SEARCH · Search PubMed

Results for “CAZymes”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 recordsLinked to original sources

PubMed2026

Isoquinoline alkaloids enhance growth performance through multifaceted modulation of the bacterial-fungal microbiome, CAZyme profiles, gut health, and neuroendocrine function in broilers.

The bacterial-fungal microbiome and its carbohydrate-active enzyme (CAZyme) capacity play critical roles in regulating gut health and growth performance in broiler chickens. This study evaluated the effects of dietary isoquinoline alkaloids (IQ) on growth performance, gut microbiome composition, CAZyme profiles, and the microbiome-gut-neuroendocrine axis in broilers. A total of 400 Ross 308 (1-day-old) chicks were randomly assigned to either a Basal diet (CON) or IQ supplemented diet (IQ). Dietary IQ supplementation significantly increased final body weight and cumulative body weight gain (P < 0.0001) and improved feed conversion ratio (P < 0.05). Intestinal permeability was reduced (lower FITC-dextran; P < 0.05), accompanied by increased serotonin and serotonin-to-corticosterone ratio and decreased corticosterone (P < 0.05). Expression of inflammatory genes (TNF-α, NF-κB, IL-4, and TLR-1) was downregulated (P < 0.05). Microbiome analysis showed increased α-diversity (P < 0.05) and clear β-diversity separation (PERMANOVA, P < 0.001), with enrichment of beneficial bacteria (Akkermansia muciniphila, Lactobacillus salivarius, Turicibacter sanguinis, Bacillus subtilis) and suppression of fungal taxa (Aspergillus, Penicillium). CAZyme-related pathways involved in lignin and carbohydrate degradation were increased (P < 0.05). Microbial diversity was negatively correlated with inflammation and gut permeability, whereas network analysis identified 164 significant associations (|ρ| ≥ 0.50), revealing strong negative correlations between beneficial bacteria and inflammatory markers (ρ = -0.65 to -0.78) and positive associations for fungal taxa (ρ = 0.62-0.81). Serotonin was positively associated with microbial diversity (ρ = 0.63-0.70). In conclusion, IQ supplementation promotes a bacteria-dominant and metabolically active microbiome, reduces inflammation and intestinal permeability, and improves neuroendocrine balance, collectively enhancing gut health and growth performance in broiler chickens.

Bacteriome↗

PubMed2006

Poplar carbohydrate-active enzymes. Gene identification and expression analyses.

Over 1,600 genes encoding carbohydrate-active enzymes (CAZymes) in the Populus trichocarpa (Torr. & Gray) genome were identified based on sequence homology, annotated, and grouped into families of glycosyltransferases, glycoside hydrolases, carbohydrate esterases, polysaccharide lyases, and expansins. Poplar (Populus spp.) had approximately 1.6 times more CAZyme genes than Arabidopsis (Arabidopsis thaliana). Whereas most families were proportionally increased, xylan and pectin-related families were underrepresented and the GT1 family of secondary metabolite-glycosylating enzymes was overrepresented in poplar. CAZyme gene expression in poplar was analyzed using a collection of 100,000 expressed sequence tags from 17 different tissues and compared to microarray data for poplar and Arabidopsis. Expression of genes involved in pectin and hemicellulose metabolism was detected in all tissues, indicating a constant maintenance of transcripts encoding enzymes remodeling the cell wall matrix. The most abundant transcripts encoded sucrose synthases that were specifically expressed in wood-forming tissues along with cellulose synthase and homologs of KORRIGAN and ELP1. Woody tissues were the richest source of various other CAZyme transcripts, demonstrating the importance of this group of enzymes for xylogenesis. In contrast, there was little expression of genes related to starch metabolism during wood formation, consistent with the preferential flux of carbon to cell wall biosynthesis. Seasonally dormant meristems of poplar showed a high prevalence of transcripts related to starch metabolism and surprisingly retained transcripts of some cell wall synthesis enzymes. The data showed profound changes in CAZyme transcriptomes in different poplar tissues and pointed to some key differences in CAZyme genes and their regulation between herbaceous and woody plants.

