AIMS Microbiology最新文献

The production of biofuels and chemicals from D-xylose is a promising option as D-xylose is the second most abundant sugar after D-glucose in lignocellulosic biomass. In microbes, efficient D-xylose uptake is a prerequisite for its utilization. Therefore, increasing D-xylose uptake efficiency by manipulation of D-xylose transporters would be an attractive strategy to improve fungal cell factories that use D-xylose as a substrate. In this study, we compared the contribution of three D-xylose transporters (XltA, XltB, XltD) from Aspergillus niger to overall D-xylose uptake at two D-xylose concentrations. XltA and XltD contributed similarly to D-xylose uptake, while the role of XltB was minimal. However, even in the absence of all three transporters, D-xylose uptake still occurred, indicating the involvement of additional transporters. Surprisingly, there was no clear correlation between the kinetic characteristics of the transporters nor the expression profile of their corresponding genes with their influence on D-xylose transport. This suggests that selection of transporters for metabolic engineering of filamentous fungal cell factories based solely on kinetic parameters originating from heterologous expression of the transporters in yeast may not be a very efficient and reliable strategy.

Enteroaggregative Escherichia coli (EAEC) causes acute and persistent diarrhea. Its antimicrobial resistance and strong biofilm formation hinder treatment, highlighting the need for new therapies. This study evaluated the antimicrobial efficacy of 1,10-phenanthroline-5,6-dione (phendione) and its copper [Cu(phendione)₃](ClO₄)₂.4H₂O (Cu-phendione) and silver [Ag(phendione)₂]ClO₄ (Ag-phendione) complexes against planktonic and biofilm-forming EAEC cells. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) values were determined for planktonic cells of 35 clinical EAEC isolates, revealing potent antibacterial activity by all test compounds, with Cu-phendione showing the greatest efficacy, followed by Ag-phendione and phendione. Most combinations of Cu-phendione or Ag-phendione with either ampicillin or tetracycline exhibited additive effects through checkerboard assays, whereas time-kill experiments revealed synergistic interactions between the complexes and those classical antibacterial agents. Minimum biofilm inhibitory concentration (MBIC) analysis identified Cu-phendione as the most effective compound for disarticulating biofilm formation (geometric MBIC = 14.61 µM), followed by Ag-phendione (24.69 µM) and phendione (67.08 µM). Notably, Cu-phendione eradicated biofilms in 24 isolates (68.6%), while Ag-phendione and phendione achieved eradication in 11 (31.4%) and 6 (17.1%) isolates, respectively. Furthermore, the test complexes were able to disrupt established mature biofilms, as demonstrated by the crystal violet assay and scanning electron microscopy. In combination therapy, complete biofilm eradication was achieved in all clinical isolates tested when Cu-phendione was paired with cefoxitin, tobramycin, tetracycline, or ciprofloxacin. Collectively, phendione-derived complexes, particularly Cu-phendione, represent promising candidates for the treatment of EAEC infections in planktonic and biofilm-associated states.

The emergence and applications of probiotic species across industries are growing rapidly, requiring the isolation, identification, and robust characterization of new strains. Enterococcus faecium, a dominant species of the genus Enterococcus, is widely distributed and has a prominent role in biotechnological applications. The probiotic potential of E. faecium is well established, and various strains have been commercially available. In this study, we aimed to provide a strategic road map to explore the probiotic potential, postbiotic production, antioxidant activities, aggregation properties, and functional characterization of the selected E. faecium strains (n = 6) isolated locally. All selected strains demonstrated significant probiotic potential, with stress tolerance, aggregation, and postbiotic production. They were free from biogenic amines while exhibiting notable free radical scavenging and reducing activities. Additionally, their ability to adhere to fibrinogen and mucin indicates enhanced potential for mucosal colonization, competitive exclusion of pathogens, and improved host interaction. All strains tolerated digestive stress, two strains (E. faecium Se142 and E. faecium F25) produced slime, and all exhibited antioxidant activity. The influence of digestive enzymes on enterocins, the production of arginine hydrolases, and the impact of glycine, arginine, and glucose on their growth performance reflected positive attributes. These attributes indicate their potential as ideal candidates for developing new probiotic formulations, with intended food and biotechnological applications. In the future, genomic and in vivo validation studies are warranted.

Objective: An increasing number of international researchers are focusing on the taxonomic composition of fecal microbiota and its correlation with disorders. Thousands of researchers compare conditionally healthy cohorts to those with specific diseases to identify potential markers. However, clinical application requires assessing the feasibility of synthesizing these findings and establishing reference intervals for normal gut flora, at least at higher taxonomic levels.

