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12 recordsLinked to original sources
PubMed2026

Five novel Paenibacillus species from the plant rhizosphere: Paenibacillus corni sp. nov., Paenibacillus vaccinii sp. nov., Paenibacillus ericacearum sp. nov., Paenibacillus polytrichii sp. nov., and Paenibacillus artemisiae sp. nov.

Bacterial strains were isolated from different locations and screened for plant growth promoting (PGP) features. Comparative analyses of the 16S gene sequences of 5 of the strains indicated taxonomic relatedness within the genus Paenibacillus. A polyphasic taxonomic approach was employed to study the strains in detail to clarify their phylogenetic position. Genome-based analyses, including digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI), revealed values consistently below the accepted species delineation thresholds when compared with closest relatives of each strain. Additionally, the strains showed clear differences in their physiological and biochemical profiles to the type strains of the closest related species. A notably diverse set of genes potentially involved in plant growth promotion was detected in all strains. With respect to the analyses reported here, the following new names are proposed: Paenibacillus corni sp. nov., with AK-167T as the type strain (= LMG 34403T = DSM 121689T); Paenibacillus vaccinii sp. nov., with AK-264T as the type strain (= LMG 34404T = DSM 121714T); Paenibacillus ericacearum sp. nov., with AK-265T as the type strain (= CCM 6913T = LMG 34405T = DSM 121715T); Paenibacillus polytrichii sp. nov., with AK-286T as the type strain (= CCM 9614T = LMG 34406T = DSM 121716T); and Paenibacillus artemisiae sp. nov., with DT-106T as the type strain (= LMG 34409T = CCM 9610T = DSM 121690T).

Paenibacillus↗
PubMed2026

Comparative Genomics of Paenibacillus Secondary Metabolism: Unveiling the Putative Biosynthetic Gene Cluster for Paenialvins in Paenibacillus Alvei Strain 32.

In this study, we used comparative genomics and culture-based methods to investigate Biosynthetic Gene Clusters (BGCs) responsible for the production of antimicrobial peptides. Paenibacillus alvei strain 32 was isolated from a cystic fibrosis sputum. Its genome was sequenced using Illumina, showing a size of 6,584,590 bp with 239 contigs assembled in 26 scaffolds, an average coverage of 243X, and 6,832 coding sequences. ANI analysis and in silico DNA-DNA hybridization showed its affiliation inside Paenibacillus alvei, with a clear separation from other related strains, leading us to propose a distinct species-level genomic clade (genomospecies) within this group. AntiSMASH analysis predicted 22 putative BGCs in the genome of strain 32. Its culture supernatant exhibited inhibitory activity against Gram-positive pathogens, including methicillin-resistant Staphylococcus aureus (MRSA), Bacillus cereus, and Enterococcus faecalis. By comparing in silico BGC predictions with activities described in the literature, we propose that strain 32 harbours a specific 110-kb cluster (cluster 6.2) with five non-ribosomal peptide synthetase (NRPS) genes. These synthetases are predicted to direct the assembly of a 16-amino acid backbone that correlates with the structure of paenialvins, which are known anti-MRSA molecules. This study describes the putative biosynthetic pathway of the paenialvins and explains structural variations, bringing useful data on Paenibacillus secondary metabolism for future antibiotic development.

Paenibacillus alvei↗
PubMed2025

The mhqPOD gene cluster in lignin-degrading Paenibacillus sp. B2 encodes a pathway for the degradation of lignin-derived 5,5'-di(dehydrovanillic acid) (DDVA).

Lignin-degrading bacteria Paenibacillus sp. B2, Agrobacterium sp. B1, and Ochrobactrum sp. each contain mhqO genes encoding ring cleavage dioxygenase enzymes whose biochemical function is unknown. Each of these strains was found to degrade the biphenyl-containing lignin fragment 5,5'-di(dehydrovanillic acid) (DDVA) on solid media. An operon of five mhq genes in Paenibacillus sp. B2 was analysed via gene expression using quantitative PCR, and all five genes were highly induced (400-1000-fold overexpression) by the presence of DDVA. Recombinant azoreductase MhqP was found to demethylate DDVA to its monodemethylated derivative. Hence, these genes are proposed to be responsible for DDVA degradation, via a pathway involving the same biochemical steps as that studied in Sphingobium lignivorans SYK-6, but using several unrelated genes. Decarboxylation of later pathway intermediate 5-carboxyvanillic acid in Paenibacillus sp. B2 is proposed to be catalysed by decarboxylase UbiD, whose gene is also upregulated in the presence of DDVA. Degradation of the other fragment 4-carboxy-2-hydroxypentadienoic acid is proposed to occur via hydratase UxuA, whose gene is also upregulated by DDVA, and 4-hydroxy-4-methyl-2-oxoglutarate aldolase.

