Search Results (1,505)

In this study, we aimed to explore the intestinal microbiota structure of Xichuan black-bone chickens (XBCs) and evaluate the effect of fecal microbiota substitute transplantation (FMST) by comparing it with traditional fecal microbiota transplantation (FMT). Metagenomic sequencing was used to analyze the microbiota composition and diversity of different intestinal segments (duodenum, jejunum, ileum, cecum, and rectum) of adult XBCs. Probiotic strains were subsequently isolated and screened from the cecal contents under anaerobic conditions to prepare FMST preparations. In total, 90 1-day-old XBCs were randomly divided into the FMT group, FMST group and control group (CK) for the transplantation experiment. The results revealed that the cecum had the highest species richness among all intestinal segments, with a mean species number of 7593.2. Three probiotic strains, namely, Lactobacillus crispatus, Weissella paramesenteroides and Bacillus amyloliquefaciens, were successfully screened and identified. In the transplantation experiment, the FMT group exhibited optimal α diversity of the cecal microbiota, while compared with the FMT group, the FMST group had significantly reduced expression of pro-inflammatory cytokines (IL-6, TNF-α, and IL-1β) and increased expression of intestinal tight junction proteins (claudin-1 and ZO-1). In conclusion, the cecum of XBCs has the most abundant microbial resources. Under the short-term intervention model tested herein, the custom FMST formulation delivers superior intestinal protective effects and shows promising potential as a standardized alternative to conventional FMT, which is highly important for the standardized application of fecal microbiota transplantation in poultry production. Full article

Vip3 proteins secreted by the entomopathogenic bacterium Bacillus thuringiensis (Bt) have an important role in biological control against economically important lepidopteran pests. The elucidation of Vip3 protein structures has helped to address the roles of domains and amino acid positions involved in toxicity, especially in the N-terminal domains I and II, thereby supporting their more efficient utilization. In this study, we evaluated the impact of combinations of critical amino acid substitutions, selected from previous studies, in domains IV and V of the Vip3Aa90 protein on its insecticidal activity against three lepidopteran pests. The double mutant S543N/I544L, triple mutants S543N/I544L/E627A and S543N/I544L/S686R, and quadruple mutant S543N/I544L/E627A/S686R were constructed in Escherichia coli by site-directed mutagenesis. Among these, only the Vip3Aa mutant proteins S543N/I544L/E627A and S543N/I544L/E627A/S686R could be expressed and purified for bioassays. Both mutant proteins had similar toxicity against Spodoptera littoralis, showing higher insecticidal activity than the wild-type (WT) Vip3Aa90 at the LC₉₀ level. However, at the LC₅₀ level, only a slight improvement in toxicity was observed for the quadruple mutant. In the case of S. exigua, no significant difference in toxicity was observed for either of the two mutant proteins with respect to the WT at either LC level. Interestingly, for G. molesta, though the toxicity of the triple mutant did not differ significantly compared to that of the WT protein, that of the quadruple mutant showed a marked decrease in toxicity of over 10-fold. This study revealed that combining selected amino acid substitutions in domains IV and V can enhance Vip3Aa90 toxicity against some lepidopteran species but can be either neutral or even deleterious in others. Full article

