Microbiol. Res., Volume 16, Issue 3 (March 2025) – 19 articles

Soda lakes are extreme saline–alkaline environments that harbor metabolically versatile microbial communities with significant biotechnological potential. This study employed shotgun metagenomics (NovaSeq PE150) to investigate the functional diversity and metabolic potential of microbial communities in Ethiopia’s Chitu and Shala Lakes. An analysis of gene content revealed 554,609 and 525,097 unique genes in Chitu and Shala, respectively, in addition to a substantial fraction (1,253,334 genes) shared between the two, underscoring significant functional overlap. Taxonomic analysis revealed a diverse phylogenetic composition, with bacteria (89% in Chitu Lake, 92% in Shala Lake) and archaea (4% in Chitu Lake, 0.8% in Shala Lake) as the dominant domains, alongside eukaryotes and viruses. Predominant bacterial phyla included Pseudomonadota, Actinomycetota, and Gemmatimonadota, while Euryarchaeota and Nitrososphaerota were prominent among archaea. Key genera identified in both lakes were Nitriliruptor, Halomonas, Wenzhouxiangella, Thioalkalivibrio, Aliidiomarina, Aquisalimonas, and Alkalicoccus. Functional annotation using the KEGG, eggNOG, and CAZy databases revealed that the identified unigenes were associated with various functions. Notably, genes related to amino acid, carbohydrate, and energy metabolism (KEGG levels 1–2) were predominant, indicating that conserved core metabolic functions are essential for microbial survival in extreme conditions. Higher-level pathways included quorum sensing, two-component signal transduction, and ABC transporters (KEGG level 3), facilitating environmental adaptation, stress response, and nutrient acquisition. The eggNOG annotation revealed that 13% of identified genes remain uncharacterized, representing a vast untapped reservoir of novel enzymes and biochemical pathways with potential applications in biofuels, bioremediation, and synthetic biology. This study identified 375 unique metabolic pathways, including those involved in pyruvate metabolism, xenobiotic degradation, lipid metabolism, and oxidative stress resistance, underscoring the microbial communities’ ability to thrive under fluctuating salinity and alkalinity. The presence of carbohydrate-active enzymes (CAZymes), such as glycoside hydrolases, polysaccharide lyases, and oxidoreductases, highlights their role in biomass degradation and carbon cycling. Enzymes such as alkaline proteases (Apr), lipases (Lip), and cellulases further support the lakes’ potential as sources of extremophilic biocatalysts. These findings position soda lakes as reservoirs of microbial innovation for extremophile biotechnology. Future research on unannotated genes and enzyme optimization promises sustainable solutions in bioenergy, agriculture, and environmental management. Full article

Multidrug-resistant (MDR) bacterial pathogens pose a serious threat to global health, underscoring the urgent need for innovative therapeutic strategies. In this work, we designed and characterized thiol-modified antisense oligonucleotide-capped gold nanoparticles (ASO-AuNPs) to resensitize antibiotic-resistant bacteria. Transmission electron microscopy and UV–Vis spectroscopy confirmed the morphology, size, and optical properties of AuNPs and ASO-AuNPs. Minimum inhibitory concentrations (MIC) of ampicillin were determined for non-resistant Escherichia coli DH5α (16 ppm) and an ampicillin-resistant E. coli DH5α strain (PSK, 32,768 ppm). When co-administered with ampicillin, ASO-AuNPs (0.1 and 0.2 nM) significantly reduced bacterial growth compared to the antibiotic-alone control (p < 0.05), demonstrating the capacity of ASO-AuNPs to restore antibiotic efficacy. These findings provide a proof of concept that antisense oligonucleotide-functionalized nanomaterials can be harnessed to overcome beta-lactam resistance, setting the stage for further optimization and translation into clinical applications. Full article