Paenibacillus↗
PubMed2026

Genome sequence data of the chitinase-producing bacterium Paenibacillus mucilaginosus YWY-5.1.

Paenibacillus mucilaginosus is a beneficial bacterium widely applied as a biofertilizer in agriculture. To date, genomic information on this species remains limited; however, no genome assemblies from Vietnam have been reported. This work presented the draft genome of P. mucilaginosus YWY-5.1, a promising strain with strong chitin-degrading capability and agricultural potential, isolated from Yok Don National Park, Vietnam, using Illumina technology. Results showed that the assembled genome comprised 48 contigs with 4,076,146 bp and 73.8% GC-content. Genome annotation identified 3,611 protein-coding genes, 2 rRNA genes, and 53 tRNA genes. A total of 150 carbohydrate-active enzyme-related genes were predicted from the genome; among them, seven putative chitinolytic genes were identified, including 4 genes related to family 18 chitinase, 2 genes to family 20 β-N-acetylglucosaminidase, and one gene to auxiliary activity family 10. In addition, at least 32 genes related to plant growth-promoting functions were identified, including those associated with indole-3-acetic acid production, phosphate and potassium solubilization, siderophore biosynthesis, iron uptake, ACC metabolism, and nitrate transport and reduction. Furthermore, genome mining identified 4 biosynthetic gene clusters probably involved in secondary metabolite production, of which 3 displayed no similarity to previously reported clusters, indicating potential for novel bioactive compounds. These genomic data improved our understanding of the biodegradation capacity and agricultural potential of P. mucilaginosus YWY-5.1 isolated from Vietnam, and provided a valuable genomic resource for future functional and biotechnological investigations toward crop production and related fields.

Chitinases↗
PubMed2026

Comparative genomics and phenotypic divergence of ERIC I and ERIC II genotypes of Paenibacillus larvae, the causative agent of American Foulbrood disease.

Honeybees of the species Apis mellifera are important pollinators of crops and wild plants. Paenibacillus larvae, a spore-forming bacterium, is a problematic pathogen that causes American foulbrood (AFB) in honeybee larvae worldwide. In many countries, AFB is a notifiable disease, requiring the destruction of diseased colonies, resulting in economic loss that impacts beekeeping and agriculture. Disease onset starts with larval ingestion of P. larvae spores, which germinate into growing cells that proliferate in the larval gut, leading to larval death and eventually bee colony collapse. As infection progresses, P. larvae produce spores, reinitiating the disease cycle. Thus, growth, sporulation and germination underlie AFB. In this study, using various microbiological assays, quantitative cell biology methods, transmission electron microscopy and genomics, we sought to identify genetic and phenotypic characteristics associated with the predominant ERIC I and ERIC II genotypes of P. larvae during growth, sporulation and germination. Extending previous findings, our data identify genetic differences between ERIC I and ERIC II strains and some genetic variation between strains of the same ERIC type. Furthermore, we describe significant differences in cellular morphology during growth, differences in spore envelope structure and differences in germination efficiency between ERIC I and ERIC II genotypes. Collectively, our findings improve understanding of P. larvae biology and provide a foundation for developing genotype-specific disease management strategies for AFB.

Animals↗
PubMed2026

Radiation-resistant and desiccation-tolerant bacteria from the Chavara-Neendakara high background radiation area, india: phenotypic characterisation and genomic insights.