Plant growth-promoting microorganisms (PGPM) may contribute to sustainable forage production, but their effects can vary with host species and plant trait. Bacillus subtilis, Pseudomonas putida, Trichoderma harzianum, and Trichoderma viride were evaluated alongside a non-inoculated control in Leucaena leucocephala and Megathyrsus maximus cv. Mombasa in northern Peru. Replicated germination and nursery experiments were complemented by a preliminary field assessment. Inoculation did not significantly affect final germination percentage in either forage species. In the nursery, L. leucocephala exhibited significant inoculant treatment effects on multiple growth traits, including positive responses in plant height and leaf number under B. subtilis, P. putida, and T. harzianum at the final evaluation. Significant treatment effects were also detected for several final aboveground and belowground growth traits, whereas total weight was not significantly affected. By contrast, growth variation in M. maximus cv. Mombasa was mainly associated with evaluation time, while microbial treatment and treatment × time effects were not significant. Multivariate analysis detected significant treatment and species × treatment effects, indicating contrasting joint growth-response profiles between the two forage species without demonstrating specificity of individual host–microorganism combinations. Preliminary field measurements showed numerical variation among treatment-associated rows, but these observations were descriptive only because treatments were neither randomized nor independently replicated. Overall, this comparative evaluation shows that PGPM responses in tropical forage species can be strongly species- and trait-dependent under nursery conditions, while validation of these responses under field conditions requires appropriately randomized and independently replicated experiments. Full article

The microbiological quality of silage, a fundamental component of cattle feed, is critical to both animal health and human safety. This long-term study evaluated the microbiological status of grass silages collected from Polish cattle farms, aiming to assess the prevalence of zoonotic agents and hygiene indicators in relation to pre-ensiling and ensiling agricultural practices. A total of 160 grass silage samples were randomly collected nationwide by veterinary officers across various municipalities. The researchers measured pH values and conducted analyses to determine the presence and loads of pathogens, including Listeria spp., Clostridium spp., Salmonella spp., Escherichia coli, and Bacillus cereus. Only 17.5% of grass silages fell within the optimal target pH range. Conversely, 80.6% exceeded the upper reference threshold, indicating widespread poor fermentation and low silage quality. Listeria species were detected in 5.6% of the forages, occurring exclusively in silages with an incorrect pH. Clostridium spp. were highly prevalent, testing positive in 82.5% of all samples, while C. perfringens (predominantly toxotype A) was identified in 26.2%. Both Salmonella spp. and botulinum neurotoxin-producing Clostridia were detected in separate, single samples, both characterized by high pH levels. Additionally, fungal counts reached high, non-feedable levels exceeding 6 log₁₀ cfu/g in 10.6% of the tested silages. Silage inoculation, practiced by 26.2% of farmers, significantly lowered pH values and reduced the counts of spoilage microorganisms. Additionally, inoculated silages had a more than three-fold greater likelihood of achieving the correct pH. In contrast, organic fertilization was associated with an increase in the mean counts of Clostridium spp. and B. cereus. In conclusion, grass silage is highly vulnerable to poor fermentation and microbial contamination. Full article

Microbe-derived elicitors can trigger plant immune responses, but elicitors from endophytic Bacillus species remain largely unexplored. Based on preliminary findings that endophytic Bacillus subtilis K1 can elicit grape immune responses, this study aimed to investigate the elicitor proteins produced by K1 and the effect on the control of gray mold in grapes. A novel elicitor protein PeBs1 screened from the genome of K1 could induce a strong hypersensitive response in Nicotiana benthamiana by Agrobacterium-mediated transformation, accompanied by significant reactive oxygen species accumulation and callose deposition. The PeBs1 gene encodes a 15.9 kDa protein consisting of 181 amino acids, which is evolutionarily conserved within the genus Bacillus. Exogenous infiltration with 10 μM purified PeBs1 protein also triggered typical hypersensitive response symptoms in N. benthamiana. Application of the purified PeBs1 to grape berries significantly reduced the incidence of gray mold and boosted the activities of defense enzymes, including peroxidase (POD), polyphenol oxidase (PPO), catalase (CAT), and phenylalanine ammonia-lyase (PAL), while also lowering the malondialdehyde (MDA) content. Meanwhile, PeBs1 treatment markedly increased the contents of total phenols and total flavonoids in grape berries, and significantly up-regulated the transcriptional levels of defense-related genes (VvPAL, VvPPO, VvPR1, VvPR2). This study suggests that PeBs1 from endophytic Bacillus may act as an immune activator to enhance grape resistance against gray mold. The findings provide a basis for exploring potential strategies to manage grape postharvest diseases. Full article