The development of microbial-based biostimulants to enhance the growth of crops and support a healthy and sustainable soil requires the isolation and large-scale industrial culture of effective microorganisms. In this study, work was undertaken to isolate and characterize free-living nitrogen-fixing bacteria capable of acting as biostimulants alone or by incorporation into and/or supplementation with a current commercial crop biostimulant for farmers. Free-living bacteria were isolated from soil, sugar cane mulch, and plant roots following preliminary culture in a nitrogen-free media that targeted specific groups of known diazotrophs. Following the identification of each isolate by 16S rDNA sequence analysis, isolates selected for further study were identified as most closely related to Priestia megaterium, Sphingobium yanoikuyae, and Burkholderia paludis. Each isolate was investigated for its capacity to promote plant growth in nitrogen-free media. Wheat seedlings were inoculated with the isolates separately, together as a consortium, or in combination with the commercial biostimulant, Great Land Plus^®. Compared to no-treatment control plants, the fresh weights were higher in both the shoots (183.2 mg vs. 330.6 mg; p < 0.05) and roots (320.4 mg vs. 731.3 mg; p < 0.05) of wheat seedlings inoculated with P. megaterium. The fresh weights were also higher in the shoots (267.8 mg; p < 0.05) and roots (610.3 mg; p = 0.05) of wheat seedlings inoculated with S. yanoikuyae. In contrast, the fresh weight of the shoot and root systems of plants inoculated with B. paludis were significantly lower (p < 0.05) than that of the no-treatment control plants. Moreover, when Great Land Plus^® was supplemented with a consortium of P. megaterium and S. yanoikuyae, or a consortium of P. megaterium, S. yanoikuyae, and B. paludis no promotion of plant growth was observed. Full article

Tilapia Parvovirus (TiPV) is a rising pathogen responsible for high mortality in tilapia aquaculture. Understanding TiPV’s pathogenesis is crucial for developing effective management strategies. This study aimed to elucidate TiPV pathogenesis by evaluating its cytotoxic effects on Danio rerio gill (DRG) cell monolayers and its impact on host immune responses. PCR-confirmed TiPV-infected DRG cell monolayers were subjected to an MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay at 24, 48, 72, and 96 h post-infection to assess cell viability and cytotoxicity. The MTT assay revealed a progressive decline in DRG cell viability over time, with viable cell percentages decreasing from 66.71% at 24 h to 31.28% at 96 h in TiPV-infected cultures, compared to consistently high viability in controls. Simultaneously, quantitative real-time PCR (qPCR) was used to assess the expression of key immune-related genes, including Interleukins (IL-1β, IL-8), Toll-like receptor 7 (TLR7), Major Histocompatibility Complex II (MHC-II), Tumor Necrosis Factor α (TNF-α), Nuclear Factor Kappa B (NF-κB), and Chemokine Receptors (CRs).qPCR analysis showed an upregulation of IL-8, IL-1β, TNF-α, and CRs, indicating an early inflammatory response. However, significant downregulation of TLR7, MHC-II, and NF-κB suggests TiPV’s ability to modulate host immune responses. The results highlight that TiPV induces significant cytotoxicity in DRG cells, leading to severe cellular damage. The virus also alters host immune responses by modulating the expression of key immune genes, which may contribute to its virulence and persistence. These findings enhance our understanding of TiPV pathogenesis and highlight the need for targeted research to develop effective control strategies for TiPV in aquaculture systems. Full article

Microbial metallophores are low-molecular-weight chelating agents produced by microorganisms to acquire essential metal ions. Their biosynthesis, transport, and regulation involve complex processes, specialized enzymatic machinery, and intricate regulatory networks. This review examines the multifaceted roles of metallophores in microbial ecology and their potential applications in sustainable agriculture, emphasizing their key role in trace metal acquisition, nutrient cycling, and plant–microbe interactions. Furthermore, it explores the potential applications of metallophores in agriculture, bioremediation, and biotechnology, connecting their potential to the development of novel strategies for sustainable agriculture. Full article

