was evaluated in vivo using the oral paracellular marker chromium (Cr)-EDTA. As anticipated, FR decreased milk production, decreased insulin, glucagon, and BUN but increased nonesterified fatty acids. During recovery, DMI rapidly increased on d 1 then subsequently decreased (4.9 kg) on d 2 before returning to baseline whereas milk yield slowly increased but remained decreased (13%) relative to P1. DFM10-fed cows had increased DMI and milk yield relative to DFM15 during P3 (10%). Overall, milk lactose content was increased in DFM cows relative to CON (0.10 percentage units), and DFM10 cows tended to have increased lactose yield relative to CON and DFM15 during P3 (8 and 10%, respectively). No overall treatment differences were observed for other milk composition variables. Circulating glucose was quadratically increased in DFM10 cows compared with CON and DFM15 during FR and recovery. Plasma Cr area under the curve was increased in all cows on d 2 (9%) and 5 (6%) relative to P1. Circulating lipopolysaccharide binding protein (LBP), serum amyloid A (SAA), and haptoglobin (Hp) increased in all cows during P2 compared with baseline (31%, 100%, and 9.0-fold, respectively). Circulating Hp concentrations continued to increase during P3 (274%). Overall, circulating LBP and Hp tended to be increased in DFM15 cows relative to DFM10 (29 and 81%, respectively), but no treatment differences were observed for SAA. Following feed reintroduction during P3, fecal pH initially decreased (0.62 units), but returned to baseline levels whereas fecal starch markedly increased (2.5-fold) and remained increased (82%). Absolute quantities of a fecal Butyryl-CoA CoA transferase (But) gene associated with butyrate synthesis, collected by fecal swab were increased in DFM10 cows compared with CON and DFM15-fed cows. In summary, FR increased GIT permeability, caused inflammation, and decreased production. Feeding DFM10 increased some key production and metabolism variables and upregulated a molecular biomarker of microbial hindgut butyrate synthesis, while DFM15 appeared to augment immune activation.

Antimicrobial use and resistance in food animal production: food safety and associated concerns in Sub-Saharan Africa

The use of antimicrobials in food animal (FA) production is a common practice all over the world, with even greater usage and dependence in the developing world, including Sub-Saharan Africa (SSA). However, this practice which serves obvious economic benefits to producers has raised public health concerns over the last decades, thus driving the selection and dissemination of antimicrobial resistance and adversely impacting food safety and environmental health. This review presents the current and comprehensive antimicrobial usage practices in food animal production across SSA. We further highlighted the overall regional drivers as well as the public health, environmental, and economic impact of antimicrobial use in the production of food animals. Antimicrobial use is likely to increase with even exacerbated outcomes unless cost-effective, safe, and sustainable alternatives to antibiotics, especially probiotics, prebiotics, bacteriocins, antimicrobial peptides, bacteriophages, vaccines, etc. are urgently advocated for and used in food animal production in SSA. These, in addition to the implementation of strong legislation on antimicrobial use, and improved hygiene will help mitigate the public health concerns associated with antimicrobial use in food animals and improve the well-being and safety of food animals and their products.

Inclusion of a Bacillus-based probiotic in non-starch polysaccharides-rich broiler diets

This study examined the effects of a 3-strain Bacillus-based probiotic (BP; Bacillus amyloliquefaciens and two Bacillus subtilis) in broiler diets with different rye levels on performance, mucus, viscosity, and nutrient digestibility. We distributed 720 one-d-old female broilers into 72 pens and designed nine diets using a 3 × 3 factorial approach, varying BP levels (0, 1.2 × 106, and 1.2 × 107 CFU/g) and rye concentrations (0, 200, 400 g/kg). On d 35, diets with 200 or 400 g/kg rye reduced broiler weight gain (BWG). Diets with 400 g/kg rye had the highest FCR, while rye-free diets had the lowest (p ≤0.05). Adding BP increased feed intake and BWG in weeks two and three (p ≤0.05). It should be noted that the overall performance fell below the goals of the breed. Including rye in diets reduced the coefficient of apparent ileal digestibility (CAID) for protein, ether extract (EE), calcium, phosphorus, and all amino acids (p ≤0.05). Rye-free diets exhibited the highest CAID for all nutrients, except for methionine, EE, and calcium, while diets with 400 g/kg of rye demonstrated the lowest CAID (p ≤0.05). BP in diets decreased phosphorus CAID (p ≤0.05). Diets containing 1.2 × 107 CFU/g (10X) of BP exhibited higher CAID of methionine than the other two diets (p ≤0.05). Diets containing 10X of BP showed higher CAID of cysteine than diets with no BP (p ≤0.05). Ileal viscosity increased as the inclusion level of rye in the diets increased (p ≤0.05). The ileal concentration of glucosamine in chickens fed diets with 400 g/kg of rye was higher than in those fed diets with no rye (p ≤0.05). Furthermore, ileal galactosamine concentrations were elevated in diets with 200 and 400 g/kg of rye when compared to rye-free diets (p ≤0.05). However, BP in diets had no impact on ileal viscosity, galactosamine, or glucosamine (p > 0.05). In conclusion, the applied Bacillus strains appeared to have a limited capacity to produce arabinoxylan-degrading enzymes and were only partially effective in mitigating the negative impacts of rye arabinoxylans on broilers.

Growth performance, nutrient utilization, rumen fermentation, blood biochemistry, and carcass traits of lambs fed Atriplex nummularia L. hay-based diet supplemented with yeast or bacterial direct- fed microbial

Direct fed microbial may enhance the utilization of halophyte forages leading to improved animal growth and productivity. This study was conducted to evaluate Atriplex hay-based diet supplemented with yeast (Saccharomyces cerevisiae; SC) or bacteria (Bacillus subtilis and Lactobacillus casei; BAC) on lamb growth performance, digestibility, rumen fermentation, and carcass characteristics. Fifteen Barki lambs (90 ± 7 days of age and 18.6 ± 0.41 kg SE body weight; BW) were randomly assigned to three treatments for 120 days as follows: Control (basal diet without supplementation), SC and BAC diets, the basal diet supplemented with SC or BAC at 2 g/head/day, respectively. All lambs had similar dry matter (DM) intake, while lambs fed SC or BAC dies had higher (P < 0.05) total gain and average daily gain than those fed the control diet. Supplementation of SC or BC increased (P < 0.05) the digestibility of DM, organic matter, and acid detergent fiber, tended to decrease (P < 0.05) the urine N excretion and enhanced the N balance compared to the control. Ruminal pH, acetate, total volatile fatty acids concentrations, and bacterial protein were increased (P < 0.05), while creatinine and urea concentrations were decreased (P < 0.05) by both additives. Compared to other diets, the BAC diet reduced (P < 0.05) triglycerides, total lipids, kidney fat, and eye muscle fat. In conclusion, both additives resulted in similar positive growth performance and feed utilization, while only the BAC additive had a beneficial advantage in reducing the fat content of the carcass.

Dietary supplementation with different alternative to in-feed antibiotic improves growth performance of broilers during specific phases

The effects of substituting Bacillus subtilis, Astragalus membranaceus, and enzymes for aureomycin to improve the growth performance of broilers during specific phases were studied to develop alternatives to in-feed antibiotics and decrease drug residues in meat food and antibiotic resistance. Six hundred one-day-old broilers were randomly assigned to 5 groups. Broilers in the control group were supplied with basal diets (CT), and those in the remaining 4 groups were supplied with feed containing aureomycin premix (AU), B. subtilis powder (BS), A. membranaceus root powder (AM), and enzyme compound powder (EN), respectively. Compared to the control group, broilers in the other groups exhibited better growth performance during different phases. Microbial analysis of cecal contents suggested that treatment with BS or EN significantly increased the abundance of Lactobacillus or Bifidobacteria but inhibited Escherichia coli or Clostridium welchii; however, these bacteria were suppressed by AU treatment except C. welchii. The digestibility of the feed in vitro was significantly enhanced by adding BS or EN to the feed, consistent with findings for growth performance. In conclusion, dietary supplementation with 3 additives could improve the growth performance of broilers during specific phases. Future studies should focus on designing suitable schedules to partially replace in-feed antibiotics.