Arabidopsis↗

PubMed2026

Host-driven evolution shapes the polysaccharide utilization profiles of alga-associated Flavobacteriaceae.

BACKGROUND: Marine algae represent major producers of complex polysaccharides and serve as hosts for diverse microbial communities in the phycosphere. Flavobacteriaceae are among the key bacterial taxa involved in polysaccharide degradation and carbon remineralization in this environment. However, the extent to which algal hosts drive the divergence of polysaccharide utilization profiles in these bacteria remains unclear. RESULTS: We conducted a genome-resolved analysis of 103 cultured Flavobacteriaceae strains isolated from red, green, and brown macroalgae, as well as from diatoms and dinoflagellates. We found that macroalga-associated strains generally harbored more abundant and diverse CAZyme-encoding genes than their microalga-associated counterparts. Moreover, strains associated with different algal phyla showed distinct metabolic specializations that aligned with the typical polysaccharides of their respective hosts, strongly supporting host-specific adaptation. In four widely distributed genera (Maribacter, Flagellimonas, Polaribacter, Winogradskyella), CAZyme profile dissimilarity and key glycoside hydrolase gene divergence exhibited phylogenetic congruence with algal host phylogeny (Mantel r up to 0.76 and 0.85, respectively), indicative of host-associated functional adaptation. Using Maribacter as a model, cultivation experiments and transcriptome characterization demonstrated that polysaccharide utilization efficiency is not solely linked to the organization of genes into polysaccharide utilization loci (PULs), but also associated with the expression dynamics of key transcription factors (TFs), particularly those from AraC and DeoR families, whose expression patterns were coordinated with laminarin degradation. Notably, these two TF families also exhibited host-associated divergence patterns similar to those of CAZyme-encoding genes. Furthermore, analysis of the Tara Oceans metagenomic data indicated that, within the AraC and DeoR families, a higher proportion of genes were positively correlated with chlorophyll a content compared to other TF families, reinforcing their specialized roles in alga-associated bacterial lifestyles. CONCLUSIONS: Our integrative genomic and transcriptomic analyses reveal evolutionary and regulatory adaptation of marine Flavobacteriaceae to distinct algal hosts. These findings highlight algae-derived habitats as specialized niches that shape microbial metabolic potential, and suggest that carbohydrate metabolism plays a key role in host-driven bacterial evolution across global oceans. Video Abstract.

Flavobacteriaceae↗

PubMed2026

Unlocking the molecular engineering of Geobacillus glycoside hydrolases as a source of industrial biocatalysts.

This review examines Geobacillus sensu stricto as a source of thermostable glycoside hydrolases (GH) for biomass conversion, food processing, and enzyme engineering. Recent peer-reviewed literature was assessed with emphasis on taxonomy, genome-based Carbohydrate-Active Enzymes (CAZyme) prediction, biochemical validation, structural data, and engineering case studies. Taxonomic boundaries were interpreted using current Anoxybacillaceae frameworks, with Parageobacillus treated as a related comparator rather than as Geobacillus. The strongest evidence supports GH13 alpha-amylases, xylan-active systems, beta-xylosidases, and selected accessory enzymes. Recent studies also show that genome mining must be coupled with enzymatic assays and product profiling because CAZyme annotation alone does not prove industrial function. Molecular engineering has improved relevant traits, including the longer thermal half-life of engineered G. stearothermophilus alpha-amylase variants, the increased catalytic efficiency of oligo-alpha-1,6-glucosidase variants, and improved AmyS expression in Bacillus subtilis. Geobacillus glycoside hydrolases are best interpreted as process-specific, engineerable biocatalytic templates. Their translation requires reliable taxonomy, functional validation, structural interpretation, scalable expression and testing on realistic substrates. This synthesis also recognises current limitations: many predicted CAZymes still lack biochemical validation, complete cellulolytic systems remain less mature than xylan- and starch-active systems, and scale-up data remain scarce.

Geobacillus↗

PubMed2026

Integrated functional genomics and safety assessment of plant-growth-promoting Caryophanales from post-maize-cultivation soils.

