BMC Microbiology最新文献

Background: Apilactobacillus kunkeei is a fructophilic lactic acid bacterium adapted to honeybees, their food sources and products. These bacteria synthesize exopolysaccharides thought to promote host colonization and protection against toxic compounds and stressful conditions. Homopolysaccharides consisting of glucose residues are synthesized by enzymes in the glycoside hydrolase family 70 (GH70), whereas polysaccharides that contain fructose are synthesized by family 32 (GH32) enzymes. However, the mechanisms whereby these enzymes diversify are not well understood. Here, we used a comparative genomics approach to investigate the evolution of GH70 and GH32 enzymes in the A. kunkeei population.

Results: Based on phylogenetic inferences, the GH70 proteins in 38 reference A. kunkeei strains were sorted into glucan-binding enzymes, which were predicted to have glucansucrase and branching sucrase activities, and non-glucan binding enzymes of unknown enzymatic functions. Genes for the glucan sucrases and the branching sucrases are clustered in a chromosomal segment that also contains genes for GH32 enzymes. The number and combination of genes for the glucan-binding GH70 enzymes were mostly strain-specific, indicative of high rates of gene turnover. Neighboring genes often displayed a dramatic variability in synonymous and nonsynonymous substitution frequencies and have only rarely co-diverged. We identified short recombination tracts and a few long tracts that spanned across the cluster of genes for GH70 and GH32 enzymes. Genes encoding GH70 and GH32 enzymes evolve faster than genes encoding core proteins. The ratios of the relative effect of recombination to mutation for the core genome were estimated to 1.6 to 5.2 for A. kunkeei strains assigned to phylogroups A and B-C, respectively.

Conclusions: Our results suggest genes for GH32 and GH70 proteins have a unique evolutionary history in each A. kunkeei strain and have diverged by duplications, deletions, fusions, recombination events and nucleotide substitutions. We suggest that genes for GH70 enzymes have escaped the homogenizing effects of homologous recombination to a greater extent than the core genes due to rampant gene gain and loss. The results imply that the clustering of the A. kunkeei-related strains into phylogroups mostly reflects the impact of homologous recombination on the core genome.

Background: Atopic dermatitis (AD) is a chronic, relapsing inflammatory skin disease in which dysbiosis of gut and skin microbiota contributes to pathogenesis and severity. Washed microbiota transplantation (WMT)-an improved form of fecal microbiota transplantation with enhanced safety and microbiota quality control-has shown efficacy in a single reported adolescent case. However, clinical data on WMT in AD and its effects on the skin and gut microbiota remain limited.

Methods: Twenty-three patients with moderate-to-severe AD received at least two courses of WMT between January 2022 and December 2023. Disease activity was evaluated using the SCORing Atopic Dermatitis (SCORAD) index, the Eczema Area and Severity Index (EASI), the Numeric Rating Scale (NRS) for itch, and the Dermatology Life Quality Index (DLQI). Peripheral blood counts, cytokine profiles, lymphocyte subsets, and gut and skin microbiota were assessed before and after treatment.

Results: WMT was well tolerated (58 sessions; 5.2% mild adverse events) and significantly improved SCORAD, EASI, DLQI, and NRS scores, with greater EASI reductions in adults than in children. Absolute basophil counts decreased significantly after treatment, whereas other hematologic and cytokine parameters remained stable. Gut microbiota showed an increased Gut Microbiome Health Index, a decreased Microbial Dysbiosis Index, and enrichment of short-chain fatty acid-producing taxa, including the Eubacterium coprostanoligenes group, Lachnospiraceae, and Coprococcus. Skin microbiota shifted from Staphylococcus dominance to higher abundances of Acinetobacter, Perlucidibaca, and other potentially protective genera, inversely correlating with disease severity and systemic inflammation.

Conclusions: WMT appears safe and effective in alleviating clinical manifestations of AD while reshaping both gut and skin microbiota. These parallel microbial shifts support the gut-skin axis as a therapeutic target and highlight WMT as a promising microbiota-centered intervention for immune-mediated skin diseases.

Background: M. abscessus (Mabs) is one of the principal pathogenic strains among nontuberculous mycobacterial. Mabs infections pose a significant global public health challenge, leading to substantial morbidity and mortality. However, a standard treatment regimen has not yet been established. The goal of this study was to provide clear insights into constructing regimens.

