Erzsébet Baka

The gut microbiota plays a central role in poultry health and production performance, yet its response to intensive fattening protocols and postbiotic supplementation in geese remains poorly characterized. This study used 16S rRNA gene amplicon sequencing to profile ileal and caecal microbial communities from geese raised under two fattening protocols, with or without postbiotic supplementation, and assessed the effect of 24 h post-mortem chilling on apparent community composition. Fattening protocol was associated with the largest differences in gut microbial structure, producing significant shifts in beta diversity in both the ileum and the caecum (although protocol, age at slaughter, and duration of postbiotic exposure co-varied between cohorts and cannot be fully disentangled), accompanied by extensive taxon-level differences identified by LEfSe. Postbiotic supplementation did not significantly alter overall community structure under force-feeding conditions but produced a taxon-specific, trend-level shift in the caecum under restricted feeding, suggesting that its effect depends on the continuity of supplementation relative to slaughter. Alpha diversity did not differ significantly in the ileum, but caecal richness differed significantly between the G2 and G5 postbiotic-supplemented groups (Conover–Iman test, adjusted p < 0.05). The warm- and chilled-dissection groups differed in ileal but not caecal community composition (individual-animal variation cannot be separated from the effect of chilling in this comparison, as the two groups consisted of different birds), indicating that dissection timing is an important methodological variable in goose microbiome research. These findings highlight cohort- and protocol-related differences as key correlates of gut microbial composition in geese and provide a framework for optimizing postbiotic supplementation strategies and sampling standardization in waterfowl production.

Rhodococcus erythropolis NI86/21, isolated from maize rhizosphere in Hungary, possesses one of the largest genomes (8.046 Mb) within the species. The genome comprises a 6.83 Mb chromosome and 1.22 Mb of extrachromosomal elements, including three circular and two fragmented linear plasmids. Comparative analysis identified five horizontally acquired genomic islands (HGTi), totaling 0.64 Mb with mosaic-like architecture derived from plasmids, phages, and chromosomal segments of other Nocardiaceae . Liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomic analysis revealed a lower expression of genes located in HGT elements (53%) compared to core chromosomal genes (73%), indicating regulatory silencing of foreign DNA. Nevertheless, an inducible cytochrome P450 monooxygenase (CYP116) responsible for thiocarbamate and atrazine degradation is encoded on HGTi_V and actively expressed upon herbicide exposure. Strikingly, an identical CYP450 locus is present on a conjugative plasmid in Rhodococcus sp. TE1 isolated from thiocarbamate-treated soil in Canada, demonstrating independent acquisition of the same catabolic module from a high GC% content Rhodococcus , under similar selective pressure. Frequent recombination between chromosomal and mobile elements generates the observed mosaic-like HGT structures, which we found common for R. erythropolis strains. These results highlight extraordinary genomic plasticity and rapid adaptive evolution in Rhodococci , enabling efficient colonization of herbicide-contaminated agro-ecosystems. IMPORTANCE: Rhodococcus erythropolis NI86/21 exemplifies how bacterial genomes evolve through horizontal gene transfer and mobile elements. Its unusually large, plastic genome contains extensive HGT islands and a high load of active transposons, which shape mosaic genomic architectures and hinder complete genome assembly. These horizontally acquired regions, although partially silenced, encode key adaptive functions such as an inducible CYP116 monooxygenase enabling thiocarbamate and atrazine degradation. Remarkably, an identical CYP116 module is present in Rhodococcus sp. TE1 from thiocarbamate-treated Canadian soil, demonstrating that similar environmental pressures can drive independent acquisition of the same biodegradation trait. Together, the dynamic transposon activity, mosaic HGT structure, and geographically convergent gene recruitment highlight the extraordinary genomic plasticity of R. erythropolis and underscore its rapid adaptive potential in agro-ecosystems, with implications for microbial evolution and bioremediation strategies.