Recurrent urinary tract infection (rUTI) is a significant public health problem in women. General measures to prevent recurrence include behavioral changes and increased fluid intake, cranberry ingest, use of methenamine hippurate, antibiotic prophylaxis, D-mannose, probiotics, or vaccines. We conducted a literature review of the latest updates on preventing rUTI in December 2024. The search concluded with 27 articles that fulfilled our inclusion criteria. Our review demonstrated that behavioral changes such as correct genital hygiene, avoiding postponing micturition or defecation, urinating after sexual intercourse, and ingesting 1.5–2 L of water could prevent rUTI. The ingestion of cranberries reduces the risk of symptomatic, culture-verified urinary tract infections in women with rUTIs. Methenamine hippurate is an alternative to antibiotics to avoid rUTI. Estrogen reduces rUTI in women with hypoestrogenism. Limited evidence supports using D-mannose, probiotics, and vaccines to prevent rUTI. In conclusion, after successful treatment of the acute episode, preventative measures are needed to reduce rUTI frequency and morbidity according to each patient’s characteristics and preferences. Full article

Invasive infection by Streptococcus agalactiae (GBS) is a significant cause of death in newborn babies. In Thailand, data on strain distribution in GBS, specific virulence genes, and susceptibility patterns are limited. Therefore, our study aimed to establish the sequence type (ST) distribution and to use a specific virulence gene in combination with a susceptibility profile for strain identification. Non-duplicate 277 isolates of GBS were tested for ST, virulence genes, and antimicrobial susceptibility profiles. Twenty-five STs were detected. The ST283 (29.24%) and ST1 (27.07%) were the most common STs. The absence of the bca gene was an excellent marker to rule out ST283. All isolates were susceptible to nearly all tested antibiotics; however, only ST283 revealed 100% susceptibility to tetracycline, while ST1 and other non-ST283 showed 21.33 and 4.96%, respectively. Therefore, combining the alpha-C protein (bca) positive and tetracycline susceptible revealed 100% sensitivity for ST283. However, to identify the ST283, this combination revealed 78.9% specificity, which increased to 80.2% when erythromycin or azithromycin-susceptible was added. The bca positive combined with tetracycline and erythromycin susceptibility results were a simple tool for predicting ST283. The bca negative profile with tetracycline and macrolides resistance was commonly non-ST283. The information gained by this tool would benefit patient management. Full article

The study of the metagenomes of bacterial communities in saline areas is relevant in connection with the global salinization of agricultural lands. The aim of this study was to investigate the biodiversity and structure of rhizobacterial communities associated with the halophyte S. marina from low and moderate sulfate–chloride salinity habitats. The bacterial community of bulk and rhizosphere soil was analyzed using high-throughput sequencing of the V1–V9 region of 16S rRNA by Oxford Nanopore Technologies. Alpha and beta diversity indices were calculated. A total of 55 phyla and 309 genera of bacteria were identified, among which Proteobacteria and Bacteroidetes dominated. The occurrence of Planctomycetes, Verrucomicrobia, and Acidobacteria in the rhizosphere was higher than in the bulk soil. Bacterial alpha diversity in the bulk soil decreased with increasing salinity, while it increased in the rhizosphere. The proportion of the halotolerant bacteria of Flavobacterium and Alteromonas genera significantly grew with increasing salinity both in the bulk and rhizosphere soil. In addition, in the rhizosphere, the percentage of Comamonas, Methylibium, Lysobacter, Planctomyces, Sphingomonas, Stenotrophomonas, and Lewinella genera increased. Among them, several genera included plant growth promoting rhizobacteria (PGPR). In the more saline bulk soil, the proportion of halotolerant genera Bacillus, Salinimicrobium, Marinobacter, Clostridium, Euzebya, KSA1, Marinobacter, Clostridium, Salinimicrobium, and Halorhodospira was also higher compared to the low saline site. Thus, increasing the salinity changed the taxonomic structure of the bacterial communities of both bulk soil and rhizosphere. Full article