Lycium barbarum polysaccharides improve lipid metabolism disorders of spotted sea bass Lateolabrax maculatus induced by high lipid diet

This experiment explored the effects of Lycium barbarum polysaccharides (LBP) on lipid metabolism of spotted sea bass Lateolabrax maculatus. Blank and experimental control diets with 100 and 150 g/kg lipid were designed, respectively, and three dosages of LBP (0.75, 1.00, 1.25 g/kg) were supplemented in the experimental control diet. A total 375 of spotted sea bass (19.33 ± 0.15) g were divided into 5 groups, and were given experimental diets for 56 days, respectively. Results showed fish were induced to lipid metabolism disorders with dietary 150 g/kg lipid intake, which manifested in reduced feeding, oxidative stress, elevated serum lipid, and more severe hepatic damage. Dietary LBP improved the lipid metabolism disorders of fish, as indicated by significant enhancements in weight gain, digestion, superoxide dismutase activity, and decreases in malonaldehyde content, and activity of alanine aminotransferase and aspartate aminotransferase. Accordingly, an improvement in the hepatic morphological and expression of lipid metabolism related genes, including FAS, PPAR-α, CPT1 and ATGL, was observed. Nevertheless, no significant variation in serum triglyceride and total cholesterol was observed. Overall, dietary LBP can improve the growth, digestion, antioxidant capacity, and liver health of spotted sea bass, thereby improving the lipid metabolism disorders induced by 150 g/kg dietary lipid intake.

Characterization of Bacillus spp. isolated from the intestines of Rhynchocypris lagowskii as a potential probiotic and their effects on fish pathogens

Probiotics sourced from fish intestinal microbiota have a merit over other bacterial sources due to colonization ability and effective time. This study aimed to evaluate the bacilli isolated from the Rhynchocypris lagowskii intestines and their validity as a probiotic. Three isolates were selected (LSG 2-5, LSG 3-7, and LSG 3-8) and defined by morphological and 16S rRNA analysis as Bacillus velezensis, Bacillus aryabhattai, and Bacillus mojavensis, respectively. Results showed the strain tolerant abilities to gastrointestinal fluid, bile salt, pH, and temperature expotures. Additionally, all bacterial strains showed anti-pathogenic activity against at least four strains out of six tested pathogen strains (Staphylococcus aureus, Aeromonas hydrophila, Escherichia coli, Aeromonas veronii, Edwardsiella, and Aeromonas sobria). The bacterial strains also showed a high percentage of co-aggregation activity, more than 70%, with Aer. hydrophile, Staph. epidermidis, and Klebsiella aerogenes. At the same time, the results of competition, rejection, and substitution activity with Aer. hydrophila and Aer. veronii indicated the ability of the isolated strains to reduce the adhesion of pathogens to mucin. All strains showed safety properties, non-hemolytic, and sensitivity characteristics for most of tested antibiotics. In vivo test after injecting these strains into fish at various concentrations showed no side effects in the internal or external organs of fish compared to controls, proving that this is safe for these fish. Furthermore, the three strains produced lipase, amylase, and protease enzymes. The strains also showed bile salt hydrolase activity and biofilm formation, allowing them to tolerate stressful conditions. Conclusion: Based on these strains characteristics and features, they could be considered a promising candidate probiotic and can be used as an anti-pathogenic, especially in aquaculture.

Safety assessment of surfactin-producing Bacillus strains and their lipopeptides extracts in vitro and in vivo

Beneficial Bacillus strains can be administered to livestock as probiotics to improve animal health. Cyclic lipopeptides produced by Bacillus such as surfactins may be responsible for some of the beneficial effects due to their anti-inflammatory and immunomodulatory activity. The aim of the present study was to isolate and evaluate the biocompatibility of native Bacillus spp. strains and their surfactin-like lipopeptides in vitro and in vivo to determine their potential to be used on animals. Biocompatibility of endospore suspensions (10⁸  UFC/mL), and different dilutions (1:10; 1:50; 1:100; 1:500, and 1:1000) of Bacillus lipopeptide extracts containing surfactin was tested on Caco-2 cells by microculture tetrazolium-based colorimetric assay. Genotoxicity was tested on BALB/c mice (n = 6) administered 0.2 mL of endospore suspensions by the bone marrow erythrocyte micronuclei assay. All the isolates tested produced between 26.96 and 239.97 µg mL^{- 1} of surfactin. The lipopeptide extract (LPE) from isolate MFF1.11 demonstrated significant cytotoxicity in vitro. In contrast, LPE from MFF 2.2; MFF 2.7, TL1.11, TL 2.5, and TC12 had no cytotoxic effect (V% > 70%) on Caco-2 cells, not affecting cell viability signifficantly in most treatments. Similarly, none of the endospore suspensions affected cell viability (V% > 80%). Likewise, endospores did not cause genotoxicity on BALB/c mice. This study was elementary as a first step for a new line of research, since it allowed us to choose the safest isolates to keep working on the search of new potentially probiotic strains destined to production animals to improve their performance and health.

The combination of multiple plant growth promotion and hydrolytic enzyme producing rhizobacteria and their effect on Jerusalem artichoke growth improvement

Rhizobacteria are well recognized for their beneficial multifunctions as key promoters of plant development, suppressing pathogens, and improving soil health. In this study, experiments focused on characterizing the plant growth promotion (PGP) and extracellular hydrolase production traits of rhizobacteria, and their impact on Jerusalem artichoke growth. A total of 50 isolates proved capable of either direct PGP or hydrolase-producing traits. Two promising strains (Enterobacter cloacae S81 and Pseudomonas azotoformans C2-114) showed potential on phosphate and potassium solubilization, IAA production, and 1-aminocyclopropane-1-carboxylic acid deaminase activity and hydrolase production. A hydrolase-producing strain (Bacillus subtilis S42) was able to generate cellulase, protease, amylase, β-glucosidase, and phosphatase. These three selected strains also gave positive results for indirect PGP traits such as siderophore, ammonia, oxalate oxidase, polyamine, exopolysaccharide, biofilm, motility, and tolerance to salinity and drought stress. Colonization was observed using a scanning electron microscope and rhizobacteria appeared at the root surface. Interestingly, inoculation with consortia strains (S42, S81, and C2-114) significantly increased all plant parameters, including height, biomass, root (length, surface, diameter, and volume), and tuber fresh weight. Therefore, we recommend that potential consortia of PGP and hydrolase-producing rhizobacteria be employed as a biofertilizer to improve soil and boost crop productivity.

Revisiting the oldest manure of India, Kunapajala: Assessment of its animal waste recycling potential as a source of plant biostimulant

India's oldest documented manure, most commonly referred to as Kunapajala, has a long history of over 1,000 years in crop cultivation. Kunapajala is primarily an in-situ decomposition technology of animal waste and can potentially provide an eco-friendly pipeline for recycling bio-waste into essential plant nutrients. This traditional animal manure, in addition, also contains dairy excreta (e.g., feces and urine), dairy products (e.g., milk and ghee), natural resources (e.g., honey), broken seeds or grains, and their non-edible by-product waste. Here, we aimed to assess the waste recycling and plant biostimulant potential of Kunapajala prepared from livestock (e.g., Black Bengal goats) or fish (e.g., Bombay duck) post-processed wastes over different decomposition periods, e.g., (0, 30, 60, and 90-days). In this study, an in-situ quantification of livestock- (lKPJ) and fish-based Kunapajala (fKPJ) reveals a dynamic landscape of essential plant primary nutrients, e.g., (0.70 &gt; NH4-N &lt; 3.40 g•L−1), (100.00 &gt; P2O5 &lt; 620.00 mg•L−1), and (175.00 &gt; K2O &lt; 340.00 mg•L−1), including other physico-chemical attributes of Kunapajala. Using correlation statistics, we find that the plant-available nutrient content of Kunapajala depicts a significant (p &lt; 0.0001) transformation over decomposition along with microbial dynamics, abundance, and diversities, delineating a microbial interface to animal waste decomposition and plant growth promotion. Importantly, this study also reports the indole 3-acetic acid (IAA) content (40.00 &gt; IAA &lt; 135.00 mg•L−1) in Kunapajala. Furthermore, the bacterial screening based on plant growth-promoting traits and their functional analyses elucidate the mechanism of the plant biostimulant potential of Kunapajala. This assay finally reports two best-performing plant growth-promoting bacteria (e.g., Pseudomonas chlororaphis and Bacillus subtilis) by the 16S ribotyping method. In support, in-planta experiments have demonstrated, in detail, the bio-stimulative effects of Kunapajala, including these two bacterial isolates alone or in combination, on seed germination, root-shoot length, and other important agronomic, physio-biochemical traits in rice. Together, our findings establish that Kunapajala can be recommended as a source of plant biostimulant to improve crop quality traits in rice. Overall, this work highlights Kunapajala, for the first time, as a promising low-cost microbial technology that can serve a dual function of animal waste recycling and plant nutrient recovery to promote sustainable intensification in agroecosystems.