Methods: We evaluated the efficacy of 7 clinically available drugs against Mabs under various environments through microplate alamar blue assay (MABA), biofilm assays, Wayne model and nutrient-starvation model. The checkerboard assay was employed to assess drug-drug interactions. Finally, we assessed the efficacy, degree of organ damage, and prevalence of resistant strains associated with different triple-drug combinations in a BALB/c mouse model.

Results: Bedaquiline (BDQ) was active against replicating and nonreplicating planktonic bacteria. Moxifloxacin (MFX) was potent in preventing biofilm formation and inhibiting the viability of biofilm-resident bacteria. ABM (Azithromycin-Bedaquiline-Moxifloxacin) and CBM (Clofazimine-Bedaquiline-Moxifloxacin) combinations were effective in bacillary load reduction and organ injury alleviation in BALB/c mouse model.

Conclusions: ABM and CBM regimens show great promise against Mabs in vivo. We strongly recommend carrying out additional clinical trials to explore their efficacy.

Background: Optimizing the silage processing technology for mulberry is essential to improve the utilization efficiency of this feed resource. This study investigated the effects of a wilting pretreatment and silage additives on fermentation dynamics, microbial community structure, metabolites, and in situ ruminal degradation characteristics of whole-plant mulberry silage. A 2 × 3 factorial arrangement with two conditions (62% vs. 73% moisture content) and three silage additives (control, Lactiplantibacillus plantarum (LP), and organic acids (OA)) was applied in a completely randomized design with 6 replications. All samples were ensiled for 60 days before analysis.

Results: The wilting procedure increased lactic acid and crude protein (CP) contents while lowering pH (P < 0.05). Both OA and LP additive treatments reduced pH and increased CP content in mulberry silage (P < 0.05). The LP treatment specifically reduced ammonia nitrogen and pH and improved lactic acid content (P < 0.05). The interaction between wilting and additive led to decreases in acetic acid and neutral detergent fiber contents (P < 0.05). 16S rRNA sequence revealed that LP inoculation enriched the relative abundance of Lactiplantibacillus while suppressing that of Enterococcus (P < 0.05). Lactiplantibacillus abundance was positively correlated with contents of lactic acid, CP, and beneficial metabolites L-arginine and salicin (P < 0.05). These two differential metabolites were enriched in phosphotransferase system and arginine biosynthesis pathways (P < 0.05). The in situ ruminal study further confirmed that wilting improved DM digestibility while reducing methane and ammonia nitrogen concentration. The LP treatment also reduced ruminal ammonia nitrogen level (P < 0.05).

Conclusion: The combined application of a wilting pretreatment and LP inoculant presents a validated and effective approach to comprehensively improve the fermentation quality and nutritive value of mulberry silage.

Background: Antibiotic-resistant Klebsiella pneumoniae (KP) poses a serious global public health threat. However, research on the resistance mechanisms and accompanying phenotypic changes in carbapenem-resistant hypervirulent KP (CR-hvKP) under antibiotic treatment remains limited. This study aims to investigate the resistance mechanisms of CR-hvKP to ceftazidime-avibactam (CAZ-AVI) and its concomitant phenotypic shifts, employing an in vitro induction assay.

Methods: Six ceftazidime-avibactam (CAZ-AVI)-susceptible CR-hvKP clinical isolates were subjected to in-vitro resistance induction. We used pulsed-field gel electrophoresis, whole-genome sequencing, biofilm formation, a Galleria mellonella infection model, and in-vitro competitive growth assays to characterize the virulence and adaptive changes of the isolates.

Results: CAZ-AVI-resistant CR-hvKP demonstrated enhanced biofilm formation capacity, but the G. mellonella infection model indicated a decrease in virulence of the drug-resistant strain. While resistant strains exhibited diminished competitive fitness in vitro, growth curves did not differ significantly. Genomic characterization identified both resistant and susceptible isolates as ST11, with resistant isolates exhibiting an expanded resistance gene profile, primarily involving KPC-2 variants. All strains carried typical virulence determinants, including iroE (a glycosidase gene within the salmochelin siderophore system), iucABCD (the aerobactin biosynthesis operon), and iutA (the gene encoding the outer membrane receptor for ferric-aerobactin).

