Microbiological research最新文献

The use of multi-omic approaches has significantly advanced the exploration of microbial traits, leading to the discovery of new bioactive compounds and their mechanisms of action. Streptomyces sp. MH71 is known for its antifungal properties with potential for use in crop protection. Using genomic, transcriptomic, and metabolomic analyses, the antifungal metabolic capacity of Streptomyces sp. MH71 was investigated. After 96 hours of liquid fermentation, cell-free spent media showed inhibitory activity against the fungal phytopathogen Verticillium dahliae, with the lowest IC₅₀ value being 0.11 % (v/v) after 144 h. Through whole-genome sequencing, we obtained a near-complete genome of 11 Mb with a G+C content of 71 % for Streptomyces sp. MH71. Genome mining identified 50 putative biosynthetic gene clusters, six of which produced known antimicrobial compounds. To link antifungal activity with candidate biosynthetic pathways, a transcriptomic approach was applied to understand antifungal induction in MH71 cells during the observed increase in antifungal activity. This approach revealed 2774 genes that exhibited differential expression, with significant upregulation of genes involved in biosynthesis of secondary metabolites during the stationary growth phase. Metabolomic analyses using LC-MS and GC-MS of secreted compounds identified a cocktail of potent antifungal metabolites, including volatiles with antifungal activity. By combining genome mining, bioactivity data, transcriptomics, and metabolomics, we describe in detail the gene expression and metabolite products driving antifungal activity during microbial fermentation.

Dietary polysaccharides function not only as indispensable nutrients and energy sources for the host organism but also as critical substrates for the gut microbiota. Gut microorganisms possess the ability to selectively degrade and metabolize specific dietary polysaccharides, thus fostering their proliferation and yielding crucial bioactive metabolites that potentially influence host metabolic and immune pathways. Dysbiosis of the gut microbiota has been extensively documented to be closely linked with the onset and progression of various diseases; in this regard, the precision modulation strategy of the gut microbiome via dietary polysaccharides holds substantial potential to enhance human health. Here, we delve into the therapeutic potential of dietary polysaccharides for the precision modulation of specific gut microorganisms via dietary interventions, with particular emphasis on their implications for the prevention and management of metabolic and inflammatory disorders. Given the complexity of the human gut microbiome and the varying degrees to which different bacterial members utilize carbohydrates, we conduct an in-depth analysis of the differential utilization of dietary polysaccharides by key gut microbiome, with particular emphasis on the role of carbohydrate-active enzymes in these processes. Furthermore, we elucidate the pivotal role of carbohydrate utilization within microbial cross-feeding networks and its significance in maintaining gut homeostasis. In summary, this review investigates the precision modulation of gut microbiota through dietary polysaccharides, with the aim of establishing a theoretical foundation for the development of personalized nutritional interventions. These strategies hold substantial potential for enhancing human health and offer valuable opportunities for the prevention and treatment of microbiota-associated diseases.

The rhizosphere microbiota, often referred to as the plant's "second genome" plays a critical role in modulating root system architecture (RSA). Despite this, existing methods to analyze root phenotypes in the context of root-microbe interactions remain limited, and the precise mechanisms affecting RSA by microbes are still not fully understood. This review comprehensively evaluates current root phenotyping techniques relevant to plant-microbe interactions, discusses their limitations, and explores future directions for integrating advanced technologies to elucidate microbial roles in altering RSA. Here, we summarized that microbial metabolite, primarily through auxin signaling pathways, drive root development changes. By harnessing advanced phenotyping tools, we aim to uncover more detailed mechanisms by which microbes modify RSA, providing valuable insights into strategies for optimizing nutrient uptake, bolstering food security, and enhancing resilience against climate-induced environmental stresses.