Dietary supplementation with full-fat Hermetia illucens larvae and multi-probiotics, as a substitute for antibiotics, improves the growth performance, gut health, and antioxidative capacity of weaned pigs

BACKGROUND

Dietary supplementation of full-fat black soldier fly larvae (BSFL full-fat meal; alone or in combination with multi-probiotics) was tested as an alternative to dietary antibiotics in weaning piglets. We also tested the effects of these diets on growth performance, nutrient digestibility coefficients, immune status, oxidative stress, intestinal histomorphology, and rectal microbial modulations in weaned pigs. A total of 80 piglets [(Landrace × Large White) × Duroc] of both sexes (a ratio of gilts and barrows; 1:1), were randomly allotted to four diet groups: positive control (PC) diet supplemented with 0.02% amoxicillin; negative control (NC) diet without supplement addition; BSFL12 diet (NC + 12% BSFL full-fat meal); and BSFL + Pro diet (BSFL full-fat meal + 0.1% multi-probiotics, including Bacillus subtilis, B. licheniformis, and Saccharomyces cerevisiae). All groups had five replicates, with four piglets per replicate.

RESULTS

Dietary BSFL + Pro improved the overall average daily gain (P = 0.013), and gain-to-feed ratio (P = 0.032). The BSFL12 and BSFL + Pro diets improved nutrient digestibility and increased the serum levels of immunoglobulin A and glutathione peroxidase, while reducing the levels of pro-inflammatory cytokines. The spleen weight was higher and caecal pH was lower in pigs fed the BSFL + Pro diet than in those fed the NC diet (P = 0.011 and P = 0.021, respectively). Pigs fed the BSFL diets had longer duodenal villi, a higher villus height-to-crypt depth ratio (P = 0.004), and shorter crypt depth (P = 0.017) than those fed NC. The BSFL + Pro diet also increased faecal Lactobacillus spp. count (P = 0.008) and reduced Escherichia coli (P = 0.021) counts compared with that seen with PC and NC diets, respectively.

CONCLUSIONS

Dietary supplementation with BSFL or BSFL + multi-probiotics can improve the growth performance and intestinal health of pigs and may be an effective strategy to replace antibiotics for weaned pigs.

Bacillus Species as Direct-Fed Microbial Antibiotic Alternatives for Monogastric Production

Antibiotic growth promoters have been utilized for long time at subtherapeutic levels as feed supplements in monogastric animal rations. Because of their side-effects such as antibiotic resistance, reduction of beneficial bacteria in the gut, and dysbiosis, it is necessary to look for non-therapeutic alternatives. Probiotics play an important role as the key substitutes to antibacterial agents due to their many beneficial effects on the monogastric animal host. For instance, enhancement of the gut microbiota balance can contribute to improvement of feed utilization efficiency, nutrients absorption, growth rate, and economic profitability of livestock. Probiotics are defined as "live microorganisms that, when administered in adequate amounts, confer a health benefit on the host." They are available in diverse forms for use as feed supplements. Their utilization as feed additives assists in good digestion of feed ingredients and hence, making the nutrients available for promoting growth. Immunity can also be enhanced by supplementing probiotics to monogastrics diets. Moreover, probiotics can help in improving major meat quality traits and countering a variety of monogastric animals infectious diseases. A proper selection of the probiotic strains is required in order to confer optimal beneficial effects. The present review focuses on the general functional, safety, and technological screening criteria for selection of ideal Bacillus probiotics as feed supplements as well as their mechanism of action and beneficial effects on monogastric animals for improving production performance and health status.

In silico, in vitro and in vivo characterization of host-associated Latilactobacillus curvatus strains for potential probiotic applications in farmed Atlantic salmon (Salmo salar)

Salmon aquaculture is the fastest growing animal protein production system in the world; however, intensive farming leads to poor weight gain, stress, and disease outbreaks. Probiotics offer the potential to enhance growth performance and feed efficiency in Atlantic salmon, as well as immunostimulate fish against common pathogens, benefitting farmers and consumers with more efficient production. Here, we isolated and identified 900 native microbial isolates including 18 Lactobacilli from the farmed salmon intestines. Based on whole-genome sequencing and phylogenetic analysis, the Lactobacillus candidates belonged to Latilactobacillus curvatus (L. curvatus) species and formed two distinct phylogenetic groups. Using bioinformatics and in vitro analyses, we selected two candidates L. curvatus ATCC PTA-127116 and L. curvatus ATCC PTA-127117, which showed desirable safety and probiotic properties. The two L. curvatus candidates were evaluated for safety and efficacy (higher final weight) in Atlantic salmon alongside spore-forming Bacilli isolated from salmon, poultry, and swine. All the tested candidates were safe to salmon with no adverse effects. While we did not see efficacy in any Bacillus supplemented groups, compared to untreated group, the group administered with the two L. curvatus strains consortium in feed for seven weeks in freshwater showed indicators of improvement in final body weight by 4.2%. Similarly, the two L. curvatus candidates were also evaluated for safety and efficacy in Atlantic salmon in saltwater; the group administered with the two L. curvatus strains consortium in feed for 11 weeks showed indicators of improvement in final body weight by 4.7%. Comprehensive metabolomics analyses in the presence of different prebiotics and/or additives identified galactooligosaccharide as a potential prebiotic to enhance the efficacy of two L. curvatus candidates. All together, these data provide comprehensive genomic, phenotypic and metabolomic evidence of safety and desirable probiotic properties as well as indicators of in vivo efficacy of two novel endogenous L. curvatus candidates for potential probiotic applications in Atlantic salmon. The in vivo findings need to be confirmed in larger performance studies, including field trials.

Assessment of probiotic and technological properties of Bacillus spp. isolated from Burkinabe Soumbala

BACKGROUND

Soumbala is a highly loved alkaline traditional fermented food condiment in Burkina Faso. It harbors various microbiota dominated by fermentative Bacillus spp. as functional microorganism with little confirmed health-promoting properties.

METHODS

The present study aimed to evaluate six Bacillus strains previously isolated and identified from soumbala. These strains were selected as presumptively safe bacteria for probiotic and technological characteristics. These strains were assessed for in vitro probiotic criteria (tolerance to acidic pH, gastric juice, 0.3% (m/v) bile salts, intestinal juice and 0.4% (w/v) phenol, cell surface hydrophobicity, auto-aggregation capacity, antimicrobial activity against foodborne pathogens, antibiotic susceptibility and biofilm production) and technological properties, including protease, amylase, lipase, and tannase activity, as well as poly-γ-glutamic acid (PGA) production and thermo-tolerance.

RESULTS

All tested Bacillus strains (B54, F20, F24, F21, F26 and F44) presented variable relevant probiotic properties (good tolerance to pH 2 and pH 4, gastric juice, bile salts, intestinal juice and phenol), with marked differences in hydrophobicity and auto-aggregation capacity ranging from 73.62-94.71% and 49.35-92.30%, respectively. They exhibited a broad spectrum of activity against foodborne pathogens depending on target pathogen, with the highest activity exhibited by strain F20 (29.52 mm) against B. cereus 39 (p <  0.001). They also showed good biofilm production as well as variable hydrolytic enzyme activities, including protease (43.00-60.67 mm), amylase (22.59-49.55 mm), lipase (20.02-24.57 mm), and tannase (0-10.67 mm). All tested Bacillus strains tolerated temperature up to 50 °C, while only strains F26 and F44 showed the best PGA production.

CONCLUSION

Overall, the tested cultures exhibiting potential probiotic and technological characteristics; particularly B. cereus F20, B. benzoevorans F21, B. cabrialessi F26, and B. tequilensis F44 could be a source of probiotic-starters of commercial interest in the production of high-quality soumbala.

Bacillus-derived probiotics: metabolites and mechanisms involved in bacteria-host interactions

Bacillus probiotics have a sporulation capacity that makes them more suitable for processing and storage and for surviving passage through the gastrointestinal tract. The probiotic functions and regulatory mechanisms of different Bacillus have been exploited in many reports, but little is known about how various Bacillus probiotics perform different functions. This knowledge gap results in a lack of specificity in the selection and application of Bacillus. The probiotic properties are strain-specific and cell-type-specific, and are related to the germination potential and to the diversity of metabolites produced following intestinal germination, as this causes the variation in probiotic function and mechanisms. In this review, we discuss the Bacillus metabolites produced during germination and sporulation in the GI tract, as well as possible processes affecting intestinal homeostasis. We conclude that the oxygen-capturing capability and the production of antimicrobials, exoenzymes, competence and sporulation factors (CSF), exopolysaccharides, lactic acid, and cell components are specifically associated with the functional mechanisms of probiotic Bacillus. The aim of this review is to guide the screening of potential Bacillus strains for probiotics and their application in nutrition research. The information provided will also promote further research on Bacillus-derived functional metabolites in human nutrition.