Radiation-resistant microorganisms that survive high doses of ionising radiation serve as valuable models for understanding stress adaptation; however, the genomic determinants underlying extreme radiation tolerance in bacteria from natural environments with high background radiation remain insufficiently characterised. Bacterial isolates from the Chavara-Neendakara HBRA (Kerala, India) were evaluated for desiccation tolerance, and the desiccation-resistant isolates were subsequently exposed to gamma irradiation (1-10 kGy) using a 60Co source. Isolates were identified through 16S rRNA sequencing, morphologically characterised by FE-SEM, and screened for antibiotic susceptibility. The highly radiation-resistant strain underwent whole-genome sequencing via Oxford Nanopore Technology, with De novo assembly, polishing, and genome annotation. Four bacterial isolates (Micrococcaceae and Paenibacillaceae) exhibited D10 values of 1-7 kGy, including one multidrug-resistant strain; no endospores were observed in the Paenibacillus isolate under the tested conditions. Paenibacillus sp. HBRA004 survived 10 kGy gamma radiation, exceeding all previously reported HBRA isolates by over fourfold. Its 5.0 Mbp genome (GC = 48.27%, ≥ 99% completeness) encodes five mechanistically independent DNA repair pathways; homologous recombination (recA, recN, radA), base excision repair (mutM, mutY, mutT), mismatch repair (mutL, mutS), nucleotide excision repair (uvrA, uvrB, uvrD), and non-homologous end joining (ku, ligD), alongside a redundant antioxidant network comprising triple-copy Fe/Mn-family superoxide dismutases and ahpC peroxiredoxin. A thioredoxin system (trxA, trxB, msrA) and manganese uptake via mntH may contribute to further layers of ROS defence. Their specific contribution to the HBRA004 phenotype remains to be experimentally and comparatively validated. These findings represent the first genomically characterised 10 kGy-resistant bacterial isolate from the Chavara-Neendakara HBRA, establishing a new benchmark for radiation tolerance within this ecologically significant environment. Pathway depth, gene copy amplification, and Mn/Fe homeostasis appear to be candidate mechanisms contributing to high-level radiation tolerance, consistent with patterns in other radiation-resistant taxa, though their contribution requires functional validation.

India↗
PubMed2025

New insights into soil amendment: Impact of humic acid on typical antibiotic resistance in agricultural soil.

Humic acid (HA) addition can improve agricultural soil, but little is known about how it affects the soil resistome. In this study, we used selective agar plate combined with quantitative PCR (qPCR) and 16S rRNA gene sequencing to investigate how HA influences antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs) in soil contaminated with erythromycin and kanamycin. 0.1 % HA reduced the abundance of culturable erythromycin-resistant bacteria (ERB), while promoting the growth of kanamycin-resistant bacteria (KRB). Lysinibacillus and Paenibacillus were the dominant genera in ERB and KRB, respectively, governing the changes in their abundances. At this concentration, the Lysinibacillus abundance in ERB decreased from 96.74 % to 70.57 %. Meanwhile, that of Paenibacillus in KRB increased from 33.40 % to 77.44 %. The copy number of ermF decreased after HA addition, while that of ermB increased. Furthermore, 0.1 % HA significantly reduced the copy number and relative abundance of aadA1 and aac(6')-Ib (aka aacA4)-03 in the soil. Changes in these two types of ARB and ARGs were primarily driven by shifts in the microbial community structure. Soil physicochemical properties, particularly increased organic matter (OM), altered the absolute abundance of ermB. Meanwhile, changes in intI1 abundance determined the risk associated with aadA1 and aac(6')-Ib (aka aacA4)-03. These findings emphasize the dual role of HA in the dissemination of antibiotic resistance in agricultural soils and highlight the necessity of considering dose-dependent effects when applying HA as a soil amendment.

Soil Microbiology↗
PubMed2026

Discovery of antimicrobial peptides from incomplete biosynthetic gene clusters to combat multidrug-resistant bacteria.

The escalating crisis of multidrug-resistant bacteria necessitates innovative antibiotic discovery platforms. Conventional antimicrobial peptide (AMP) mining often relies on complete biosynthetic gene clusters (BGCs), leaving fragmented genomic resources underexplored. Here, we present an evolution-inspired approach to reconstruct and predict AMPs from partial BGCs. Applying this strategy to 954 Paenibacillus genomes identifies five polymyxin-like peptides, NP001-NP005, with broad in vitro activity. Crucially, in murine models of polymyxin-resistant infection, NP001 reduced bacterial burdens by up to 1,000-fold in a thigh infection model and improved survival (50% vs. 0%) in a lethal peritonitis model. Structural simulations and biophysical assays revealed that NP001 maintains high affinity for bacterial membranes and effectively binds to MCR-1-modified lipid A, a key colistin-resistance mechanism. Moreover, Leu at position 10 of NP001 plays a key role in antibacterial activity against MCR-1-resistant bacteria. Our work establishes a generalizable framework for AMP discovery and introduces a promising therapeutic candidate, NP001, which effectively counteracts polymyxin-resistant pathogens.