Antimicrobial resistance is a growing global challenge, rendering many standard treatments ineffective. Essential oils (EOs) of cinnamon (Cinnamomum aromaticum Nees) and clove (Syzygium aromaticum (L.) Merr. et Perry) may offer an alternative solution due to their high antimicrobial properties and their abilities to fight resistant pathogens. This study evaluates the antimicrobial activity of these two EOs, and their synergistic potential when combined with two antibiotics (ciprofloxacin and vancomycin) and two antifungals (fluconazole and amphotericin B) against various bacterial and yeasts strains. The antimicrobial activities of each EO were evaluated by agar diffusion and broth microdilution assays, while the synergetic effects with antimicrobials were determined by calculating the fractional inhibitory concentration index (FICI) using the checkerboard method. The chemical composition of the EOs was analyzed using Gas Chromatography-Mass Spectrometry (GC-MS). The identification of individual components in the EOs was achieved by comparing their mass spectra with the NIST MS Search database and by correlating their retention times with those of known standards. GC-MS analysis revealed that the main constituents of S. aromaticum EO were eugenol (71.49%) and β-caryophyllene (23.43%), while C. aromaticum EO were dominated by cinnamaldehyde (47,04%) and cinnamyl acetate (18.93%). Antimicrobial activity showed that cinnamon EO exhibits highest effectiveness against all tested strains, with inhibition zones (IZ) ranging from 16.99 mm to 53.16 mm, and minimum inhibitory concentrations (MIC) and minimum microbicidal concentrations (MMC) ranging from 0.039 mg/mL to 0.156 mg/mL. However, for clove EO, the IZ ranged from 9.31 mm to 29.91 mm, with MIC and MMC values from 0.313 mg/mL to 1.25 mg/mL. In combination with antibiotics (ciprofloxacin and vancomycin), the studied EOs showed promising synergistic effects with reduction up to 128-fold. As regards antifungals (amphotericin B, and fluconazole), the synergistic effects were recorded with MIC gains up to 32-fold. Our findings demonstrate that the EOs from C. aromaticum and S. aromaticum exhibit significant broad-spectrum antimicrobial activity against diverse yeast and bacterial strains. This highlights their potential as bases for the development of novel plant-based antimicrobial agents. Importantly, the observed synergistic effects of these EOs with conventional antibiotics support their integration into medical treatments as a strategy to address microbial resistance. Future research should aim to elucidate the mechanisms underlying these synergistic actions, optimize their application, and enhance their therapeutic efficacy. Full article

In this study, biofilm formation and the production of key virulence factors were systematically evaluated across 33 strains of Pseudomonas aeruginosa isolated from diverse hospital environments in Tunisia. Among these, 13 strains demonstrated strong biofilm-forming capacities. Adding glucose (9%, w/v) to the culture medium generally enhanced biofilm development, indicating that glucose supplementation may promote biofilm formation in clinical isolates. The 13 selected biofilm-forming strains exhibited a consistent production of critical virulence factors, including pyocyanin, rhamnolipid, and LasA protease, known for its staphylolytic activity. However, profiles of extracellular polysaccharide (EPS) production and motility showed considerable heterogeneity among the strains, suggesting a strain-specific regulation of these traits. Based on a comprehensive analysis of biofilm formation and virulence expression, strain 2629 was chosen as a model organism due to its robust biofilm-producing ability and high virulence factor output. This strain was used in subsequent in vitro assays to evaluate the anti-biofilm potential of a commercial disinfectant containing peracetic acid and other active agents. Results indicated that a 3% (v/v) concentration of the disinfectant, applied for 5 min, was nearly sufficient to eradicate the biofilm formed by the model strain. These findings underscore the importance of selecting a representative biofilm-forming strain for accurate in vitro assessments of disinfectant activity. Full article