In vitro and in vivo evaluation of probiotic potential and safety assessment of Bacillus coagulans SKB LAB-19 (MCC 0554) in humans and animal healthcare

Bacillus coagulans is Gram positive, spore forming and high lactic acid producing bacteria; however, probiotic and safety assessment of the isolated strain need to be investigated for commercial applications. Current study aimed to screen SKB LAB-19 for potential probiotic characteristics viz. enzyme production, antimicrobial properties, pH/bile salt tolerance, temperature stability, antidiarrheal activity in Swiss albino mice and Wistar rats; and acute oral toxicity in mice. The results showed that, SKB LAB-19 produces eight potential enzymes, effective against E. coli and C. perfringensis, tolerant to bile salt (0.3%)/gastric pH (2.5), stable at 40-90 °C and nontoxic to cells. SKB LAB-19 was found to be safe and displayed promising results to reverse E. coli and castor oil induced diarrhoea. Histopathological studies showed repair to damaged mucosal epithelium cells and improves integrity of the goblet cells of colon. SKB LAB-19 showed immunomodulatory effects with increased immunoglobulins in blood and augmented weight of spleen and thymus. In addition, SKB LAB-19 showed significant in-vitro antioxidant activity (82.93%), reducing capacity and ascorbate auto-oxidation inhibition effect (94.62%). These preliminary results suggested that, SKB LAB-19 was found to be safe and has the potential to be used as effective probiotic and anti-diarrhoeal agent in humans and animal healthcare.

In ovo Inoculation of Bacillus subtilis and Raffinose Affects Growth Performance, Cecal Microbiota, Volatile Fatty Acid, Ileal Morphology and Gene Expression, and Sustainability of Broiler Chickens (Gallus gallus)

Banning antibiotic growth promoters has negatively impacted poultry production and sustainability, which led to exploring efficient alternatives such as probiotics, probiotics, and synbiotics. Effect of in ovo injection of Bacillus subtilis, raffinose, and their synbiotics on growth performance, cecal microbial population and volatile fatty acid concentration, ileal histomorphology, and ileal gene expression was investigated in broilers (Gallus gallus) raised for 21 days. On 300 h of incubation, a total of 1,500 embryonated eggs were equally allotted into 10 groups. The first was non-injected (NC) and the remaining in ovo injected with sterile distilled water (PC), B. subtilis 4 × 10⁵ and 4 × 10⁶ CFU (BS1 and BS2), Raffinose 2 and 3 mg (R1 and R2), B. subtilis 4 × 10⁵ CFU + raffinose 2 mg (BS1R1), B. subtilis 4 × 10⁵ CFU + raffinose 3 mg (BS1R2), B. subtilis 4 × 10⁶ CFU + raffinose 2 mg (BS2R1), and B. subtilis 4 × 10⁶ CFU + raffinose 3 mg (BS2R2). At hatch, 60 chicks from each group were randomly chosen, divided into groups of 6 replicates (10 birds/replicate), and fed with a corn–soybean-based diet. In ovo inoculation of B. subtilis and raffinose alone or combinations significantly improved body weight, feed intake, and feed conversion ratio of 21-day-old broilers compared to NC. Cecal concentrations of butyric, pentanoic, propionic, and isobutyric acids were significantly elevated in R1, R2, BS2R1, and BS2R2, whereas isovaleric and acetic acids were significantly increased in R1 and BS2R1 compared to NC. Cecal microbial population was significantly altered in treated groups. Ileal villus height was increased (p < 0.001) in BS1, R2, and BS2R2 compared to NC. The mRNA expression of mucin-2 was upregulated (p < 0.05) in synbiotic groups except for BS1R1. Vascular endothelial growth factor (VEGF) expression was increased (p < 0.05) in BS2, R1, BS1R1, and BS1R2 compared to NC. SGLT-1 expression was upregulated (p < 0.05) in all treated birds except those of R1 group compared to NC. The mRNA expressions of interleukin (IL)-2 and toll-like receptor (TLR)-4 were downregulated (p < 0.05) in BS2 and R1 for IL-2 and BS1R1 and BS2R2 for TLR-4. It was concluded that in ovo B. subtilis, raffinose, and synbiotics positively affected growth performance, cecal microbiota, gut health, immune responses, and thus the sustainability of production in 21-day-old broilers.

Medium for the Production of Bacillus-Based Biocontrol Agent Effective against Aflatoxigenic Aspergillus flavus: Dual Approach for Modelling and Optimization

One of the leading limiting factors for wider industrial production and commercialization of microbial biopesticides refers to the high costs of cultivation media. The selection of alternative sources of macronutrients crucial for the growth and metabolic activity of the producing microorganism is a necessary phase of the bioprocess development. Gaining a better understanding of the influence of the medium composition on the biotechnological production of biocontrol agents is enabled through bioprocess modelling and optimization. In the present study, after the selection of optimal carbon and nitrogen sources, two modelling approaches were applied to mathematically describe the behavior of the examined bioprocess—the production of biocontrol agents effective against aflatoxigenic Aspergillus flavus strains. The modelling was performed using four independent variables: cellulose, urea, ammonium sulfate and dipotassium phosphate, and the selected response was the inhibition-zone diameter. After the comparison of the results generated by the Response Surface Methodology (RSM) and the Artificial Neural Network (ANN) approach, the first model was chosen for the further optimization step due to the better fit of the experimental results. As the final investigation step, the optimal cultivation medium composition was defined (g/L): cellulose 5.0, ammonium sulfate 3.77, dipotassium phosphate 0.3, magnesium sulfate heptahydrate 0.3.

Development and Evaluation of a Commercial Direct-Fed Microbial (Zymospore®) on the Fecal Microbiome and Growth Performance of Broiler Chickens under Experimental Challenge Conditions

Simple Summary

Probiotics are recognized for their beneficial health-promoting properties, through competitive exclusion, promoting maintenance of intestinal epithelial integrity and host immune system homeostasis. The use of some spore-forming bacteria from the genus Bacillus has earned interest as a direct-fed microbial in recent years as a potential alternative to antibiotic growth promoters and growth enhancers. The present study evaluates the use of a Bacillus subtilis spore-based direct-fed microbial (Zymospore^®, Vetanco, Villa Martelli, Argentina) compared to an antibiotic growth promoter on the performance of broiler chickens under experimental intestinal challenge conditions. The results suggest that Zymospore^® increases the diversity of the broiler fecal microbiota and is an acceptable substitute for commonly used antibiotic growth promoters under defined and non-defined intestinal dysbiosis conditions.

Abstract

Direct-fed microbials (DFM) are added to broiler chicken diets in order to promote the proliferation of beneficial intestinal bacterial populations, which may lead to gains in performance efficiency and, potentially, reduce the level of enteric pathogens in the broiler chickens. The selection and laboratory evaluation of Bacillus subtilis strains as well as the experimental trial results of a novel Bacillus-based commercial DFM product are described. Fifteen wild-type Bacillus subtilis strains were characterized and assayed for their enzyme production capability, spore resistance to pH, salinity, and temperature, and ability to inhibit the growth of E. coli and Salmonella spp. The final DFM formulation was evaluated and compared to an antibiotic growth promoter (AGPs) in two experimental trials. In Experiment 1, broilers were given a defined challenge of Eimeria spp. and Clostridium perfringens to induce intestinal dysbiosis. The optimal dose of the DFM was determined to be 0.3 kg/ton of feed. At this dose, the broilers fed the DFM performed as well as the Flavomycin^®-fed broilers. Further, intestinal microbiome analysis indicates that the use of the DFM enhances bacterial diversity of the gut flora by day 5 of age, increasing levels of lactic acid bacteria (LAB) and Clostridiales by 25 days of age, which may enhance the digestion of feed and promote growth of the birds. In Experiment 2, the broilers were raised on recycled litter and given an undefined challenge orally to mimic commercial growth conditions. In this trial, the DFM performed as well as the bacitracin methylene disalicylate (BMD)-11%-fed birds. The results of the present studies suggest that this novel DFM, Zymospore^®, improves the performance of broiler chickens under experimental challenge conditions as effective as an AGP, providing a safe and effective substitute to the poultry industry.