Foodborne pathogens such as E. coli, B. cereus, L. monocytogenes, and S. aureus cause many illnesses in Europe each year due to traits like biofilm formation, spore production, and high resistance to harsh conditions. This study investigated plasma-treated water (PTW) as an eco-friendly antimicrobial approach and examined its effect on bacterial growth curves to improve food safety. PTW was generated using a microwave plasma source, then applied to bacterial cultures that were monitored by optical density and colony counts. The bacterial growth was described by application of a logistic growth model to the optical density and colony count data. Results show that PTW mainly prolonged the lag phase of growth, with a stronger effect on Gram-positive bacteria than on Gram-negative bacteria. Although PTW initially reduced viable cell numbers, most bacteria eventually recovered and reached the stationary phase after a delay of about 2 to 11 h depending on the species. These effects may be due to cell damage, cell death, viable but nonculturable state induction, or stress responses such as spore formation. Further studies are needed to confirm how PTW performs in real food systems and biofilm settings. Full article

Antimicrobial resistance (AMR) in aquaculture environments has become an increasing concern due to the dissemination of antibiotic-resistant bacteria in aquatic ecosystems. This study investigated the occurrence of presumptive antimicrobial-resistant bacteria in commercial fish farms in Hajdú-Bihar county, Hungary. Between 2023 and 2024, water samples were collected from fishponds from Hajdúszoboszló, Biharugra, and Debrecen, followed by membrane filtration with 0.45 µm pore size mixed cellulose ester membrane filters, bacterial isolation using selective media including vancomycin-resistant enterococci (VRE) agar, Eosin Methylene Blue (EMB) agar, and Endo’s medium. The phenotypic characterization revealed the presence of diverse bacterial populations that could be associated with potential antimicrobial resistance. Bacterial identification using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) showed several bacterial genera, predominantly Acinetobacter, Pseudomonas, Enterococcus, Bacillus, and Escherichia. A total of 16 presumptive antimicrobial-resistant bacterial isolates recovered from selective media were identified using MALDI-TOF MS. Several detected species, including Acinetobacter baumannii, Pseudomonas aeruginosa, Enterococcus faecium, and Enterococcus faecalis, are recognized as opportunistic bacteria associated with antimicrobial resistance dissemination. The findings demonstrate that aquaculture waters in Hajdú-Bihar county may serve as reservoirs of antimicrobial-resistant bacteria. Full article

Cowpea (Vigna unguiculata subsp. sesquipedalis, also known as yardlong bean) is an important winter horticultural crop in Hainan, and Fusarium wilt seriously threatens its yield and quality. To clarify the pathogen and screen antagonistic bacteria, surveys were conducted in 14 fields across Hainan’s major cowpea-growing areas. The causal agent was isolated, tested for pathogenicity, and identified using morphological and multigene molecular methods. Meanwhile, rhizosphere and endophytic bacteria from healthy plants were screened by dual culture, and candidate strains were phylogenetically analyzed using whole-genome sequencing (285 orthologous single-copy genes). Fusarium wilt occurred in all 14 fields (mean incidence 15.35%, range 3.20–76.40%). Of 44 fungal isolates, six were highly pathogenic and identified as Fusarium oxysporum. Twenty-two bacterial strains showed stable antagonism against F. oxysporum, with inhibition rates ranging from 42.62% to 68.47%. Phylogenetic analysis based on whole-genome sequences identified 15 Bacillus strains to the species level (12 B. velezensis, 2 B. subtilis, 1 B. tropicus), while the remaining seven strains belonged to Lysinibacillus (1), Pantoea (1), Klebsiella (1), Serratia (2), and Pseudomonas (2). Draft genome sequences of all 22 strains were obtained. This study provides a collection of biocontrol bacterial resources and genomic information for managing cowpea Fusarium wilt. Full article