This study aimed to evaluate six environmental bacterial strains isolated from post-maize cultivation soils as candidates for agricultural biopreparation development, using an integrated functional genomic and safety assessment framework. Building on experimental validation of plant-growth-promoting activities, the analysis included: plant-growth-promoting traits (PGPT-Pred) using PLABase; carbohydrate-active enzymes (CAZymes) relevant for lignocellulosic crop residue degradation (dbCAN3); secondary metabolite profiles (antiSMASH); and screening for virulence factors and antibiotic resistance genes (ABRicate, BTyper3).All analyzed strains possess 1,449-1,617 predicted PGPT-encoding genes (24.1-35.9% of total genes), which are strongly shaped by taxonomic relatedness, as confirmed by congruence testing against ANI-based genomic divergence. Paenibacillus amylolyticus 5mez and Priestia megaterium 7psych showed distinct functional profiles compared to Bacillus spp., while Bacillus subtilis sensu lato strains were most similar to each other. Genomic predictions suggest involvement in nutrient acquisition (N, P, K, Fe) and stress mitigation. Secondary metabolite analysis revealed high biosynthetic potential, with non-Bacillus species harbouring a large proportion of unknown gene clusters, indicating underexplored metabolite diversity. CAZyme profiling identified P. amylolyticus 5mez as the most enzyme-rich strain, while B. cereus s.s. zielonkawy showed ligninolytic potential despite low overall CAZyme abundance. The safety assessment identified B. cereus s.s. zielonkawy as toxigenic and unsuitable for use. Of the remaining strains, P. amylolyticus 5mez and Pr. megaterium 7psych demonstrated the most favourable safety profiles, exhibiting no detectable virulence factors or antibiotic resistance genes, justifying their priority use in agricultural biopreparations, pending phenotypic validation. Given the high-dimensional, low-sample-size nature of multi-trait datasets in applied microbial genomics, tailored statistical approaches, including noise-reduction-validated PCA and distance-based congruence testing, were applied; their rationale and limitations are discussed.

Soil Microbiology↗

PubMed2025

Biosynthetic potential of the culturable foliar fungi associated with field-grown lettuce.

Fungal endophytes and epiphytes associated with plant leaves can play important ecological roles through the production of specialized metabolites encoded by biosynthetic gene clusters (BGCs). However, their functional capacity, especially in crops like lettuce (Lactuca sativa L.), remains poorly understood. We sequenced the genomes of nine fungal isolates, representing Fusarium sp., Fulvia sp., Alternaria alternata, and Alternaria postmessia, from leaves of lettuce grown under field conditions in Arizona, USA. We used antibiotics and secondary metabolite analysis shell (antiSMASH) and the database for automated carbohydrate-active enzyme annotation (dbCAN3), to predict BGCs and carbohydrate-active enzymes (CAZymes) for each strain, and then compared them to conspecific strains from other environments and substrates. Foliar lettuce-associated fungi featured 39-95 BGCs per genome, with substantial overlap between isolates occurring in association with lettuce leaves vs. from other substrates. Species identity was a significant determinant of BGC count, while host type, isolation source, and lifestyle were not. Several BGCs, including those for alternariol and 1,3,6,8-Tetrahydroxynaphthalene (T4HN), showed 100% similarity to characterized minimum information about a biosynthetic gene cluster (MIBiG) clusters based on antiSMASH predictions. Although analysis by biosynthetic gene similarity clustering and prospecting engine (BiG-SCAPE) identified gene cluster families (GCFs) across the dataset, these reference-matching clusters were not always grouped, reflecting methodological differences in how the tools assess similarity. Comparative CAZyme analysis in a focal species (Fulvia sp.) revealed higher gene counts in a foliar lettuce-derived isolate than in tomato (Solanum lycopersicum)-associated strains, challenging assumptions about host chemical complexity. These results highlight the importance of phylogenetic context in shaping fungal functional potential and suggest that selection on microbial traits in edible leafy crops may be more subtle and species-specific than previously assumed. KEY POINTS: • Lettuce-associated fungi feature diverse biosynthetic potential • Phylogeny predicts fungal BGC content more strongly than ecological lifestyle • Findings support genome-informed microbiome strategies for leafy crops.