Genome mining reveals polysaccharide-degrading potential and new antimicrobial gene clusters of novel intestinal bacterium Paenibacillus jilinensis sp. nov

Background

Drug-resistant bacteria have posed a great threat to animal breeding and human health. It is obviously urgent to develop new antibiotics that can effectively combat drug-resistant bacteria. The commensal flora inhabited in the intestines become potential candidates owing to the production of a wide range of antimicrobial substances. In addition, host genomes do not encode most of the enzymes needed to degrade dietary structural polysaccharides. The decomposition of these polysaccharides mainly depends on gut commensal-derived CAZymes.

Results

We report a novel species isolated from the chicken intestine, designated as Paenibacillus jilinensis sp. nov. and with YPG26^T (= CCTCC M2020899^T) as the type strain. The complete genome of P. jilinensis YPG26^T is made up of a single circular chromosome measuring 3.97 Mb in length and containing 49.34% (mol%) G + C. It carries 33 rRNA genes, 89 tRNA genes, and 3871 protein-coding genes, among which abundant carbohydrate-degrading enzymes (CAZymes) are encoded. Moreover, this strain has the capability to antagonize multiple pathogens in vitro. We identified putative 6 BGCs encoding bacteriocin, NRPs, PKs, terpenes, and protcusin by genome mining. In addition, antibiotic susceptibility testing showed sensitivity to all antibiotics tested.

Conclusions

This study highlights the varieties of CAZymes genes and BGCs in the genome of Paenibacillus jilinensis. These findings confirm the beneficial function of the gut microbiota and also provide a promising candidate for the development of new carbohydrate degrading enzymes and antibacterial agents.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08623-4.

Bacillus Probiotics as Alternatives to In-feed Antibiotics and Its Influence on Growth, Serum Chemistry, Antioxidant Status, Intestinal Histomorphology, and Lesion Scores in Disease-Challenged Broiler Chickens

In commercial poultry production, chickens are reared under intensive conditions, which may allow infections to spread quickly. Antibiotics are used at sub-therapeutic doses in livestock and poultry feed to prevent diseases and improve productivity. However, restrictions on the use of antibiotics at sub-therapeutic concentrations in livestock feed due to growing concerns of antimicrobial resistance (AMR), together with antibiotic residues in meat and eggs has prompted poultry researchers and feed producers to look for viable alternatives. Thus, there is increasing interest in developing natural alternatives to in-feed antibiotics to improve chicken productivity and health. Probiotics, specifically from the genus Bacillus have proven to be effective due to their spore-forming capabilities. Furthermore, their ability to withstand heat during feed processing and be stored for a long time without losing viability as well as their potential to function in the acidic medium of the chicken gut, provide them with several advantages over conventional probiotics. Several studies regarding the antimicrobial and antioxidant activities of Bacillus probiotics and their positive impact in chicken nutrition have been documented. Therefore, the present review shields light on the positive effect of Bacillus probiotics as alternatives to in-feed antibiotics on growth performance, serum chemistry, antioxidant status, intestinal histomorphology and lesion scores of disease-challenged broiler chickens and the mechanisms by which they exert their actions. It is concluded that Bacillus probiotics supplementation improve growth, health and productive indices of disease-challenged broiler chickens and can be a good alternative to in-feed antibiotics. However, more studies are required on the effect of Bacillus probiotics supplementation in broiler chickens to maximize productivity and achieve the ultimate goal of stopping the usage of antibiotics at sub-therapeutic doses in broiler chicken feed to enhance performance.

Effects of a direct fed microbial (DFM) on broiler chickens exposed to acute and chronic cyclic heat stress in two consecutive experiments

Two consecutive 35 d experiments were conducted to investigate the effects of a multistrain DFM fed continuously to broiler chickens exposed to HS from 28 to 35 d on broiler performance, body composition, ileal digestibility, and intestinal permeability using serum Fluorescein Isothiocyanate Dextran (FITC-d) concentration. The treatments were arranged as a 2 × 2 factorial with temperature: Elevated (HS: 33 ± 2°C for 6 h and 27.7°C for the remaining 18 h from 28 to 35 days of age) and Thermoneutral (TN: 22 to 24°C over the entire 24-h day from 28 to 35 days of age) and diet: corn-soybean meal based with and without DFM (3-strain Bacillus; Enviva PRO) fed over the entire 35-d period as the two factors. Experimental diets were formulated to meet all nutrient recommendations based on breed standards using a starter (0–10 d), grower (10–21 d), and finisher (21–35 d) period. For each of the 2 experiments, 648 Ross 708 broiler chicks were allotted among the treatments with 9 replicate pens of 18 broilers. Data were analyzed as a 2 × 2 factorial within each experiment in JMP 14. In both experiments, cloacal temperatures were increased (P ≤ 0.05) in the broilers subjected to the HS treatment at both 28 d (acute) and 35 d (chronic). Supplementing birds with DFM reduced cloacal temperatures in the Experiment 1 at 28 d, but not at the other time periods. The HS treatment reduced body weight gain and lean tissue accretion from 0 to 35 d in both experiments (P ≤ 0.05). In Experiment 2, when the litter was reused BWG was increased by 36 g/bird with supplementation of DFM (P ≤ 0.05). Ileal digestibility at 28 d (2 h post HS) was improved with DFM supplementation in both experiments (P ≤ 0.05). Serum FITC-d increased with HS at both 28 and 35 d. Serum FITC-d was generally decreased with DFM at 28 d but the response was inconsistent at 35 d. Overall, the results suggest that HS reduced broiler performance and DFM treatment improved intestinal permeability and nutrient digestibility responses to HS in both experiments but did not improve performance until built up litter was used in Experiment 2.

Bacterial Community of Galchi-Baechu Kimchi Based on Culture-Dependent and - Independent Investigation and Selection of Starter Candidates

In this study, the bacterial community of galchi-baechu kimchi was determined using culture-based and culture-independent techniques (next generation sequencing:NGS), and showed discrepancies between results. Weissella koreensis and Pediococcus inopinatus were the dominant species according to the NGS results, while Bacillus species and P. inopinatus were dominant in the culture-dependent analysis. To identify safe starter candidates, sixty-five Bacillus strains isolated from galchi-baechu kimchi using culture-dependent methods were evaluated for their antibiotic resistance, presence of toxin genes, and hemolytic activity. Strains were then assessed for salt tolerance and protease and lipase activity. As a result, four strains-B. safensis GN5_10, B. subtilis GN5_19, B. velezensis GN5_25, and B. velezensis GT8-were selected as safe starter candidates for use in fermented foods.

Whole-Genome and Transcriptome Sequencing-Based Characterization of Bacillus Cereus NR1 From Subtropical Marine Mangrove and Its Potential Role in Sulfur Metabolism

Sulfur, organosulfur compounds, and sulfides are essential parts of life. Microbial sulfate assimilation is among the most active and ancient metabolic activities in the sulfur cycle that operates in various ecosystems. We analyzed the molecular basis of bacterial characterization. NR1 was isolated and purified from mangrove sediments. Whole-genome sequencing indicated that the NR1 isolate was closely related to Bacillus cereus. The genome contained 5,305 functional genes with a total length of 5,420,664 bp, a GC content of 35.62%, 42 rRNA, and 107 tRNA. DBT-grown cultures exhibited DBT utilization, fleeting emergence of DBT sulfone (DBTO2), and formation of 2-hydroxybiphenyl (2-HBP). Molecular analysis of the PCR products’ dsz operon revealed the presence of dszA, dszB, and dszC genes, which encoded for NR1’s 90% DBT desulfurization activity. Furthermore, 17 sulfur metabolism-related genes, including genes involved in assimilation sulfate reduction, APS and PAPS, and the cys, ssu, and TST gene families, were identified. In sulfate media, alkenesulfonate was converted to sulfite and inhibited ssu enzymes. Downregulated cysK variants were associated with nrnA expression and the regulation of L-cysteine synthesis. These findings established a scientific foundation for further research and application of bacteria to mangrove rehabilitation and ecological treatment by evaluating the bacterial characterization and sulfur degradation metabolic pathway. We used whole-genome and transcriptome sequencing to examine their genetic characteristics.