Precision nutrigenomics requires a diet–microbiome–host perspective because microorganisms can transform feed substrates, generate bioactive metabolites, compete with pathogens, and modify intestinal and systemic gene regulation. This structured narrative review synthesizes representative controlled feeding trials, transcriptomic and targeted gene-expression studies, microbiome analyses, and complementary multi-omic evidence concerning dietary regulations in cultured finfish. The available evidence is concentrated particularly on soybean-derived proteins, lipid-source replacements, selected amino acids and micronutrients, functional additives, probiotics, and fermented ingredients in a limited range of cultured finfish species; therefore, the synthesis is not intended to provide exhaustive coverage of every dietary intervention or finfish taxon. Recurrent host responses involve intestinal inflammation and barrier integrity, nutrient transport, lipid and bile-acid metabolism, long-chain polyunsaturated fatty-acid biosynthesis, targets of rapamycin/insulin-like growth factor (TOR/IGF) signaling, and nuclear factor erythroid 2-related factor 2/Kelch-like ECH-associated protein 1 (Nrf2/Keap1) antioxidant defense. The expanded microorganism-centered synthesis shows that dietary effects depend on microbial niche, substrate availability, community succession, metabolite production, and strain-specific probiotic or pathobiont activity. Lactic-acid bacteria, Bacillus-associated interventions, butyrate-generating strategies, fermented ingredients, and microbial biomass may support digestion, immune balance, and disease resistance, but taxonomic shifts alone do not demonstrate functional benefit. Current evidence is limited by extensive reliance on 16S ribosomal RNA (16S rRNA) relative-abundance data, inconsistent digesta-versus-mucosa sampling, inadequate feed and water controls, and weak causal validation. Future precision aquafeed studies should combine host transcriptomics with absolute microbial quantification, shotgun metagenomics, metatranscriptomics, metabolomics, culturomics, histology, and pathogen challenge. Integrating microbial function with host phenotype can improve sustainable feed design, intestinal health, and resilience. Full article

The study evaluated the bioremediation potential of a commercial probiotic composed of multi-strain Bacillus (B. subtilis CCT 0089, B. amyloliquefaciens ATCC 31592, B. licheniformis CCT 7836 and B. megaterium CCT 7935) in biofloc technology (BFT). In vitro, the ideal dosage was identified between concentrations [0.01], [0.10], [1.00], and [10.00] g m⁻³. Additionally, the growth of probiotic species was characterised in different temperature and oxygen conditions, resistance in 3.0% sodium chloride culture medium, enzyme production (protease, amylase, and lipase) and antibacterial activity. The in vivo experiment evaluated the bioremediation potential of the probiotic and its impact on the growth performance of Nile tilapia Oreochromis niloticus raised in BFT conditions. The group that received the multi-strain Bacillus probiotic at a dosage of 0.10 g m⁻³ experienced a decrease in floc volume, toxic ammonia, and nitrate levels, leading to environmental enhancements and improved well-being for the cultured organisms. It is advisable to use the multi-strain probiotic at a dosage of 0.10 g m⁻³ in BFT conditions. Full article

Potato peel waste (PPW) represents a low-cost and eco-friendly by-product with potential for use as a fermentation substrate for the production of antibacterial metabolites by Bacillus species. This study evaluated PPW as a fermentation matrix for Bacillus velezensis and demonstrated that 2% PPW supported optimal production of antibacterial compounds. The cell-free supernatant obtained after 96 h of fermentation exhibited the strongest activity against E. coli 18/22, with a MIC of 62.5 µg/mL. The ethyl acetate extract exhibited rapid bactericidal activity, killing E. coli 18/22 within 30 min at 2× MIC and within 120 min at MIC. The antibacterial activity remained stable up to 80 °C, across pH 4–12, and after treatment with pepsin and chymotrypsin. LC/HR-ESI-MS analysis identified oxydifficidin and surfactins C14 and C15 as the main active compounds. Molecular docking revealed that oxydifficidin and surfactin C15 exhibited the strongest binding affinity toward Shiga toxin II, while surfactin C14 displayed a weaker interaction, suggesting the role of acyl chain length in toxin binding. Both oxydifficidin and surfactins interacted with key residues within the catalytic pocket of the AcrB subunit of the AcrAB–TolC multidrug efflux pump, indicating potential inhibition of multidrug resistance mechanisms. To our knowledge, this is the first report describing the use of PPW as a fermentation substrate for Bacillus velezensis B38 to produce oxydifficidin and surfactin C14 and C15 exhibiting antimicrobial activity against multidrug-resistant E. coli. These findings provide a promising strategy for transforming agro-industrial waste into value-added antimicrobial metabolites, contributing to the circular bioeconomy strategies within the One Health framework. Full article

