AIMS Microbiology最新文献

Fungal co-culture is a method that allows the detection of interactions between fungi, enabling the examination of bioactive novel metabolites induction that may not be produced in monocultures. Worldwide, Fusarium basal rot is a primary limitation to onion yield, being caused by different Fusarium species. Current research directions encourage biological control of plant diseases as a replacement for routine chemical treatments. The current study aimed to investigate the co-culturing technique for mining new sources of bioagents that could be used as fungicides. Aspergillus ochraceus AUMC15539 was co-cultured with Penicillium chrysogenum AUMC15504, and their ethyl acetate extract was tested in vitro and in a greenhouse against Fusarium proliferatum AUMC15541. The results showed that Aspergillus-Penicillium (AP) co-culture extract significantly inhibited the growth of F. proliferatum with an MIC value of 0.78 mg/mL and showed antioxidant efficiency with an IC₅₀ value of 1.31 mg/mL. The brine shrimp toxicity testing showed a LC₅₀ value of 2.77 mg/mL. In addition, the co-culture extract showed the highest phenolic content at 114.71 GAE mg/g, with a 27.82 QE mg/g flavonoid content. Profiling of AP co-culture and its monoculture extracts by HPLC revealed a change in the metabolites profile in AP co-culture. Principal component analysis verified a positive correlation between the obtained HPLC data of A. ochraceus (A), P. chrysogenum (P), and AP extracts. Greenhouse experiments demonstrated that treating infected onion plants with the AP co-culture extract significantly enhanced all growth parameters. Additionally, the co-culture extract treatment resulted in the highest levels of total pigments (3.46 mg/g), carbohydrates (52.10 mg/g dry weight), proteins (131.44 mg/g), phenolics (41.66 GAE mg/g), and flavonoids (9.43 QE mg/g) compared with other treatments. This indicates a promising potential for fungal co-cultures in discovering new bioagents with antifungal properties and growth-promoting capabilities.

Little is known regarding the diversity patterns of Xylariaceae and Hypoxylaceae (Ascomycota) fungi taking part in the lignin decomposition of leaf litter from different tree species and under different climatic regions. The alpha and beta diversity of Xylariaceae and Hypoxylaceae fungi was investigated on bleached leaf litter from nine subtropical and cool temperate tree species in Japan. A total of 248 fungal isolates, obtained from 480 leaves from the nine tree species, were classified into 43 operational taxonomic units (OTUs) with a 97% similarity threshold and were assigned to nine genera of Xylariaceae and Hypoxylaceae. There was no overlap of fungal OTUs between subtropical and cool temperate trees. The mean number of fungal OTUs was generally higher in subtropical than cool temperate trees, whereas rarefaction curves depicting the numbers of OTU with respect to the number of leaves from which fungi were isolated were less steep in subtropical trees than in cool temperate trees, reflecting the dominance of major OTUs in the subtropical trees and indicating a higher species richness in cool temperate regions. Nonmetric multidimensional scaling showed general overlaps of fungal OTU compositions among tree species in the respective climatic regions, and one-way permutational multivariate analysis of variance indicated that the OTU composition was not significantly different between the tree species. These results suggest a wide host range and some geographic and climatic structures of distribution of these ligninolytic fungi.

Probiotics, known for their health benefits as living microorganisms, hold significant importance across various fields, including agriculture, aquaculture, nutraceuticals, and pharmaceuticals. Optimal delivery and storage of probiotic cells are essential to maximize their effectiveness. Biopolymers, derived from living sources, plants, animals, and microbes, offer a natural solution to enhance probiotic capabilities and they possess distinctive qualities such as stability, flexibility, biocompatibility, sustainability, biodegradability, and antibacterial properties, making them ideal for probiotic applications. These characteristics create optimal environments for the swift and precisely targeted delivery of probiotic cells that surpass the effectiveness of unencapsulated probiotic cells. Various encapsulation techniques using diverse biopolymers are employed for this purpose. These techniques are not limited to spray drying, emulsion, extrusion, spray freeze drying, layer by layer, ionic gelation, complex coacervation, vibration technology, electrospinning, phase separation, sol-gel encapsulation, spray cooling, fluidized, air suspension coating, compression coating, co-crystallization coating, cyclodextrin inclusion, rotating disk, and solvent evaporation methods. This review addresses the latest advancements in probiotic encapsulation materials and techniques, bridging gaps in our understanding of biopolymer-based encapsulation systems. Specifically, we address the limitations of current encapsulation methods in maintaining probiotic viability under extreme environmental conditions and the need for more targeted and efficient delivery mechanisms. Focusing on the interactions between biopolymers and probiotics reveals how customized encapsulation approaches can enhance probiotic stability, survival, and functionality. Through detailed comparative analysis of the effectiveness of various encapsulation methods, we identify key strategies for optimizing probiotic deployment in challenging conditions such as high-temperature processing, acidic environments, and gastrointestinal transit. The findings presented in this review highlight the superior performance of novel encapsulation methods using biopolymer blends and advanced technologies like electrospinning and layer-by-layer assembly, which provide enhanced protection and controlled release of probiotics by offering insights into the development of more robust encapsulation systems that ensure the sustained viability and bioavailability of probiotics, thus advancing their application across multiple industries. In conclusion, this paper provides the foundation for future research to refine encapsulation techniques to overcome the challenges of probiotic delivery in clinical and commercial settings.