Composition of the ileum microbiota is a mediator between the host genome and phosphorus utilization and other efficiency traits in Japanese quail (Coturnix japonica)

Background

Phosphorus is an essential nutrient in all living organisms and, currently, it is the focus of much attention due to its global scarcity, the environmental impact of phosphorus from excreta, and its low digestibility due to its storage in the form of phytates in plants. In poultry, phosphorus utilization is influenced by composition of the ileum microbiota and host genetics. In our study, we analyzed the impact of host genetics on composition of the ileum microbiota and the relationship of the relative abundance of ileal bacterial genera with phosphorus utilization and related quantitative traits in Japanese quail. An F2 cross of 758 quails was genotyped with 4k genome-wide single nucleotide polymorphisms (SNPs) and composition of the ileum microbiota was characterized using target amplicon sequencing. Heritabilities of the relative abundance of bacterial genera were estimated and quantitative trait locus (QTL) linkage mapping for the host was conducted for the heritable genera. Phenotypic and genetic correlations and recursive relationships between bacterial genera and quantitative traits were estimated using structural equation models. A genomic best linear unbiased prediction (GBLUP) and microbial (M)BLUP hologenomic selection approach was applied to assess the feasibility of breeding for improved phosphorus utilization based on the host genome and the heritable part of composition of the ileum microbiota.

Results

Among the 59 bacterial genera examined, 24 showed a significant heritability (nominal p ≤ 0.05), ranging from 0.04 to 0.17. For these genera, six genome-wide significant QTL were mapped. Significant recursive effects were found, which support the indirect host genetic effects on the host’s quantitative traits via microbiota composition in the ileum of quail. Cross-validated microbial and genomic prediction accuracies confirmed the strong impact of microbial composition and host genetics on the host’s quantitative traits, as the GBLUP accuracies based on the heritable microbiota-mediated components of the traits were similar to the accuracies of conventional GBLUP based on genome-wide SNPs.

Conclusions

Our results revealed a significant effect of host genetics on composition of the ileal microbiota and confirmed that host genetics and composition of the ileum microbiota have an impact on the host’s quantitative traits. This offers the possibility to breed for improved phosphorus utilization based on the host genome and the heritable part of composition of the ileum microbiota.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12711-022-00697-8.

Whole-Genome Sequence and Interaction Analysis in the Production of Six Enzymes From the Three Bacillus Strains Present in a Commercial Direct-Fed Microbial (Norum™) Using a Bliss Independence Test

The three Bacillus strains present in Norum™ were initially selected by their excellent to good relative enzyme activity (REA) production score for amylase, protease, lipase, phytase, cellulase, β-glucanase, and xylanase. Further studies confirmed that the three isolates also showed an antibacterial activity, Gram-positive and Gram-negative poultry pathogens. Norum™ (Eco-Bio/Euxxis Bioscience LLC) is a Bacillus spore direct-fed microbial (DFM). The Bacillus isolates were screened and selected based on in vitro enzyme production profiles. Moreover, in chickens fed high non-starch polysaccharides, this DFM demonstrated to reduce digesta viscosity, bacterial translocation, increase performance, bone mineralization, and balance the intestinal microbiota. In the present study, we present the whole-genome sequence of each of the three isolates in Norum™, as well as the synergistic, additive, or antagonistic effects on the enzyme production behavior of the three Bacillus strains and their combinations when grown together vs. when grown individually. The whole-genome sequence identified isolate AM1002 as Bacillus subtilis (isolate 1), isolate AM0938 as Bacillus amyloliquefaciens (isolate 2), and isolate JD17 as Bacillus licheniformis (isolate 3). The three Bacillus isolates used in the present study produce different enzymes (xylanase, cellulase, phytase, lipase, protease, and β-glucanase). However, this production was modified when two or more Bacillus strains were combined, suggesting possible synergistic, antagonistic, or additive interactions. The Bliss analysis suggested (p < 0.05) that the combination of Bacillus strains 1–2 and 1–2–3 had intermediate effects and predicted that the combination of Bacillus strains 2–3 could have better effects than the combination of all the three Bacillus strains. In summary, the current study demonstrated the need of selecting Bacillus strains based on quantitative enzyme determination and data analysis to assess the impacts of combinations to avoid antagonistic interactions that could limit treatment efficacy. These results suggest that using Bacillus strains 2–3 together could lead to a new generation of DFMs with effects superior to those already examined in Bacillus strains 1–2–3 and, therefore, a potential alternative to growth-promoting antibiotics. More research utilizing poultry models is being considered to confirm and expand the existing findings.

Effect of Bacillus subtilis C-3102 Spores as a Probiotic Feed Supplement on Growth Performance, Nutrient Digestibility, Diarrhea Score, Intestinal Microbiota, and Excreta Odor Contents in Weanling Piglets

It has been well-documented that the dietary supplementation of Bacillus subtilis could improve piglet performance. The present study was conducted to investigate the effect of Bacillus subtilis C-3102 spores as a probiotic feed supplement on growth performance, nutrient digestibility, fecal score, intestinal microbiota, and excreta odor contents in weanling piglets. A total of 150 crossed ((Yorkshire × Landrace) × Duroc) weanling piglets (28-days-old), with an average initial body weight of 7.53 ± 1.23 kg, were divided into two treatment groups according to sex and initial body weight (BW) for a 6-week experiment. In each group, fifteen replicate pens consisting of five piglets per pen (three gilts and two barrows) were used in a randomized complete block design. Treatments consisted of (1) CON, a basal diet; (2) BSC, a diet of CON + 300 g Bacillus subtilis (B. subtilis) C-3102 spores per ton of feed. Supplementation with the B. subtilis C-3102 spores in the diet increased the BW, average daily gain (ADG), and gain-to-feed ratio (G:F) throughout the whole trial (p < 0.05). Weanling piglets that were fed B. subtilis C-3102 spores had increased dry matter (DM), crude protein (CP), and energy (E) digestibility compared to the CON group (p < 0.05). Lower diarrhea scores were observed in the B. subtilis C-3102 spores group on Day 7 (p < 0.05). Taken together, our results suggest that dietary supplementation with B. subtilis C-3102 spores could benefit the BW, ADG, and G:F of weanling piglets and improve the apparent total tract digestibility (ATTD) of the DM, CP, and E.

Selection of Bacteriocinogenic Bacillus spp. from Traditional Fermented Korean Food Products with Additional Beneficial Properties

Two Bacillus spp. isolated from kimchi, Bacillus tequilensis ST816CD and Bacillus subtilis ST830CD, were characterized for their antimicrobial properties and safety. The proteinaceous nature of their inhibitory metabolites was confirmed after exposure to proteolytic enzymes, resulting in partial loss of the antimicrobial effect. This indicated that different non-proteinaceous antimicrobial substances may also be produced by these strains. This hypothesis was later confirmed when genes associated with the production of surfactants were detected in their DNA. The expressed antimicrobial metabolites were not affected by treatment at different temperatures and pH levels, including exposure to selected chemicals. Their strong adherence to susceptible pathogens was not significantly affected by different temperatures, chemicals, or pH values. Both Bacillus strains showed inhibitory activity against clinical and food-associated pathogens, including Listeria monocytogenes ATCC 15313, and some Staphylococcus species. Several genes associated with the production of antimicrobial metabolites were detected, but key virulence and beneficial genes were not present in these strains. Even though only B. tequilensis ST816CD displayed γ-hemolysin production, both selected strains were found to produce gelatinase and biogenic amines, which are considered as either potential virulence- or health-related factors. Moreover, the strains were susceptible to a variety of antibiotics except for the penicillin G [1 IU/disc] resistance of B. tequilensis ST816CD. Both strains showed proteolytic activity. Additionally, both strains showed low hydrophobicity based on bacterial adherence measured by hydrocarbons (n-hexadecane).

Multi-Omics Characterization of Host-Derived Bacillus spp. Probiotics for Improved Growth Performance in Poultry

Microbial feed ingredients or probiotics have been used widely in the poultry industry to improve production efficiency. Spore-forming Bacillus spp. offer advantages over traditional probiotic strains as Bacillus spores are resilient to high temperature, acidic pH, and desiccation. This results in increased strain viability during manufacturing and feed-pelleting processes, extended product shelf-life, and increased stability within the animal’s gastrointestinal tract. Despite numerous reports on the use of Bacillus spores as feed additives, detailed characterizations of Bacillus probiotic strains are typically not published. Insufficient characterizations can lead to misidentification of probiotic strains in product labels, and the potential application of strains carrying virulence factors, toxins, antibiotic resistance, or toxic metabolites. Hence, it is critical to characterize in detail the genomic and phenotypic properties of these strains to screen out undesirable properties and to tie individual traits to clinical outcomes and possible mechanisms. Here, we report a screening workflow and comprehensive multi-omics characterization of Bacillus spp. for use in broiler chickens. Host-derived Bacillus strains were isolated and screened for desirable probiotic properties. The phenotypic, genomic and metabolomic analyses of three probiotic candidates, two Bacillus amyloliquefaciens (Ba ATCC PTA126784 and ATCC PTA126785), and a Bacillus subtilis (Bs ATCC PTA126786), showed that all three strains had promising probiotic traits and safety profiles. Inclusion of Ba ATCC PTA12684 (Ba-PTA84) in the feed of broiler chickens resulted in improved growth performance, as shown by a significantly improved feed conversion ratio (3.3%), increased of European Broiler Index (6.2%), and increased average daily gain (ADG) (3.5%). Comparison of the cecal microbiomes from Ba PTA84-treated and control animals suggested minimal differences in microbiome structure, indicating that the observed growth promotion presumably was not mediated by modulation of cecal microbiome.