A novel carbon monoxide (CO)-oxidizing bacterial strain designated as SB112 ^T was enriched and isolated from Ilex aquifolium leaves from Tocil Wood Nature Reserve in Coventry, UK. The strain was Gram reaction-negative, aerobic, rod-shaped, motile with a polar flagellum and non-spore-forming. Growth of strain SB112 ^T was observed at 10–45 °C, pH 6.0–12.0 and NaCl concentrations of 1–3%. The genomic DNA G+C content was 58.3 mol%, and the major fatty acids (>10%) of strain SB112 ^T were C _18 : 1 ω7c, C _18 : 1 ω7c 11-methyl and C _19 : 0 cyclo ω7c. Major polar lipids were phosphatidylcholine, diphosphatidylglycerol, phosphatidylglycerol and a phospholipid. Strain SB112ᵀ contains ubiquinone-10 as the major respiratory quinone. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SB112 ^T formed a separate lineage within the family Phyllobacteriaceae , showing sequence identities of 97.7%, 97.6% and 97.5%, with its closest relatives Aminobacter niigataensis , Aminobacter aminovorans and Mesorhizobium plurifarium , respectively. Phylogenomic analyses using whole-genome sequences consistently placed this strain within the family Phyllobacteriaceae . However, its phylogenetic position did not correspond to any known genus within this family. The genome of strain SB112 ^T was found to possess the form II coxL gene, which encodes the large subunit of the CO dehydrogenase and potentially enables CO oxidation. The average nucleotide identity and digital DNA–DNA hybridization with members of closely related genera yielded values below the thresholds for prokaryotic species delineation (95–96 and 70%, respectively). Based on the phenotypic, chemotaxonomic, phylogenetic, genomic and physiological properties, strain SB112 ^T is considered to represent a novel species of a new genus Foliimonas within the family Phyllobacteriaceae for which the name Foliimonas ilicis gen. nov., sp. nov. is proposed. The type of strain is SB112 ^T (=LMG 33802 ^T , =NCAIM B.02691 ^T ).

Thermobifida alba DSM43795 ^T , a mesophilic actinobacterium isolated from garden soil, plays a vital role in lignocellulose degradation and holds biotechnological and pharmaceutical potential. We present a high-quality, complete de novo genome assembly of T. alba DSM43795 ^T using combined PacBio long-read and Illumina short-read sequencing, resulting in a single circular chromosome of 4.9 Mbp with 72.1% GC content. Comparative genomics with the thermophilic relative T. fusca YX revealed 83.39% average nucleotide identity and extensive genome synteny alongside niche-specific differences. Functional annotation identified 4345 genes, including a rich complement of carbohydrate-active enzymes (CAZymes) such as glycoside hydrolases (GHs), esterases, and polysaccharide lyases, supporting versatile plant biomass degradation. GH gene sets were largely conserved between the species in both gene number and distribution, but T. alba uniquely encodes a novel GH10 endo-xylanase near a characterised palindrome regulatory sequence, indicating species-specific regulation. We hypothesise that thermophilic adaptation in T. fusca requires more proteins for ribosome integrity and amino acid metabolism, with reduced emphasis on carbohydrate metabolism and defence compared to T. alba . Moreover, T. alba harbours a broader array of defence-related genes and mobile genetic elements, including integrases and transposases. Although lacking a complete CRISPR-Cas system, two CRISPR arrays were detected, suggesting alternative immune strategies. Virulence factor homologs shared by both species likely reflect environmental survival rather than pathogenicity. This genomic characterisation elucidates T. alba ’s metabolic versatility and ecological adaptations, laying the groundwork for its potential applications in biomass conversion, environmental biotechnology, and drug discovery.

Most of the agricultural products can potentially be exposed to mycotoxins—especially to ochratoxin A (OTA)—, which may cause foodborne diseases such as renal toxicity and notable economic losses worldwide. Biological detoxification is the most promising method to control OTA contamination. To provide a comprehensive understanding, this review summarizes the biodegradation pathways of OTA and discusses microbes capable of degrading OTA and their detoxification strategies. A detailed analysis of potentially useful enzymes for food and feed detoxification will be reported, highlighting specific enzymatic strategies identified in scientific literature. A comparative analysis of the functional capabilities of different OTA hydrolases demonstrates significant variation in degradation efficiency, thus the optimization of these enzymes is essential for the development of effective detoxification strategies. This review underscores the potential of harnessing these microorganisms and their enzymes for mitigating the toxic effects of OTA in contaminated environment and examining the essential requirements that must be met for the successful application of OTA degrading enzyme technology for promoting public health and food safety.

Aflatoxin B1 (AFB1) is a potent mycotoxin and natural carcinogen. The primary producers of AFB1 are Aspergillus flavus and A. parasiticus. Sterigmatocystin (STC), another mycotoxin, shares its biosynthetic pathway with aflatoxins. While there are abundant data on the biological effects of AFB1, STC is not well characterised. According to published data, AFB1 is more harmful to biological systems than STC. It has been suggested that STC is about one-tenth as potent a mutagen as AFB1 as measured by the Ames test. In this research, the biological effects of S9 rat liver homogenate-activated and non-activated STC and AFB1 were compared using two different biomonitoring systems, SOS-Chromotest and a recently developed microinjection zebrafish embryo method. When comparing the treatments, activated STC caused the highest mortality and number of DNA strand breaks across all injected volumes. Based on the E. coli SOS-Chromotest, the two toxins exerted the same genotoxicities. Moreover, according to the newly developed zebrafish microinjection method, STC appeared more toxic than AFB1. The scarce information correlating AFB1 and STC toxicity suggests that AFB1 is a more potent genotoxin than STC. Our findings contradict this assumption and illustrate the need for more complex biomonitoring systems for mycotoxin risk assessment.