Root endophytic microbial communities play a key role in plant health and productivity, yet the extent to which these communities vary across different crop species remains underexplored. This study aimed to investigate the root endophytic bacterial diversity of two important crops—hybrid tomato (Lycopersicon esculentum Mill. var. TNAU CO3) and finger millet (Eleusine coracana L. var. TNAU CO13)—to understand how crop-specific microbiomes contribute to agricultural sustainability and productivity. Targeted 16S rDNA amplicon sequencing was performed on tomato and finger millet root samples. A total of 165,772 and 181,327 16S rRNA gene sequences were generated from tomato and finger millet roots, respectively. These sequences were processed to identify amplicon sequence variants (ASVs), which were then classified taxonomically to assess community composition and functional prediction. Across the two hybrid crops, 1400 ASVs were detected in tomato and 1838 in finger millet. Proteobacteria (52.61–62.09%) were the dominant phylum in both, followed by Actinobacteria, Firmicutes, Bacteroidota, unidentified bacteria, Myxococcota, Verrucomicrobiota, Acidobacteriota, Fusobacteriota, and Chloroflexi. Finger millet roots harbored a more diverse and robust microbial assemblage, particularly enriched with nitrogen-fixing and oxidative stress-mitigating bacteria. In contrast, tomato roots showed a higher abundance of phosphate-solubilizing and biofilm-forming taxa, potentially enhancing resilience to environmental stress. These findings highlight the crop-specific nature of endophytic bacterial communities and their diverse functional capabilities. By revealing distinct microbial profiles in tomato and finger millet, this work provides a valuable foundation for developing strategies to optimize soil health, crop performance, and abiotic stress tolerance. Full article

The aim of this study was to compare the human intestinal microbiota in different age groups, elucidating the precise stages of life in which the gut microbiota evolves its specific characteristics in terms of composition and diversity, as well as associating different bacterial groups for prediction of their intertwined metabolic role, considering their importance in human health. The quantitative composition, Bacteroidetes/Firmicutes (B/F) ratio, counts and diversity indices of faecal samples obtained from infant, child, adult and elderly individuals were assessed via quantitative real-time polymerase chain reaction (qPCR). The intestinal microbiota of infants expressed the highest B/F ratio and diversity. The total bacteria counts, Bacteroides-Prevotella and Blautia coccoides-Eubacterium rectale groups were the most abundant in adults and infants, while child and elderly individuals presented the highest counts of Firmicutes and Lactobacillus sp. In infants, the counts of Enterococcus sp., Streptococcus sp., Enterobacteriaceae, Veillonella sp. and Clostridium perfringens groups were higher, when compared to the other age groups. The tightest positive correlations between bacteria within age groups were found for the B. coccoides-E. rectale, C. leptum (incl. Faecalibacterium prausnitzii), Bacteroidetes-Prevotella and Atopobium groups. Through the stages of life, the quantitative composition and diversity of intestinal microbiota evolves with two changing maximal peaks of predominant groups, with bacterial diversity decreasing from infant to child stage, showing unitary stabilization in adults and presenting a wide individual range in the elderly. The high counts of Bacteroidetes and Clostridium from the phylum Firmicutes, present throughout all life stages, mainly influence the composition and metabolic activity of other bacteria. Recognizing age-specific differences may provide a basis for comparing different geographic populations and predicting the intertwined metabolites of various bacteria, which have certain implications for health. Full article

Extraintestinal pathogenic Escherichia coli (ExPEC) is a group of Escherichia coli strains that can cause severe infectious diseases outside the gastrointestinal tract, such as urinary tract infections, meningitis, septicemia, etc. We report a case of a calf herd infection by ExPEC with high rates of morbidity and mortality. The research purpose of this study was to thoroughly investigate the characteristics of the ExPEC responsible for the calf herd infection. Specifically, we aimed to understand the mechanisms underlying its multidrug resistance and high pathogenicity. Clinical samples were collected for the isolation and identification of ExPECs, cultured on MacConkey agar, and further tested by PCR for the uidA gene, 16S rRNA gene sequencing, and adhesion patterns on HEp-2 cells. The antimicrobial activity was determined using the disk diffusion method according to Clinical & Laboratory Standards Institute (CLSI) guidelines. The pathogenicity was assessed through the experimental infection of Kunming mice, tracking their survival and weight changes, and performing autopsies for bacterial counts and histopathological analysis. Additionally, whole-genome sequencing (WGS) and a comprehensive analysis were performed, including multilocus sequence typing (MLST), serotyping, drug-resistance gene analysis, virulence factor analysis, metabolic pathway analysis, and enrichment analysis, using various online tools and databases. An ExPEC strain named RZ-13 was responsible for this case and was identified as ST345 and O134: H21. Among the 14 antibiotics tested, 13 showed resistance, indicating that the RZ-13 strain is a multidrug-resistant (MDR) bacterium. The experimental infection of Kunming mice proved the greater pathogenicity of RZ-13 than that of CICC 24186. The comprehensive WGS revealed the presence of 28 antibiotic resistance genes and 86 virulence-related genes in the genome of the strain, corroborating its clinical manifestations of MDR and high pathogenicity. Our study isolated a MDR ExPEC strain, RZ-13, with a strong pathogenicity. This is the first case report of ExPEC leading to severe mortality in calf herds in China, underscoring the need for the rational use of antibiotics to reduce the risk of the generation and transmission of MDR bacteria from food-producing animals to ensure food safety and public health. Full article