Lactuca↗

PubMed2026

Multi-omics analysis reveals Protein Kinase A-associated regulatory remodeling during adaptation of Trichoderma reesei to lignocellulosic substrate.

The filamentous fungus Trichoderma reesei is a major industrial source of holocellulolytic enzymes, and its response to complex carbon sources is regulated by nutrient-sensing mechanisms, including the cyclic adenosine monophosphate (cAMP)-protein kinase A (PKA) signaling pathway. Here, we integrated transcriptomics, quantitative proteomics, and phosphoproteomics to analyze PKAc1-associated responses in the parental strain QM9414 and a Δpkac1 strain cultivated under glucose or sugarcane bagasse conditions. Deletion of pkac1 was associated with altered growth-related phenotypes and reduced extracellular activities of selected biomass-depolymerizing enzymes. Multi-omics profiling revealed condition-dependent changes affecting subsets of carbohydrate-active enzymes (CAZymes) genes and proteins, nutrient transporters, stress-associated proteins, and regulatory factors. Phosphoproteomics identified phosphorylation-state changes associated with pkac1 deletion, including reduced phosphorylation at sites enriched for the PKA consensus motif. In silico peptide docking was used to prioritize candidate PKAc1-associated substrates for future validation, including a Sec 7-derived peptide with favorable docking behavior relative to the control peptide. Together, these data support a working model in which PKAc1 contributes to regulatory and phosphorylation-state remodeling during adaptation to sugarcane bagasse, with effects on the magnitude and/or timing of selected CAZyme-related outputs in T. reesei.

Trichoderma↗

PubMed2026

Whole-genome sequencing and analysis of the endophytic fungus Alternaria alternata Y-2 from Leymus chinensis.

To explore the genetic basis and functional potential of beneficial symbiosis between the endophytic fungus Alternaria alternata Y-2 and its host Leymus chinensis, we performed Illumina-based draft whole-genome sequencing and systematic bioinformatic analysis. Although this assembly does not reach telomere-to-telomere completeness, it provides high-quality gene-level information for gene prediction, functional annotation, carbohydrate-active enzyme (CAZyme) identification, and secondary metabolite biosynthetic gene cluster analysis. The final genome size of A. alternata Y-2 was 34,383,676 bp with a GC content of 51.0%, containing 12,724 predicted protein-coding genes, 90 tRNAs, and 12 rRNAs. BUSCO assessment showed 98.9% completeness, supporting the high quality of this draft genome. A total of 12,627 genes were successfully annotated in the NCBI NR database, and 17,183 genes were functionally categorized using GO terms. In total, 448 CAZyme genes and 21 secondary metabolite biosynthetic gene clusters were identified, which are potentially involved in lignocellulose degradation, cellular redox homeostasis and biosynthesis of bioactive metabolites. Based on ITS sequence alignment, NR annotation, and phylogenetic analysis of single-copy orthologous genes, the strain was confidently identified as A. alternata. This study firstly reports the draft genome of an endophytic A. alternata strain derived from L. chinensis and provides valuable genetic resources for exploring the endophytic lifestyle, stress tolerance, and bioactive metabolite potential of this fungus.

Alternaria↗

PubMed2024

Characterizing the gut microbiome of diarrheal mink under farmed conditions: A metagenomic analysis.

This study aimed to comprehensively characterize the gut microbiota in diarrheal mink. We conducted Shotgun metagenomic sequencing on samples from five groups of diarrheal mink and five groups of healthy mink. The microbiota α-diversity and Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology did not show significant differences between the groups. However, significant differences were observed in microbiota β-diversity and the function of carbohydrate-active enzymes (CAZymes) between diarrheal and healthy mink. Specifically, The relative abundance of Firmicutes was lower, whereas that of Bacteroidetes was higher in diarrheal mink. Fusobacteria were enriched as invasive bacteria in the gut of diarrheal mink compared with healthy mink. In addition, Escherichia albertii was identified as a new bacterium in diarrheal mink. Regarding functions, nicotinate and nicotinamide metabolism and glycoside hydrolases 2 (GH2) family were the enhanced KEGG orthology and CAZymes in diarrheal mink. Furthermore, the diversity and number of antibiotic-resistant genes were significantly higher in the diarrheal mink group than in the healthy group. These findings enhance our understanding of the gut microbiota of adult mink and may lead to new approaches to the diagnosis and treatment of mink diarrhea.