Sustainable alternatives are essential to improving agriculture production to meet the growing world's critical demands. Cyanobacteria and microalgae are considered renewable resources with a wide range of potential uses in the agricultural sector. We aimed to isolate cyanobacteria and microalgae from the mud of a carbon dioxide-rich sulfur pond and to investigate their plant growth-promoting (PGP) and soil bio-consolidating ability. Mud samples were subjected to DNA extraction and 16S rRNA gene sequencing to characterize the prokaryotic community. Phototrophic culturable microbiota was isolated and evaluated for different PGP properties. The most relevant isolates were combined in a consortium and used for in vitro bioconsolidation activity. In a greenhouse experiment, the isolates were evaluated for their ability to promote salinity stress tolerance in sunflower plants. Metabarcoding results showed that most Amplicon Sequence Variants (ASV) were associated with Actinobacteriota (35%), Proteobacteria (19%), and Acidobacteriota (11%) at the phylum level and Unknown (32%) and uncultured (31%) lineages at the genus level. The culture-dependent method yielded eight isolates associated with cyanobacteria and microalgae genera. The isolates obtained showed interesting PGP activities. Isolates C1, C2, and M1 were selected based on phosphate solubilization (85.6 µg PO₄ ^3- mL^-1 on average), indoles (C1 and M1 0.54 µg mL^-1 IAA equivalents on average), and ACC deaminase activity (C2 and M1 6.00 µmol α-KB mg proteins^-1 h^-1). The consortium efficiently consolidated sand particles in the presence of calcium carbonate by forming biomineralized aggregates. In planta results showed positive effects of the consortium on Helianthus annuus L., plant growth under normal conditions and salt stress. The positive effects on soil and plants indicated their effectiveness as bioconsolidants and biostimulant agents. Our findings highlight the interesting potential of cyanobacteria and microalgae applications in sustainable agriculture.

Rat-bite fever (RBF) is a zoonotic infection and systemic febrile illness transmitted to humans by Rattus spp. contacts following a scratch, bite, or touching excrement, such as urine, feces, and oral secretions. Infection with members of the genus Streptobacillus is the most common cause of this infectious disease. In this review article, we updated the knowledge on the RBF caused by the genus Streptobacillus based on the isolation and identification methods, virulence factors, clinical signs, differential diagnoses, antibiogram, treatment, geographical distribution, and epidemiology. Moreover, the present paper's comprehensive analysis of over 200 infection cases attributed to this genus, spanning from 1915 to 2023, sheds light on its epidemiology and provides valuable insights for the future.

The scab disease, caused by Elsinoe perseae, poses a significant risk to avocado (Persea americana) production in countries with warm and humid climates. Although the genome has been published, the precise virulence factors accountable for the pathogenicity of E. perseae have not yet been determined. The current study employed an in silico approach to identify and functionally characterize the secretory proteins of E. perseae. A total of 654 potential secretory proteins were identified, of which 190 were classified as carbohydrate-active enzymes (CAZymes), 49 as proteases, and 155 as potential effectors. A comparison to six other closely related species identified 40 species-specific putative effectors in E. perseae, indicating their specific involvement in the pathogenicity of E. perseae on avocado. The data presented in this study might be valuable for further research focused on understanding the molecular mechanisms that contribute to the pathogenicity of E. perseae on avocado.

Staphylococcus lugdunensis is a coagulase-negative species responsible for a multitude of infections. These infections often resemble those caused by the more pathogenic staphylococcal species, Staphylococcus aureus, such as skin and soft tissue infections, prosthetic joint infections, and infective endocarditis. Despite a high mortality rate and infections that differ from other coagulase-negative species, little is known regarding S. lugdunensis pathogenesis. The objective of this study is to identify the essential factors for biofilm formation in S. lugdunensis. S. lugdunensis was mutagenized through ethyl methanesulfonate (EMS) exposure, and the individual cells were separated using a cell sorter and examined for biofilm formation at 8 hr and 24 hr timepoints. Mutations that resulted in either increased or decreased biofilm formation were sequenced to identify the genes responsible for the respective phenotypes. A mutation within the S. lugdunensis surface protein A (slsA) gene was common among all of the low biofilm formers, thus suggesting that high expression of this protein is important in biofilm formation. However, other mutations common among the mutants with decreased biofilm formation were in the putative divalent cation transport gene, mgtE. Conversely, a mutation in the gene that codes for the von Willebrand factor binding protein, vwbl, was common among the mutants with increased biofilm formation. Following proteinase K treatment, a significant dispersal of the S. lugdunensis biofilm matrix occurred, thus confirming the presence of primarily protein-mediated biofilms; this is in agreement with previous S. lugdunensis studies. Additionally, all low biofilm formers exhibited decreased protein levels (1.95-2.77 fold change) within the biofilm matrix, while no difference was observed with extracellular DNA (eDNA) or polysaccharides. This study presents a unique methodology to identify genes that affect biofilm formation and sheds light on S. lugdunensis pathogenesis.