Toxocariasis is a parasitic zoonosis caused by ascarid nematodes of dogs (Toxocara canis) or cats (Toxocara cati). Transmission to humans can occur in various ways, most commonly through the ingestion of infective embryonated eggs in soil or on vegetables or fruits and less frequently through ingestion of raw or undercooked meat contaminated with larvae. The disease manifestations span a broad clinical spectrum, ranging from asymptomatic seropositivity to severe systemic complications including sepsis and septic shock, with the presentation varying according to the affected organ systems. Cardiac involvement is a rare but potentially life-threatening complication and consists of myocarditis, pericarditis or Loeffler’s endocarditis (eosinophilic myocarditis). We present a case of eosinophilic myocarditis associated with Toxocara canis infection in a 54-year-old woman living in a rural area near the forest and provide a brief review of the literature. Full article

Cassida vittata Vill. is a major pest of sugar beet crops worldwide. This study evaluated the efficacy of Streptomyces sp. strains E23-2, E23-9, E23-3, and E25-12 in managing this pest under both laboratory bioassays (26 ± 2 °C, 60 ± 10% RH, and 12 h of photoperiod) and field conditions. In the laboratory bioassays, insecticidal and repellent activities were assessed using topical and leaf dip methods. The insecticidal activity test involved five concentrations of bacterial suspensions (10² to 10¹⁰ cfu. mL⁻¹ (Colony-Forming Units per milliliter)) against pest larvae and adults. Only E23-2 and E23-9 strains at concentrations of 10¹⁰ and 10⁸ cfu. mL⁻¹, exhibiting the highest insecticidal activity, were used for the field bioassay. Carbosulfan at 0.25 g/L served as a positive control. Results indicated E23-2’s high efficacy against C. vittata, with the lowest LC₅₀ values: 323.5 (larvae) and 5.1 × 10³ (adults) cfu. mL⁻¹ in topical contact, and 1.9 × 10³ (larvae) and 3.1 × 10⁴ (adults) cfu. mL⁻¹ in the leaf dip method. LT₅₀ values of 3 days for larvae and adults in the topical contact method supported E23-2’s efficacy. E23-2, at 10¹⁰ cfu. mL⁻¹, displayed notable repellency against C. vittata adults (RI = 84.9% at 48 h). In field trials, Henderson–Tilton adjusted rates revealed E23-2’s substantial reductions of 88.6% (larvae) and 85.9% (adults), aligning closely with Carbosulfan’s efficacy. Enzymatic analysis underscored the versatile biocontrol attributes of E23-2, E23-3, and E23-9, providing insights for targeted pest management strategies. Field conditions, notably temperature, can influence the establishment and efficacy of EP bacteria. Further field studies are imperative for a comprehensive understanding of these influencing factors. Full article

This study aimed to isolate AHL-degrading bacteria from the intestine of Penaeus vannamei and evaluate their ability to control pathogenic Vibrio harveyi in P. vannamei larvae. Twenty-seven isolates were obtained from the digestive tract of healthy Pacific white shrimp juveniles (P. vannamei) after six cycles of pasteurization at 70 °C, but only three isolates (E₁LP₂, E₂LP₁, and E₂LP₂) could degrade AHL. The 16S sequence results gave a high identity (>95%) with Bacillus sp. The isolates exhibited quorum-quenching abilities by degrading AHLs, thereby disrupting Vibrio quorum sensing and virulence. In Zoea and Mysis, the challenged larvae plus the administration of E₁LP₂ resulted in the lowest survival compared to the other groups. Isolates degrading N-acyl homoserine lactone improved the survival of shrimp Zoea and Mysis larvae when challenged with pathogenic V. harveyi. This is the first report on the use of quorum-sensing disrupter bacteria in P. vannamei larval shrimp culture. Our findings suggest that these Bacillus spp. strains have potential as biocontrol agents for sustainable shrimp aquaculture, reducing the reliance on antibiotics while mitigating vibriosis outbreaks. Full article