Animals↗

PubMed2026

Genome analysis and antagonistic activity of Streptomyces sp. strain J36 against Phytophthora cactorum.

The Phytophthora blight of Panax notoginseng, caused by Phytophthora cactorum, is a devastating oomycete disease. Biocontrol strategies hold immense potential for inhibiting the spread of P. cactorum. We isolated 72 actinobacteria from soil and screened their antagonistic activity against P. cactorum. Both strain J36 and its cell-free filtrate exhibited strong antagonistic activity against P. cactorum and were therefore selected. Based on the 16S rRNA gene phylogenetic tree, strain J36 formed a well supported subclade with Streptomyces zaomyceticus NRRL B-2038 (bootstrap value 100%). However, because 16S rRNA sequences often lack sufficient resolution for species-level discrimination, we performed multilocus sequence analysis (MLSA) using three housekeeping genes (rpoB, recA, and atpD). The MLSA results consistently placed strain J36 within the same cluster as S. zaomyceticus NRRL B-2038, with a bootstrap support of 99%, indicating a close phylogenetic relationship. To further clarify the taxonomic status, we calculated the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain J36 and the type strain of S. zaomyceticus NBC-00415T. The ANI value was 90.91% and the dDDH value was 39.30%, both well below the accepted thresholds for species demarcation (ANI < 95%, dDDH < 70%). These genomic indices therefore strongly support that strain J36 represents a novel species within the genus Streptomyces. Through whole-genome sequencing and CAZymes analysis, a total of 98 carbohydrate-active enzymes (CAZymes) were detected, including 2 cellulase and 2 β-1,3-glucanases. The cell-free filtrate, which exhibited strong antagonistic activity against P. cactorum, also showed high activities of cellulase and β-1,3-glucanase, suggesting that these enzymes may be involved in its anti-oomycete activity. These findings suggest that J36 has potential as a biocontrol candidate, although further in vivo evaluation is needed to confirm its efficacy against Phytophthora blight of P. notoginseng.

Panax notoginseng↗

PubMed2026

Genome-Resolved Functional Profiling of Osteoporosis-Associated Gut Bacteria Highlights Putative Metabolic and Immunogenic Signatures of the Gut-Bone Axis.

The gut microbiota has emerged as a potential regulator of bone metabolism, but the genome-encoded functional repertoire of osteoporosis-associated gut bacteria remains insufficiently characterized. This study performed in silico functional profiling of gut bacterial taxa associated with osteoporosis, low bone mineral density, or comparator bone-related phenotypes. Twenty candidate taxa were selected from evidence in the human microbiome and represented by 26 curated bacterial reference genomes. Genome-wide annotations were used to map predicted gut-bone axis signatures, carbohydrate-active enzyme (CAZyme) repertoires, selected Kyoto Encyclopedia of Genes and Genomes pathways, and gutSMASH-predicted metabolic gene clusters. Functional burdens were normalized as hits per 1000 annotated proteins and integrated into metabolic, immunogenic, CAZyme, KEGG, and metabolic gene cluster profiles. Twelve predicted gut-bone axis signatures were identified, comprising 3337 primary candidate protein hits and a strict high-confidence subset of 2497 hits. Dominant signatures included vitamin B12/cobalamin metabolism, folate/one-carbon metabolism, peptidoglycan/cell-wall biosynthesis, and short-chain fatty acid-related functions. Dialister invisus, Dialister succinatiphilus, Megamonas funiformis, and Megamonas hypermegale showed the strongest normalized predicted gut-bone axis signal. These hypothesis-generating findings prioritize microbial metabolic and immunogenic features for future metagenomic, metabolomic, and experimental validation studies.

Osteoporosis↗

PubMed2026

Hybrid genome assembly of Penicillium oxalicum UV4 delineates cryptic secondary metabolite pathways and robust lignocellulolytic potential.