In this study, bacteria associated with licorice (Glycyrrhiza glabra L.) were characterized through 16S rRNA gene analysis. Profiling of endophytic bacteria isolated from Glycyrrhiza glabra tissues revealed 18 isolates across the following genera: Enterobacter (4), Pantoea (3), Bacillus (2), Paenibacillus (2), Achromobacter (2), Pseudomonas (1), Escherichia (1), Klebsiella (1), Citrobacter (1), and Kosakonia (1). Furthermore, the beneficial features of bacterial isolates for plants were determined. The bacterial isolates showed the capacity to produce siderophores, hydrogen cyanide (HCN), indole-3-acetic acid (IAA), chitinase, protease, glucanase, lipase, and other enzymes. Seven bacterial isolates showed antagonistic activity against F. culmorum, F. solani, and R. solani. According to these results, licorice with antimicrobial properties may serve as a source for the selection of microorganisms that have antagonistic activity against plant fungal pathogens and may be considered potential candidates for the control of plant pathogens. The selected bacterial isolates, P. polymyxa GU1, A. xylosoxidans GU6, P. azotoformans GU7, and P. agglomerans GU18, increased root and shoot growth of licorice and were able to colonize the plant root. They can also serve as an active part of bioinoculants, improving plant growth.

Staphylococcus aureus is one of the leading agents of nosocomial and community-acquired infections. In this study, we explored the genomic characterization of eight methicillin-resistant clinical isolates of S. aureus from Dhaka, Bangladesh. Notably, all strains were resistant to penicillin, cephalosporins, and monobactams, with partial susceptibility to meropenem and complete susceptibility to amikacin, vancomycin, and tigecycline antibiotics. The strains were found to have an average genome size of 2.73 Mbp and an average of 32.64% GC content. Multi-locus sequence typing analysis characterized the most predominant sequence type as ST361, which belongs to the clonal complex CC361. All isolates harbored the mecA gene, often linked to SCCmec_type IV variants. Multidrug resistance was attributed to efflux pumps NorA, NorC, SdrM, and LmrS alongside genes encoding beta-lactamase BlaZ and factors like ErmC and MepA. Additionally, virulence factors including adsA, sdrC, cap8D, harA, esaA, essC, isdB, geh, and lip were commonly identified. Furthermore, genes associated with heme uptake and clumping were present, highlighting their roles in S. aureus colonization and pathogenesis. Nine secondary metabolite biosynthetic gene clusters were found, of which six were common in all the strains. Numerous toxin-antitoxin systems were predicted, with ParE and ParB-like nuclease domains found to be the most prevalent toxin and antitoxin, respectively. Pan-genome analysis revealed 2007 core genes and 229 unique genes in the studied strains. Finally, the phylogenomic analysis showed that most Bangladeshi strains were grouped into two unique clades. This study provides a genomic and comparative insight into the multidrug resistance and pathogenicity of S. aureus strains, which will play a crucial role in the future antibiotic stewardship of Bangladesh.

Colorectal cancer (CRC) continuously ranks as the third most common cause of cancer-related deaths worldwide. Based on anatomical classifications and clinical diagnoses, CRC is classified into right-sided, left-sided, and rectal CRC. Importantly, the three types of positional-specific CRC affect the prognosis outcomes, thus indicating that positional-specific treatments for CRC are required. Emerging evidence suggests that besides host genetic and epigenetic alterations, gut mucosal microbiota is linked to gut inflammation, CRC occurrence, and prognoses. However, gut mucosal microbiota associated with positional-specific CRC are poorly investigated. Here, we report the gut mucosal microbiota profiles associated with these three types of CRC. Our analysis showed that the unique composition and biodiversity of bacterial taxa are linked to positional-specific CRC. We found that a combination of bacterial taxa can serve as potential biomarkers to distinguish the three types of CRC. Further investigations of the physiological roles of bacteria associated with positional-specific CRC may help understand the mechanism of CRC progression in different anatomical locations under the impact of gut mucosal microbiota.