A detailed diversity analysis of the prokaryotic and fungal communities in soil impacted by an underground fire located in the Trans-Mexican volcanic belt, Mexico, is described. Microbial diversity data obtained from soils at different depths and temperatures (27 °C, 42 °C, 50 ºC and 54 ºC) were analyzed, and Firmicutes increased in abundance as the temperature augmented, and Proteobacteria mainly decreased in abundance at high temperatures compared to unaffected soils. The fungal phylum Ascomycota was the most abundant, with no significant changes. A clear reduction in the richness of both prokaryotic and eukaryotic operational taxonomic units (OTUs) was observed in the affected soils. At the genus level, Bacillus species were the most abundant among bacteria, while Aspergillus, Penicillium, and Mortierella were dominant fungal genera at higher temperatures. Interestingly, the physicochemical parameters of the affected soils modified organic matter, which was indirectly correlated with the presence of some microbial taxa. Likewise, we obtained 308 soil bacterial isolates from both control and affected soils. Among these, the taxa from the phyla Actinobacteria and Firmicutes demonstrated the highest thermotolerance in the affected soils. Our findings shed light on the impact of underground fires on the structure of microbial communities, favoring an abundance of thermotolerant microbes.

Cover crops can suppress the following crop diseases and alter soil microbial communities, but the mechanisms of such disease suppressive effects remain uncertain. Here, we studied the effects of brassica and cereal cover crops, along with decomposition solutions from these crop residues, on tomato growth and bacterial wilt. Moreover, tomato rhizosphere microorganisms were analyzed by qPCR and high-throughput sequencing. Rhizosphere transplant experiment was conducted to validate the disease suppressive potential of rhizosphere microorganisms mediated by decomposition solutions from these crop residues. Our findings revealed that brassica and cereal cover crops especially wheat, pakchoi and rape significantly enhanced tomato growth and inhibited bacterial wilt disease. Decomposition solutions from brassica and cereal residues had inhibitory effects on Ralstonia solanacearum and this disease. Moreover, such decomposition solutions can differently alter the abundances, compositions and diversities of tomato rhizosphere bacterial and fungal communities. Notably, decomposition solutions from wheat, pakchoi and rape residues increased the inverse Simpson diversity and the abundances of Bacillus spp. community. In addition, decomposition solutions from wheat and pakchoi residues significantly increased bacterial beta diversity, and decomposition solutions from rape residue significantly increased fungal beta diversity. Rhizosphere transplant experiment confirmed that the rhizosphere microbial changes induced by decomposition solutions contributed to the suppressiveness of tomato bacterial wilt disease. These suppressive effects were stronger in decomposition solutions from wheat, pakchoi and rape residues than those from oilseed rape, wild rocket and Indian mustard residues. Overall, our results demonstrated that decomposition solutions from brassica and cereal residues enhance disease suppression by shaping a beneficial rhizosphere microbiota, providing a promising strategy for sustainable management of bacterial wilt in tomato cultivation.

Over the past decade, Italian kiwifruit orchards and overall production have faced a significant threat from Kiwifruit Vine Decline Syndrome (KVDS). Despite the insights gained from metagenomics studies into the microbial communities associated with the disease, unanswered questions still remain. In this study, the evolution of bacterial, fungal, and oomycetes communities in soil and root endosphere at three different time points during the vegetative season was investigated for the first time in a KVDS-affected orchard in the Lazio Region. The fungal and oomycetes genera previously associated with the syndrome, including Fusarium, Ilyonectria, Thelonectria, Phytophthora, Pythium and Globisporangium, were identified in both groups. In contrast, the characterization of bacterial communities revealed the first instance of the presence of the genus Ralstonia in soil and root samples. The microbiome composition shifts between KVDS-affected and asymptomatic plants were significant as evidenced by the results, particularly after a temperature increase. This temperature change coincided with the onset of severe disease symptoms and may indicate a key role in the progression of KVDS.