Penicillium oxalicum is a saprophytic fungus well-known for its hydrolytic potential; however, little is known about its metabolic flexibility and secondary metabolite biosynthesis, especially in isolates from underrepresented areas. In this study, we sequenced the genomic DNA of Penicillium oxalicum UV4 using Illumina and Oxford Nanopore platforms, generating a high-quality hybrid genome assembly of 30.28 Mb. The genome features 7,944 predicted genes (7,747 protein-coding sequences and 197 tRNAs) and demonstrates high completeness (99.0% BUSCO). Genomic analysis revealed 40 Biosynthetic Gene Clusters (BGCs), including distant orthologs of the Alternaria phytotoxin ACT-toxin II and the mycotoxin alternariol, as well as a putative clavaric acid-like biosynthetic cluster. Further investigation revealed an expanded CAZyme repertoire comprising 150 secreted proteins, featuring an AA16 lytic polysaccharide monooxygenase and putative multi-domain architectures, such as a pectin methylesterase-polygalacturonase fusion. This comprehensive genomic profiling highlights the dynamic metabolic capacity of P. oxalicum UV4, establishing it as a highly promising candidate for bio-refining studies and the discovery of cryptic bioactive metabolites.

Penicillium↗

PubMed2026

Hybrid genome assembly and phenotypic assays reveal carbohydrate metabolism diversity in Lacticaseibacillus strains.

Investigation of carbohydrate metabolism in lactic acid bacteria is essential for the rational selection of strains for fermentation processes, particularly in emerging applications involving non-conventional substrates or building of synthetic microbial consortia. However, establishing robust genotype-phenotype relationships remains challenging, as gene presence alone often fails to explain observed metabolic traits without considering the genomic context and regulatory architecture. In the present study, we combined hybrid genome assembly (Illumina and Oxford Nanopore) with high-throughput phenotype profiling (Biolog GENIII and PM2A) to investigate carbohydrate utilization in five Lacticaseibacillus strains. Phenotypic assays revealed clear intra- and inter-specific variability in substrate utilization. We therefore investigated whether such differences could be attributed to the organization and regulatory context of carbohydrate-associated loci, rather than to gene presence alone. Functional annotation based on COG and CAZyme databases revealed candidate genomic regions potentially involved in carbohydrate metabolism. Comparative analysis between predicted and experimentally observed substrate usage highlighted specific loci associated with carbohydrate utilization profile. The trehalose (tre) operon was conserved across all strains, while at least two distinct cellobiose-associated loci were detected in each genome. Despite the presence of these loci, L. paracasei strains were unable to metabolize cellobiose, a phenotype likely linked to the presence of a downstream TetR-type transcriptional repressor within the cellobiose (cel) operon. Additionally, a genomic region uniquely found in L. rhamnosus strains was associated with gentiobiose utilization, consistent with phenotypic observations. Overall, these findings highlight the importance of integrating phenotypic validation with complete genome context to support the identification of candidate structural and regulatory determinants of carbohydrate utilization in lactic acid bacteria. KEY POINTS: • Phenotype microarrays reveal metabolic traits of interest in isolated strains. • Regulatory context is key to understanding carbohydrate metabolism differences. • Basis of subspecies-dependent cellobiose metabolism in L. paracasei is provided.

Carbohydrate Metabolism↗

PubMed2026

Genomic signatures of host-range divergence in the generalist Beauveria bassiana and the specialist Beauveria brongniartii.