Conclusions: CAZ-AVI resistance acquisition in CR-hvKP primarily occurs through KPC-2 mutations. Strains harboring such mutations exhibit enhanced biofilm formation capacity but attenuated virulence and competitiveness. Research into these adaptive changes will facilitate the development of improved clinical strategies for the treatment and control of carbapenem-resistant hypervirulent Klebsiella pneumoniae.

Background: In recent years, the inappropriate use of antibiotics has led to the widespread emergence of multidrug-resistant Klebsiella pneumoniae (MDR-K. pneumoniae), resulting in infections that are increasingly challenging to manage clinically. Bacteriophages (phages) are emerging as promising alternatives to antibiotics. This study aimed to isolate and characterize lytic phages targeting MDR-K. pneumoniae, providing biological resources and experimental data for phage-based control of MDR-K. pneumoniae infections.

Results: A lytic phage, designated vB_KpnA_Pkp-1 (Pkp-1), was successfully isolated. TEM revealed that Pkp-1 belongs to the Caudoviricetes class, featuring an icosahedral head (62 ± 2 nm) and a short tail (17 ± 1 nm), with plaques displaying clear centers and translucent halos. Pkp-1 exhibited strict specificity for porcine-derived ST967 K. pneumoniae isolates. Its optimal MOI was 0.00001, with a latent period of 25 min and a burst size of 108 PFU/cell. Pkp-1 demonstrated high stability at 40 °C-60 °C and pH 4.0-11.0, effectively inhibiting planktonic bacteria and suppressing/eradicating biofilms. Genomic analysis revealed a 38,455 bp dsDNA genome with 48 open reading frames (ORFs), functions of 30 proteins were predicted (e.g., DNA polymerase, tail fiber), while the remaining 18 proteins were annotated as hypothetical. Genomic analysis confirmed the absence of virulence, lysogeny-related, and antibiotic resistance genes. Pkp-1 shared high identity with phages phi1_146013 (98.71%) and P7124 (97.25%). Recombination analysis revealed 19 recombination events, with two specifically located within the tail protein gene. Notably, this tail protein gene exhibits significant divergence from those of other classified Kayfunavirus phages.

Conclusion: The lytic phage Pkp-1 represents a novel recombinant chimera within the Kayfunavirus genus, characterized by rapid replication, strict host specificity, environmental resilience, potent bactericidal activity, and biofilm clearance capability. The significant divergence of its tail protein from other Kayfunavirus phages suggests unique adaptive evolution. It represents a novel recombinant chimeric phage of the genus Kayfunavirus, with multiple recombination events in its genome. Its tail protein exhibits significant differences from those of other phages in the genus Kayfunavirus, indicating that it possesses adaptive evolutionary characteristics. These attributes position Pkp-1 as a potential biocontrol agent against MDR-K. pneumoniae infections, particularly in livestock and clinical settings. Further studies on in vivo efficacy and safety are warranted.

Diet regulates the gut microbiota, which in turn affects animal performance, but how diet shapes the animal performance and gut microbiota remains largely unknown. To fill this gap, the author conducted a comprehensive study of the influence of total mixed ration (TMR) or fermented TMR (FTMR) on the animal performance and gut microbiome. Sixteen Simmental male cattle were randomly allocated to two treatments (one cattle per pen). The animals were fed with the TMR and FTMR diets respectively. The results showed that the contents of ADF, NDF, cellulose and total cellulose in the FTMR were significantly decreased (p < 0.05), the average daily weight gain of the Simmental male cattle shows an increasing trend (TMR: 0.31 vs. FTMR: 0.62), while no significant (p = 0.2382) difference was found between the two treatments. The metagenomics analysis showed significant (p < 0.05) difference in the α-diversity and β-diversity, and the dominant bacterial genera were Weissella, Lactiplantibacillus, Levilactobacillus and Companilactobacillus. The 16S rRNA sequencing indicated that a significant (p = 0.018) difference in the bacterial communities between the cattle fed with TMR or FTMR diet, while no significant (p < 0.05) differences were detected on the primary genus. It can be found that the FTMR diet increased the average daily gain of cattle by improving the chemical composition and microbial functional profile of the FTMR diet, and affected the growth performance of cattle.