Salt stress is a prevalent abiotic stress worldwide, which markedly inhibits crop growth and triggers yield losses. In this study, salt-tolerant plant-growth-promoting rhizobacteria of Cerasus humilis—Bacillus pumilus and B. velezensis, which possess nitrogen-fixing, phosphate-solubilizing, and indole-3-acetic acid (IAA) and 1-aminocyclopropane-1-carboxylate (ACC) deaminase-producing traits—were co-inoculated with Sinorhizobium meliloti. The effects of these bacterial combinations on alfalfa (Medicago sativa L.) were systematically evaluated during seed germination and plant growth under salt stress simulated using NaCl, Na₂SO₄, NaHCO₃, and Na₂CO₃ at varying intensities. The results showed that under salt stress, inoculation significantly increased the seed germination rate by 11.33–41.33%. Pot experiments further revealed that inoculation significantly enhanced symbiotic nitrogen fixation efficiency in alfalfa and effectively maintained K⁺/Na⁺ homeostasis (K⁺ concentration increased by 4.23–125.34%, while Na⁺ concentration decreased by 7.15–102.09%). Concurrently, inoculation upregulated antioxidant enzyme activities and promoted the accumulation of non-enzymatic antioxidants, thereby significantly reducing reactive oxygen species levels. Moreover, inoculation substantially increased the content of osmoregulatory substances such as proline and soluble protein; proline accumulation surged more than fivefold (39.97–551.05%) compared with the non-inoculated control, effectively alleviating cellular dehydration. Through these multi-pathway regulations mediated by Bacillus sp. and S. meliloti, the inhibitory effect of salt stress on alfalfa growth was significantly mitigated, with dry weight increasing by 45.9–92.4%. Principal component analysis indicated that inoculation with the B. velezensis–S. meliloti microbial combination was the most promising strategy for promoting alfalfa growth and alleviating salt stress. The results provide a theoretical basis for developing microbial fertilizers and establishing alfalfa pastures in saline lands, thereby promoting their sustainable utilization. Full article

Post-weaning diarrhea caused by pathogenic Escherichia coli is a significant economic challenge in global swine production. Rising antimicrobial resistance linked to traditional antibiotics necessitates safe, sustainable alternatives. This study isolated and characterized host-associated Bacillus species from the gastrointestinal tracts of healthy pigs to evaluate their probiotic potential. Fifty-nine Bacillus isolates were screened for safety, gastrointestinal tract survivability, mucosal adhesion, and antimicrobial efficacy. Several isolates demonstrated robust tolerance to simulated gastrointestinal stress (acidic pH and bile salts), non-hemolytic profiles, and strong mucosal adhesion. Multiple isolates displayed inhibitory activity against pathogenic Escherichia coli in vitro. The most promising candidate, Bacillus subtilis 1BP1Co1, underwent Nanopore whole-genome sequencing. Genomic profiling confirmed its safety, revealing a complete absence of known virulence factors and high-risk antimicrobial resistance genes. Furthermore, genome annotation identified multiple biosynthetic gene clusters responsible for the production of antimicrobial secondary metabolites, including surfactin, fengycin, bacillaene, and subtilosin A, which mechanistically supports its pathogen-inhibitory properties. Collectively, these findings highlight indigenous Bacillus strains, particularly Bacillus subtilis 1BP1Co1, as promising probiotic candidates with the potential to be developed to mitigate Escherichia coli-associated enteric disorders in swine production systems. Full article