Entomopathogenic fungi of the genus Beauveria are widely used biological control agents that infect diverse insect hosts and can also associate with plants as rhizosphere colonizers and endophytes. Within this genus, Beauveria bassiana is a cosmopolitan generalist, whereas Beauveria brongniartii exhibits a narrower host range, primarily targeting soil-dwelling coleopteran larvae with limited evidence of plant colonization. To explore genomic differentiation associated with this ecological divergence, the commercially exploited B. brongniartii strain BIPESCO2 and B. bassiana ATHUM 4946 were sequenced using Oxford Nanopore technology, followed by comparative genomic analyses across multiple strains. Orthology identified species-specific gene families, although overall genome architecture and core gene content were highly conserved. The CAZyme repertoires were nearly identical, indicating retention of a versatile enzymatic toolkit supporting plant association, saprotrophy, and insect pathogenicity. In contrast, biosynthetic gene clusters displayed substantial variation, including structural remodeling of Beauveria-specific virulence-associated clusters and expansion of type I polyketide synthase clusters in B. brongniartii. Effector prediction revealed a conserved core of largely uncharacterized proteins alongside species-specific orthogroups enriched in adhesion-, immunity-, and cuticle-interaction domains. Together, these findings indicate that host-range divergence in Beauveria is associated with compartmentalized genomic differentiation, particularly in secondary metabolism and a limited subset of lineage-specific virulence factors, rather than in the conserved core infection machinery.

Beauveria↗

PubMed2026

Spore type-specific gene expression profiles underlying development and leaf infection processes of Colletotrichum graminicola.

Colletotrichum graminicola causes significant losses of the staple crop maize worldwide. The fungus produces two distinct asexual spore types, oval and falcate conidia, which show unique processes in development and plant interaction. Based on genome resequencing of our laboratory strain (CgM2/M1.001), we investigated the gene expression profiles of oval and falcate conidia during development and early leaf infection using RNA-seq. Our results reveal specific gene expression profiles between the two spore types, indicating fundamental differences in their developmental programs that reflect different modes of infection. We identified expression patterns discriminating both conidia types from mycelium and spore type-specific ones for genes encoding transcription factors, conserved fungal developmental genes, transporters, genes of secondary metabolite clusters, and pathogenicity-related functions, including effectors and carbohydrate-active enzymes (CAZymes). Our study shows that despite the identical genomic basis, oval and falcate conidia show unique transcriptomes across vegetative development and early plant interaction. Taking together, these results provide new insights into the molecular mechanisms determining the biology of C. graminicola and its interaction with the plant host.

Colletotrichum graminicola↗

PubMed2026

Characterization and genomic analysis of Bacillus halotolerans G3-2: a potential biocontrol agent against apple Alternaria leaf blotch disease.

BACKGROUND: Apple Alternaria leaf blotch (ALB) is a devastating disease threatening the apple industry worldwide. Biocontrol offers an effective and environmentally friendly alternative for disease management. RESULTS: Bacillus strain G3-2 exhibits strong antagonistic activity against Alternaria alternata (a major causal pathogen of ALB). In dual-culture assays, G3-2 inhibited A. alternata by 88.39%; in detached-leaf inoculation assays, it reduced the lesion area by >88%. 16S rRNA sequencing and phylogenetic analysis identified this strain as Bacillus halotolerans. Oxford Nanopore Technology (ONT) sequencing generated a 4.18-Mb complete genome (43.8% G + C) containing 4149 protein-coding genes, 30 rRNAs and 86 tRNAs. CAZy annotation identified 182 genes encoding carbohydrate-active enzymes (CAZymes), including glycoside hydrolases, glycosyltransferase, and carbohydrate esterases, suggesting potential for glycosylated secondary metabolite production. AntiSMASH analysis detected nine biosynthetic gene clusters, including those for surfactin, fengycin, bacillaene and laterocidine. Plate assays confirmed that G3-2 has the ability to produce protease, cellulase and siderophore. Moreover, it exhibits ~70% inhibition against several other phytopathogenic fungi. CONCLUSIONS: These findings demonstrate that G3-2 suppresses A. alternata through antibiosis (lipopeptides and polyketides), nutrient competition (siderophores) and cell-wall degradation (proteases and cellulases). Moreover, our study revealed that it has great potential to be used as a broad-spectrum, environmentally friendly biocontrol agent. © 2026 Society of Chemical Industry.

Alternaria↗

PubMed2026

Genomic Insights Into the Probiotic and Safety Attributes of Pediococcus acidilactici BC-7 for its Potential Application in Livestock Health.