Potential of an Eco-Sustainable Probiotic-Cleaning Formulation in Reducing Infectivity of Enveloped Viruses

The COVID-19 pandemic has deeply influenced sanitization procedures, and high-level disinfection has been massively used to prevent SARS-CoV-2 spread, with potential negative impact on the environment and on the threat of antimicrobial resistance (AMR). Aiming to overcome these concerns, yet preserving the effectiveness of sanitization against enveloped viruses, we assessed the antiviral properties of the Probiotic Cleaning Hygiene System (PCHS), an eco-sustainable probiotic-based detergent previously proven to stably abate pathogen contamination and AMR. PCHS (diluted 1:10, 1:50 and 1:100) was tested in comparison to common disinfectants (70% ethanol and 0.5% sodium hypochlorite), in suspension and carrier tests, according with the European UNI EN 14476:2019 and UNI EN 16777:2019 standards. Human alpha- and beta-coronaviruses hCoV-229E and SARS-CoV-2, human herpesvirus type 1, human and animal influenza viruses, and vaccinia virus were included in the study. The results showed that PCHS was able to inactivate 99.99% of all tested viruses within 1-2 h of contact, both in suspension and on surface. Notably, while control disinfectants became inactive within 2 h after application, the PCHS antiviral action persisted up to 24 h post-application, suggesting that its use may effectively allow a continuous prevention of virus spread via contaminated environment, without worsening environmental pollution and AMR concern.

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.

Genome assisted probiotic characterization and application of Bacillus velezensis ZBG17 as an alternative to antibiotic growth promoters in broiler chickens

The present study describes genome annotation and phenotypic characterization of Bacillus velezensis ZBG17 and evaluation of its performance as antibiotic growth promoter substitute in broiler chickens. ZBG17 comprises 3.89 Mbp genome with GC content of 46.5%. ZBG17 could tolerate simulated gastrointestinal juices prevalent in the animal gut. Some adhesion-associated genomic features of ZBG17 supported the experimentally determined cell surface hydrophobicity and cell aggregation results. ZBG17 encoded multiple secondary metabolite gene clusters correlating with its broad-spectrum antibacterial activity. Interestingly, ZBG17 completely inhibited Salmonella enterica and Escherichia coli within 6 h and 8 h in liquid co-culture assay, respectively. ZBG17 genome analysis did not reveal any genetic determinant associated with reported safety hazards for use as a poultry direct-fed microbial. Dietary supplementation of ZBG17 significantly improved feed utilization efficiency and humoral immune response in broiler chickens, suggesting its prospective application as a direct-fed microbial in broiler chickens.

Assessing the Impact of Flavophospholipol and Virginiamycin Supplementation on the Broiler Microbiota: a Prospective Controlled Intervention Study

The antibiotic growth promoters (AGPs) flavophospholipol and virginiamycin have been widely used for decades in food animal production. AGP activity is believed to be partly modulated by gut microbial composition although exact AGP-induced changes remain unclear. In a controlled intervention study, we studied the effect of flavophospholipol and virginiamycin on the broiler chicken ileal microbiota spanning from birth to 39 days. Using 16S rRNA gene profiling and prediction of metabolic activity, we show that both AGPs result in dynamic microbial shifts that potentially increase anti-inflammatory mechanisms and bioavailability of several essential nutrients by decreasing degradation (flavophospholipol) or increasing biosynthesis (virginiamycin). Further, virginiamycin-supplemented broilers showed increased colonization with potentially pathogenic bacteria, Clostridium perfringens, Campylobacter, and Escherichia/Shigella spp. Overall, we show that both AGPs induce microbial changes potentially beneficial for growth. However, the increase in (foodborne) pathogens shown here with virginiamycin use could impact not only broiler mortality but also human health. IMPORTANCE Antibiotic growth promoters (AGPs) are commonly used within poultry farming to increase muscle growth. Microbial composition in the gut is known to be influenced by AGP use although exact AGP-induced changes remain unclear. Utilizing 16S rRNA gene profiling, this study provides a first head-to-head comparison of the effect of the two most commonly used AGPs, flavophospholipol and virginiamycin, on the broiler chicken ileum microbiota over time. We found that supplementation with both AGPs altered ileal microbial composition, thereby increasing potential bioavailability of essential nutrients and weight gain. Flavophospholipol showed a slight benefit over virginiamycin as the latter resulted in more extensive microbial perturbations including increased colonization by enteropathogens, which could impact broiler mortality.

A probiotic and mixed-enzymes combination reduces the inflammatory response, faecal shedding and systemic spread of Campylobacter jejuni in broilers

Recent research has questioned the notion that Campylobacter jejuni is a harmless resident of the avian gastrointestinal tract (GIT). The following trial examined the effect of dietary supplementation with a mixture of enzymes and Bacillus-based probiotics on growth performance, C. jejuni colonisation, GIT immune responses, faecal shedding and extra-intestinal spread in broilers. Fifty-eight, Ross 308 d-old broilers were randomly assigned to one of four treatments, giving 14 or 15 birds/pen. Birds were given nutritionally complete, complex, phased diets unsupplemented (two treatments) or supplemented (two treatments) with a multi-enzyme containing 2,000 U/kg xylanase, 200 U/kg amylase and 4,000 U/kg protease, and 75,000 cfu/g of a combination of three strains of Bacillus amyloliquefaciens. One control and one supplemented diet group contained birds orally challenged with 105 cfu C. jejuni strain M1 on d 21 of age. Among challenged birds, the mixed-enzymes and probiotic combination numerically reduced faecal C. jejuni shedding (-98% vs challenged control) three days-post-infection (d.p.i.), and at 7 d.p.i. numerically reduced C. jejuni colonisation of the ileal mucosa (-1000-fold vs control) and totally inhibited systemic spread of C. jejuni to the liver, compared to the control (P<0.05). It suppressed early pro-inflammatory chemokine response seen in the ileum, caecum and caecal tonsil tissues (at 3 d.p.i.) in challenged control birds (-18 to -46-fold; P<0.05) and altered expression of pro-inflammatory (IL-1β, IL-6, IL-17A and IL-17F) and regulatory (IL-10 and TGF-β) cytokines. The data demonstrated inhibition of a sustained pro-inflammatory response to C. jejuni infection and improved intestinal barrier integrity in supplemented birds. This highlighted the importance of looking beyond simple measurements of feed conversion and body weight gain when seeking to understand the effects and mode of action of poultry dietary interventions. Achieving a favourable balance between the gut, immune function, microbiome and nutrition should be the goal for achieving good gastrointestinal health and optimal performance.

Antimicrobial Effects of Potential Probiotics of Bacillus spp. Isolated from Human Microbiota: In Vitro and In Silico Methods

The variable taxa components of human gut microbiota seem to have an enormous biotechnological potential that is not yet well explored. To investigate the usefulness and applications of its biocompounds and/or bioactive substances would have a dual impact, allowing us to better understand the ecology of these microbiota consortia and to obtain resources for extended uses. Our research team has obtained a catalogue of isolated and typified strains from microbiota showing resistance to dietary contaminants and obesogens. Special attention was paid to cultivable Bacillus species as potential next-generation probiotics (NGP) together with their antimicrobial production and ecological impacts. The objective of the present work focused on bioinformatic genome data mining and phenotypic analyses for antimicrobial production. In silico methods were applied over the phylogenetically closest type strain genomes of the microbiota Bacillus spp. isolates and standardized antimicrobial production procedures were used. The main results showed partial and complete gene identification and presence of polyketide (PK) clusters on the whole genome sequences (WGS) analysed. Moreover, specific antimicrobial effects against B. cereus, B. circulans, Staphylococcus aureus, Streptococcus pyogenes, Escherichia coli, Serratia marcescens, Klebsiella spp., Pseudomonas spp., and Salmonella spp. confirmed their capacity of antimicrobial production. In conclusion, Bacillus strains isolated from human gut microbiota and taxonomic group, resistant to Bisphenols as xenobiotics type endocrine disruptors, showed parallel PKS biosynthesis and a phenotypic antimicrobial effect. This could modulate the composition of human gut microbiota and therefore its functionalities, becoming a predominant group when high contaminant exposure conditions are present.