Multigene Family↗
PubMed2026

An Acetyltransferase Conferring Self-Resistance of the Producer to Lasso Peptide Antibiotic Lariocidin.

The soil microbiome, a reservoir of antibiotic-producing bacteria, also harbors resistance determinants encoded within antibiotic biosynthetic gene clusters (BGCs). Studying self-resistance mechanisms, which have evolved in producers to protect against their own toxic metabolites, provides critical insights into the evolution of resistance and the potential vulnerabilities of new antibiotics and can facilitate the production of natural products in heterologous hosts. Here, we describe the self-resistance mechanism to lariocidin (LAR), a recently discovered lasso peptide antibiotic that inhibits the ribosomal machinery and exhibits antibacterial activity against key pathogens. We identified and characterized an N-acetyltransferase enzyme (LrcE) encoded within the LAR BGC that mediates self-resistance in LAR-producing Paenibacillus sp. M2. LrcE is a member of the GCN5-related N-acetyltransferase (GNAT) superfamily and performs site-specific acetylation of LAR at a critical lysine residue. This modification disrupts ribosomal binding, thereby reducing LAR's antibacterial activity. Using in silico modeling, we predicted a conserved acetyl-CoA-binding motif and an LAR-binding region on LrcE. Bioinformatic analysis revealed LrcE homologues in environmental but not clinically relevant pathogens, suggesting a limited risk of horizontal gene transfer and, therefore, supporting the further development of LAR as a next-generation antibiotic.

Anti-Bacterial Agents↗
PubMed2024

Effects of initial corncob particle size on the short-term composting for preparation of cultivation substrates for Pleurotus ostreatus.

The short-term composting based on corncob for preparing Pleurotus ostreatus cultivation medium originated from agricultural production practices and so lacked systematic investigation. In this study, the influences of a Dafen (15 mm, DFT) and Xiaofen (5 mm, XFT) initial particle size (IPS) of corncob on the microbial succession and compost quality were examined. Results demonstrated that XFT compost was better suited for mushroom cultivation due to its high biological efficiency of 70 % and the absence of contamination. The composting microbes differed significantly between the DFT and XFT composts. During composting, the genera of Bacillus, Acinetobacter, Lactobacillus, Streptomyces, and Paenibacillus were majorly found in the DFT compost, while Acinetobacter, Lactobacillus, Puccinia, Bacteroides, and Bacillus genera dominated the XFT compost. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that throughout the thermophilic phase, XFT compost had much greater relative abundances of sequences relevant to energy, carbohydrate, and amino acid metabolism than DFT compost. Analysis of network correlations and Mantel tests indicated that IPS reduction could increase microbial interactions. Overall, adjusting the IPS of corncob to 5 mm increased microbial interactions, improved compost quality, and thereby boosted the P. ostreatus yield. These findings will be pertinent in optimizing the composting process of cultivation medium for P. ostreatus.

Composting↗
PubMed2026

Pilot metaproteomic profiling reveals bacterial diversity and potential medical and veterinary relevance of tick microbiomes in northern Algeria.

Ticks are major ectoparasites and vectors of pathogens affecting humans, livestock, and wildlife. They harbor diverse microbial communities that may influence tick biology and interactions with microorganisms; however, functional information on tick-associated microbiomes remains limited, particularly in North Africa. In this pilot study, we applied a metaproteomic approach based on high-resolution tandem mass spectrometry to characterize bacterial communities associated with three tick species collected in Algeria: Rhipicephalus sanguineus sensu lato, Hyalomma aegyptium, and Hyalomma dromedarii. Peptide spectra were assigned to taxa using a two-step database search strategy based on NCBInr, and bacterial composition and relative abundance were compared across tick species and sampling locations. A total of 40 bacterial genera belonging to 32 families and four phyla were identified. Microbiome composition differed significantly between tick genera and collection locations, suggesting an influence of species-specific and geographical factors on microbial community structure. Dominant genera included Streptomyces, Bacillus, Clostridium, Escherichia, Flavobacterium, Paenibacillus, and Providencia. Peptides related to Coxiella spp. were frequently detected, consistent with previous reports of Coxiella-like endosymbionts in ticks. This pilot study provides a first metaproteomic characterization of tick-associated communities in Algeria. The results reveal species- and location-associated differences in microbial composition and highlight the potential of metaproteomics for exploring tick-associated microbiomes in North Africa.

Animals↗
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↗