Temperate bacteriophages are crucial for maintaining the pathogenicity and fitness of S. aureus, which also show promise as a biocontrol agent for S. aureus. However, the fitness benefit and cost of lysogeny by S. aureus temperate phages and their underlying mechanisms remain unexplored. In this study, phage resistance, virulence, antimicrobial resistance (AMR), transcriptome, and metabolome of phage SapYZUs7 lysogenic and non-lysogenic S. aureus strains were compared. Whole-genome analysis revealed that SapYZUs7 harbouring smaII associated with a single-protein MazF-like antiphage system could be integrated into the genome of S. aureus isolates. Notably, lysogenic S. aureus exhibited higher phage resistance, a lower growth rate, and inhibited metabolic activity compared to the parental strains, indicating interference of phage reproduction by smaII. Moreover, prophages carrying smaII are widely distributed across S. aureus and harboured other virulence factor (VF) and AMR genes. Besides, the SapYZUs7-integration increased phagocytosis resistance but decreased adhesion, biofilm formation, and AMR. The combined use of SapYZUs7 and antibiotics exhibited a better bactericidal effect than SapYZUs7 or the antibiotics alone. Consistently, integrated omics analysis suggested that SapYZUs7-lysogeny downregulated multiple VF and AMR genes. Our analysis suggests that SmaII drives mutualistic phage-host interactions through lysogenic conversion. The fitness cost of SapYZUs7-integration is the downregulated expression of VF and AMR genes, serving as an alternative candidate as a biocontrol agent for methicillin-resistant S. aureus and multidrug-resistant S. aureus.

The widespread antimicrobial resistance (AMR) problem poses a serious health threat, leaving few drug choices, including tigecycline, to treat multidrug resistance pathogens. However, a plasmid-borne tigecycline resistance gene cluster, tmexCD1-toprJ1, emerged and conferred tigecycline resistance. In this study, we identified two novel subtypes, tmexCD2.3-toprJ2.3 and tmexCD2.4-toprJ1b, obtained from three chicken-origin Pseudomonas putida isolates. Two types of megaplasmids were found as the vital vehicle of these tmexCD-toprJ variants. Phylogenetic and genomic analysis indicated the two variants were mainly distributed in Pseudomonas and acted as an evolved intermediated state precursor of tmexCD2-toprJ2. Further gene cloning assay revealed both the expression of tmexCD2.3-toprJ2.3 and tmexCD2.4-toprJ1b could confer multiple antimicrobial resistance, mediating 8- to 16-fold increase of tigecycline MIC. Importantly, two key nucleotide differences in promoter region influence the promoter activity between P_tmexC2.3 and P_tmexC2.4, while the downregulation effect of TNfxB on the transcriptional expression level of tmexCD2.3-toprJ2.3 and tmexCD2.4-toprJ1b were observed. The emergency of two novel tmexCD-toprJ variants necessitates preventive measures to curb their spread and highlights concerns about more emerging tmexCD-toprJ variants.

The ApxIVA protein belongs to a distinct class of a "clip and link" activity of Repeat-in-ToXin (RTX) exoproteins. Along with the three other pore-forming RTX toxins (ApxI, ApxII and ApxIII), ApxIVA serves as a major virulence factor of Actinobacillus pleuropneumoniae, the causative agent of porcine pneumonia. The gene encoding ApxIVA is located on a bicistronic operon downstream of the orf1 gene and is expressed exclusively under in vivo conditions. Both ApxIVA and ORF1 are essential for full virulence of A. pleuropneumoniae, but the molecular mechanisms by which they contribute to the pathogenicity are not yet understood. Here, we provide a comprehensive structural and functional analysis of ApxIVA and ORF1 proteins. Our findings reveal that the N-terminal segment of ApxIVA shares structural similarity with colicin M (ColM)-like bacteriocins and exhibits an antimicrobial activity. The ORF1 protein resembles the colicin M immunity protein (Cmi) and, like Cmi, is exported to the periplasm through its N-terminal signal peptide. Additionally, ORF1 can protect bacterial cells from the antimicrobial activity of ApxIVA, suggesting that ORF1 and ApxIVA function as an antibacterial toxin-immunity pair. Moreover, we demonstrate that fetal bovine serum could elicit ApxIVA and ORF1 production under in vitro conditions. These findings highlight the coordinated action of various RTX determinants, where the fine-tuned spatiotemporal production of ApxIVA may enhance the fitness of A. pleuropneumoniae, facilitating its invasion to a resident microbial community on the surface of airway mucosa.