Orchid root-associated fungal endophytes (ORAFEs) represent an important component of fungal biodiversity with potential applications in orchid conservation and sustainable production. ORAFEs were isolated from the roots of four orchid species in Veracruz, Mexico: Gongora galeata, Maxillaria densa, Maxillaria tenuifolia, and Maxillaria variabilis to investigate their diversity and plant-growth-promoting (PGP) properties. Taxonomic identification relied on morphological and molecular phylogenetic analyses using ITS, TEF1-α, β-tubulin (TUB2), and actin (ACT). Fifty-six isolates were grouped into 20 morphotypes representing 15 genera, including Aspergillus, Biscogniauxia, Chaetomium, Colletotrichum, Thelonectria, Diaporthe, Fusarium, Geotrichum, Hypoxylon, Lasiodiplodia, Mucor, Periconia, Pestalotiopsis, Trichoderma, Xylaria, and two isolates that may represent undescribed taxa requiring further polyphasic taxonomic investigation. Functional experiments indicated a wide range of PGP activities: ten strains solubilized phosphate, eight produced siderophores, twelve synthesized indole-3-acetic acid, fourteen produced pectinases, six fungi exhibited antibacterial activity against Bacillus subtilis, and five inhibited Staphylococcus aureus. Furthermore, Trichoderma atroviride TR1-T2 and Xylaria multiplex XY1-D42 showed antagonistic activity against Phytopythium vexans, characterized by a contact-dependent displacement effect. Five strains were chosen for further research as orchid bioinoculants based on their PGP and antagonistic traits: Chaetomium cochliodes CH1-V10, Mucor pseudolusitanicus MU2-T6, Thelonectria veuillotiana TH1-T3, Trichoderma atroviride TR1-T2, and Xylaria multiplex XY1-D42. These endophytes have the potential to improve in vitro propagation and facilitate ex vitro acclimatization of orchids, highlighting their importance in sustainable orchid production. Full article

Largemouth bass (Micropterus salmoides) is a major freshwater farmed species in China, making substantial economic contributions owing to its desirable flesh quality, rapid growth, and strong acceptance of formulated feeds. This study assessed the effects of dietary supplementation (intermittent and continuous feeding group, n = 3) with the probiotic Bacillus velezensis (1.0 × 10⁹ CFU/g) on growth performance, intestinal morphology, digestive enzyme activities, and gut microbial diversity in this fish. The results indicated that continuous B. velezensis administration significantly increased percentage weight gain, specific growth rate, and survival, while concurrently reducing feed conversion ratio relative to the basal diet (p < 0.05). Intermittent feeding also resulted in a markedly higher survival rate and a lower FCR. Histological examination of intestinal sections revealed elevated villus height, villus width, and muscularis thickness in the B. velezensis supplemented groups, with the intermittent regimen producing more pronounced effects. Compared with the control, the intermittent group exhibited substantially decreased the pepsin and lipase activities of the serum. In the continuous group, serum globulin levels rose noticeably, accompanied by significant declines in total complement and superoxide dismutase. Moreover, continuous B. velezensis supplementation markedly upregulated the expression levels of TGFβ, myd88, IL34, IL8, and TNFα in the head-kidney of the largemouth bass, whereas intermittent supplementation significantly increased TGFβ, Gpx, Nrf2, and Acp transcript levels. Dietary inclusion of B. velezensis was also found to enhance intestinal microbial richness and greatly increase the abundance of potentially beneficial bacteria. Collectively, these results indicate that B. velezensis supplementation exerts beneficial effects on intestinal digestive capacity, growth, and innate immunity, thereby lowering disease susceptibility in largemouth bass. Full article