It is known that plant-associated microorganisms must be considered as key drivers for plant health, productivity, community composition, and ecosystem functioning. Much attention has been paid to the exploration of the plant-associated microbiome in search of new microorganisms with antagonistic activity against various phytopathogens. P. viticola represents one of the main fungal agents of grape yield losses during the pre-harvest stage. To date, the use of chemical pesticides is the main method to control downy mildew infection in vineyards. In recent years, innovative and more environmentally suitable control strategies, such as Biological Control Agents (BCAs), have been greatly improved. In this study, 16 new bacterial strains, isolated from the leaves of three table grape cultivars, were tested for their in vivo effectiveness against downy mildew of grape, resulting in one B. velenzensis (‘BLG_B4), one P. pleuroti (‘BLG_B5), one P. psychrotolerans (‘BLG_B1.3’) and one B. subtilis (‘BLG_B1.1.1’) bacterial strains that were marked as good BCAs. As possible mechanisms of action, a genetic analysis was performed to evaluate the ability of selected bacterial strains to reduce the expression of two P. viticola effectors. Finally, their effectiveness against a wide range of fungal pathogens and their safety for human health was also evaluated. Full article

The early growth phase is a critical period for the development of the chicken gut microbiome. In this study, the spatiotemporal diversity of the gastrointestinal microbiota, shifts in taxonomic composition, and relative abundances of the main bacterial taxa were characterized in Kadaknath, a high-value indigenous Indian chicken breed, using sequencing of the V3–V4 region 16S rRNA gene. To assess microbiome composition and bacterial abundance shifts, three chickens per growth phase (3, 28, and 35 days) were sampled, with microbiota analyzed from three gut regions (crop, small intestine, and ceca) per bird. The results revealed Firmicutes as the most abundant phylum and Lactobacillus as the dominant genus across all stages. Lactobacillus was particularly abundant in the crop at early stages (3 and 28 days), while the ceca exhibited a transition towards the dominance of genus Phocaeicola by day 35. Microbial richness and evenness increased with age, reflecting microbiome maturation, and the analyses of the microbial community composition revealed distinct spatiotemporal differences, with the ceca on day 35 showing the highest differentiation. Pathogen analysis highlighted a peak in poultry-associated taxa Campylobacter, Staphylococcus, and Clostridium paraputrificum in 3-day-old Kadaknath, particularly in the small intestine, underscoring the vulnerability of early growth stages. These findings provide critical insights into age-specific microbiome development and early life-stage susceptibility to pathogens, emphasizing the need for targeted interventions to optimize poultry health management and growth performance. Full article

In this study, the acid resistance and desiccation tolerance of 20 strains of Cronobacter malonaticus were explored, and their genetic variances with respect to their survival in stressful conditions were identified by genomic analysis. The strains showed significant variances in acid tolerance when exposed to simulated gastric acid (pH 3.5) for 2 h. Strain 685 demonstrated less viability, suggesting greater susceptibility. Desiccation in infant formula also yielded sub-lethally injured cells, with variable strain recovery, highlighting strain 685 as the strain with the lowest recovery. Strains were determined to contain single nucleotide polymorphisms (SNPs) in the ompR and rpoS genes, suggesting loss-of-function mutations and potentially elucidating the stress sensitivity mechanism of strain 685. This study underscores the importance of genetic factors in C. malonaticus resilience and the necessity for developed detection methods for assessing food safety risk, especially in relation to powdered infant formulas. Our results provide important information on the pathogenic potential of C. malonaticus and help guide future research priorities to mitigate risks associated with foodborne pathogens. Full article