Pediococcus acidilactici is widely recognized for its health-beneficial aspects and has gained increasing interest for use in livestock industry. It shows strong probiotic efficacy, antimicrobial activity, cholesterol-lowering potential, immune modulation, and other therapeutic attributes. The novel strain from indigenous habitats mainly depicted potent probiotic efficacy and high adaptability. In this study, we evaluated the probiotic characteristics and genomic features of strain BC-7 obtained from a Nili - Ravi buffalo calf raised under domestic conditions using phenotypic assessment, genomic analysis and in vivo studies. The strain BC-7 exhibited key probiotic traits i.e., gut tolerance (70.43% - 97.5%), auto-aggregation (85.24%), co-aggregation (14.33% - 25.88%), hydrophobicity (78.33% - 88%), antioxidant potential (54%), and antibacterial activity (16.47-18 mm). The safety analysis revealed that BC-7 exhibited susceptibility and resistance to various antimicrobial agents and showed no β hemolytic activity. BC-7 was taxonomically classified as Pediococcus acidilactici by 16 S rRNA gene sequencing. Whole genome sequence (WGS) analysis showed that P. acidilactici BC-7 contains a 1.9 Mb genome with 42% GC content. Pediococccus acidilactici BC-7 harbored 1900 genes, which were mainly associated with metabolism and genetic processes. Based on genomic comparison, BC-7 shared 99% average nucleotide identity and strong genomic collinearity with P. acidilactici NARCC1 which is a TYPE strain having potent probiotic potential. Probiotic strain BC-7 shared 1,664 core genes with reference strains and 69 unique genes specific for metabolism and genetic processes. The BC-7 strain contained unique bacteriocins-associated genes and defense-related CAzymes, it harbors only vancomycin resistance genes and lacked true virulence determinants. In vivo trial showed that BC-7 treated mice showed increased growth rate, improved immune modulation, and membrane integrity. These significant findings revealed that BC-7 emerging as a potential probiotic strain with strong functionality and efficacy. Thus, our strain BC-7 could be used as a promising candidate for applications in the animal health industry.

Gastrointestinal tract↗

PubMed2026

Comprehensive profiling of antibiotic resistance genes and functional clusters of orthologous groups annotation of gut microbiota in Indonesian Kedu chickens.

Antibiotic resistance is a growing global health concern, with poultry systems acting as important reservoirs of antibiotic resistance genes (ARGs). However, resistome and functional profiles of indigenous chickens raised under traditional systems remain underexplored. This study aimed to characterize the antibiotic resistome, virulence factor genes, and metabolic potential of gut microbiota in Indonesian Kedu chickens using a shotgun metagenomic approach. Digesta samples from five gastrointestinal segments of 21 healthy adult chickens were analyzed through high-throughput sequencing. ARGs were identified using the Comprehensive Antibiotic Resistance Database (CARD) and Antibiotic Resistance Genes Databases (ARDB), while virulence factors and functional genes were annotated using Virulence Factor Database (VFDB), Clusters of Orthologous Groups (COG), and Carbohydrate-Active EnZymes (CAZy) databases. Results revealed a diverse resistome dominated by multidrug resistance and efflux pump mechanisms, with prominent genes associated with fluoroquinolone, tetracycline, β-lactam, and glycopeptide resistance. The detection of clinically relevant ARGs suggests that genetic determinants associated with antimicrobial resistance are present in the gut microbiota of traditionally raised Kedu chickens, although metagenomic data alone cannot determine whether these genes are actively expressed or confer phenotypic resistance. Virulence factor analysis showed functions related to adherence, immune evasion, iron acquisition, quorum sensing, and efflux activity, reflecting strong microbial adaptability. Functional profiling demonstrated enrichment in translation, carbohydrate and amino acid metabolism, genome maintenance, and cell envelope biogenesis. Additionally, CAZyme analysis indicated a high capacity for complex polysaccharide degradation, supporting efficient utilization of fiber-rich traditional diets. In conclusion, this study provides a comprehensive metagenomic overview of antibiotic resistance and functional potential in Kedu chicken gut microbiota, emphasizing the importance of incorporating indigenous poultry into antimicrobial resistance surveillance within a One Health framework.

Antibiotic resistance genes↗