Benefit of Dietary Supplementation with Bacillus subtilis BYS2 on Growth Performance, Immune Response, and Disease Resistance of Broilers

A strain of Bacillus subtilis (B. subtilis) BYS2 was previously isolated from Mount Tai, which is located in Tai'an City in the Shandong Province of China. The strain was then stored in the Environmental Microbiology Laboratory at Shandong Agricultural University. To evaluate the effect of the bacterium preparation in broiler production, we fed the bacterium (10⁶ CFU/g) to 1-day-old broilers and continued this feeding for 6 weeks to analyze its effect on growth and immune performance. We found that the average weight of the bacterium-fed group increased by 17.19% at weeks 5 compared to the control group (P < 0.05). The height of the villi in the duodenum and jejunum and the ratio of villi to crypt were significantly increased in the bacterium-fed group at weeks 5 (P < 0.05). Also, the IgG in the serum of broilers in the experimental group increased by 31.60% (P < 0.05) and IgM 30.52% (P < 0.05) compared with those in the control group. The expressions of the major pattern recognition receptors (PRRs), antiviral proteins, pro-inflammatory cytokines, and β-defensins were significantly higher than those in the control group (P < 0.05). Meanwhile, the bursa immune organ indices of broilers in the experimental group were significantly higher than those in the control group (P < 0.05). Also, after 5 weeks of continuous feeding, when infected with Escherichia coli (E. coli) O1K1 and Newcastle disease virus (NDV) F48E8, the content of bacteria and virus in tissues and organs of the experimental group decreased significantly, and the survival rate of infected chickens increased by 31.1% and 17.7%, respectively (P < 0.05). These results show that the anti-infective B. subtilis BYS2 could, to some extent, replace antibiotics to promote growth, improve innate immunity, and enhance disease resistance in broilers.

Representative Bacillus sp. AM1 from Gut Microbiota Harbor Versatile Molecular Pathways for Bisphenol A Biodegradation

Human gut microbiota harbors numerous microbial species with molecular enzymatic potential that impact on the eubiosis/dysbiosis and health/disease balances. Microbiota species isolation and description of their specific molecular features remain largely unexplored. In the present study, we focused on the cultivation and selection of species able to tolerate or biodegrade the endocrine disruptor bisphenol A (BPA), a xenobiotic extensively found in food plastic containers. Chemical xenobiotic addition methods for the directed isolation, culturing, Whole Genome Sequencing (WGS), phylogenomic identification, and specific gene-encoding searches have been applied to isolate microorganisms, assess their BPA metabolization potential, and describe encoded catabolic pathways. BPA-tolerant strains were isolated from 30% of infant fecal microbial culture libraries analyzed. Most isolated strains were phylogenetically related to the operational taxonomic group Bacillus amyloliquefaciens spp. Importantly, WGS analysis of microbial representative strain, Bacillus sp. AM1 identified the four complete molecular pathways involved on BPA degradation indicating its versatility and high potential to degrade BPA. Pathways for Exopolysaccharide (EPS) and Polyhydroxyalkanates (PHA) biopolymer synthesis were also identified and phenotypically confirmed by transmission electronic microscopy (TEM). These microbial biopolymers could generally contribute to capture and/or deposit xenobiotics.

Bacteriocinogenic Bacillus spp. Isolated from Korean Fermented Cabbage (Kimchi)—Beneficial or Hazardous?

Bacillus velezensis ST03 and ST32, Bacillus amyloliquefaciens ST06 and ST109, and Bacillus subtilis ST08 were isolated from artisanal-produced kimchi and were identified based on 16S rRNA partial sequencing. DNA obtained from the investigated bacilli generated positive results for lichenicidin, iturin, subtilosin, and surfactin on a strain-specific basis. The strains were found to produce antimicrobial metabolites with activity levels ranging between 800 and 1600 AU/mL on a strain-specific basis, as determined against Listeria monocytogenes ATCC15313. Moreover, all tested strains in this study were still active after treatment with proteolytic enzymes, even with reduced inhibition zones compared to the controls, pointing to additional antimicrobial activity possibly related to a non-proteinaceous molecular structure. Most probably these strains may express surfactin as an additional factor in their complex antimicrobial activity. B. amyloliquefaciens ST09 and B. velezensis ST03 and ST32 were characterized as positive for β-hemolysis. B. subtilis ST08 was shown to be positive for hblC and nheC and B. amyloliquefaciens ST109 for nheB. B. amyloliquefaciens ST109 generated positive results for gelatinase activity. The ability of the studied Bacillus strains to metabolize different carbohydrate sources was done based on the API50CHB test, while the enzyme production profile was recorded by the APIZym kit. All studied strains were positive producers for biogenic amines production. Studied Bacillus spp. strains were resistant to some of the evaluated antibiotics, tested according to recommendations of CLSI and EFSA.

Effects of feed supplementation with 3 different probiotic Bacillus strains and their combination on the performance of broiler chickens challenged with Clostridium perfringens

The application of probiotics in broiler feed, to alleviate performance deficiencies due to mild infections by coccidia and Clostridium perfringens, is of increasing interest for the poultry industry. Therefore, our objective was to evaluate the capacity of 3 Bacillus strains and their combination as probiotics in vitro and in vivo. Thus, protein and carbohydrate degradation and C. perfringens growth inhibition capabilities were assessed by colometry measurement and an agar diffusion bioassay, respectively. A total of 2,250 1-day-old male broiler chicks were assigned to 5 dietary treatments: 1) non-probiotic-supplemented control (control); 2) control + DSM 32324 at 0.8 × 106 cfu/g of feed; 3) control + DSM 32325 at 0.5 × 106 cfu/g of feed; 4) control + DSM 25840 at 0.3 × 106 cfu/g of feed; and 5) control + DSM 32324 + DSM 32325 + DSM 25840 at 1.6 × 106 cfu/g of feed. A pathogenic field strain of C. perfringens was used to induce the necrotic enteritis challenge on day 19, 20, and 21. All birds and remaining feed were weighed on pen basis on day 0, 21, 35, and 42, to calculate BW gain and mortality-adjusted feed conversion. Mortality and mortality due to necrotic enteritis were recorded daily. On day 21, 45 birds per treatment were evaluated for macroscopic intestinal necrotic enteritis lesions. Performance data were statistically analyzed using an ANOVA and subjected to a least significant difference comparison. Necrotic enteritis lesion scores were statistically analyzed using nonparametric Kruskal-Wallis test. Dunn's test was used for treatment comparison. The tested strains showed different abilities of degrading protein and carbohydrates and inhibiting C. perfringens growth in vitro. The birds fed the multi-train combination presented significantly better performance and lower necrotic enteritis lesion score than those in the control group. Dietary supplementation with probiotics resulted in significantly lower necrotic enteritis mortality. The results demonstrate the suitability of the evaluated Bacillus multistrain combination as an effective probiotic in C. perfringens-challenged chickens.

Bioprospecting potentials of moderately halophilic bacteria and the isolation of squalene producers from Kuwait sabkha

Sabkhas in Kuwait are unique hypersaline marine environments under-explored for bacterial community composition and bioprospecting. The 16S rRNA sequence analysis of 46 isolates with distinct morphology from two Kuwait sabkhas recovered 11 genera. Phylum Firmicutes dominated these isolates, and Bacillus (32.6%) was recovered as the dominant genera, followed by Halococcus (17.4%). These isolates were moderately halophilic, and some of them showed tolerance and growth at extreme levels of salt (20%), pH (5 and/or 11), and temperature (55 °C). A higher percentage of isolates harbored protease (63.0), followed by DNase (41.3), amylase (41.3), and lipase (32.6). Selected isolates showed antimicrobial activity against E. faecalis and isolated Halomonas shengliensis, and Idiomarina piscisalsi harbored gene coding for dNDP-glucose 4,6-dehydratase (Glu 1), indicating their potential to produce biomolecules with deoxysugar moieties. Palmitic acid or oleic acid was the dominant fatty acid, and seven isolates had some polyunsaturated fatty acids (linolenic or γ-linolenic acid). Interestingly, six isolates belonging to Planococcus and Oceanobacillus genus produced squalene, a bioactive isoprenoid molecule. Their content increased 30-50% in the presence of Terbinafine. The potential bioactivities and extreme growth conditions make this untapped bacterial diversity a promising candidate for future bioprospecting studies.