Design: This study involves a systematic review and meta-analysis of human gut microbiota research based on 16S rRNA gene next-generation sequencing (NGS). Relevant research was sourced following the PRISMA guidelines. Descriptive statistics, linear regression analysis by weighted least squares method, Mann-Whitney test, and Benjamini-Hochberg procedure adjustments were employed. The study has been registered with PROSPERO (CRD42023431467).

Results: Of the 4,346 studies initially identified, 86 publications involving 20,748 unique participants met the quality criteria and were included in the analysis of the impact of fecal sample preparation on taxonomic composition. The phylotype composition, in relation to preprocessing methods and cohort locations, are presented as relative abundances (%): Bacillota (median 49.5-59.6%), Bacteroidota (28.0-33.4%), Pseudomonadota (3.4-5.9%), Actinomycetota (2.3-3.7%), Verrucomicrobiota (0.5-1.0%), Fusobacteriota (maximum 4.6%), and Euryarchaeota (maximum 2.11%). The content of 27 key family-level representatives was also evaluated. The well-known hypothesis regarding the influence of the homogenization stage on taxonomic composition was examined using generalized results.

Conclusion: While supported by a strong theoretical basis and evidence from individual practical cases, none of the phyla showed a statistically significant association and consistent relationship with sample preparation or cohort location when generalizing across studies after the two exceptionally large cohorts exclusion, both originating from a single research group. These findings underscore the need for strict methodological standardization in microbiome studies. Key features of the 16S NGS process accounting for these results are outlined, along with proposed optimizations for microbiome research.

Rosmarinus officinalis has attracted significant attention due to its broad-spectrum antimicrobial activity, largely attributed to its bioactive essential oils (EOs). Several studies indicate that the flowering period is crucial for harvesting rosemary's aerial parts for optimal EO extraction. However, its prolonged flowering period complicates the determination of an optimal harvest time, potentially affecting yield, chemical composition, and efficacy. This study provides, for the first time, a systematic month-by-month evaluation of EO yield, chemical composition, and synergistic antimicrobial potential of rosemary cultivated under arid Mediterranean conditions during its flowering period (September to March). EO samples were analyzed by GC-MS and assessed for antimicrobial activity against clinically relevant pathogens, including S. aureus, E. coli, S. enterica, and four Candida species. The synergistic potential was further evaluated with two conventional antimicrobials (streptomycin and amphotericin B). The results showed that the EO yields ranged from 1.73% to 2.75%, with a clear peak in autumn. GC-MS analysis identified 31 compounds, dominated by 1,8-cineole (27.57 ± 0.76%-36.28 ± 0.26%), α-pinene (15.36 ± 0.23%-28.97 ± 0.10%), and camphor (7.12 ± 0.00%-15.37 ± 0.12%), confirming the prevalence of the 1,8-cineole/α-pinene/camphor chemotype. Antimicrobial assays demonstrated stronger activity against fungal strains, particularly C. krusei and C. albicans, with enhanced efficacy observed in EOs collected in October-November. Synergy assays showed significant potentiation of streptomycin activity, particularly against E. coli in autumn, with up to a 32-fold increase in efficacy. In contrast, only limited synergistic effects were observed with amphotericin B. Overall, our findings emphasize the clinical relevance of optimizing harvest timing, as autumn-harvested rosemary EOs exhibit the greatest potential as natural antibiotic adjuvants against multidrug-resistant pathogens. Nevertheless, the partial antagonism with amphotericin B highlights the need for strain-specific compatibility assessments to avoid compromising drug efficacy in combinatory therapies.

Probiotics are living microbes that impart overall health benefits when introduced appropriately. They play important roles in enhancing immunity, inhibiting harmful bacteria, balancing the gut microbiota, and increasing poultry growth performance. In this manuscript, we address the classifications of probiotics, the compositions and functions of the gut microbiota in poultry, and examine the connection between probiotics and the gut microbiota and their roles in promoting the poultry growth. Probiotics are widely used in poultry production, including Lactobacillus, Bacillus, Bifidobacterium, Streptococcus, Enterococcus, and Clostridium, which can exert beneficial effects through various mechanisms, such as increasing the abundance and diversity of the gut microbiota, promoting the secretion of digestive enzymes and antimicrobial substances, optimizing immune microenvironment homeostasis, and enhancing the intestinal barrier. Furthermore, new probiotic products are emerging in poultry production, including prebiotics, synbiotics, and postbiotics. Other novel approaches are used in poultry production to improve their growth and immune performances and inherit beneficial microbial communities, including the integration of probiotics with gut health-promoting agents and the genetic selection of microbiota. The paper demonstrates the potential of probiotics as effective alternatives of antibiotic growth promoters (AGPs) for the promotion of growth performance and intestinal health in poultry production.

In Saccharomyces cerevisiae, the molecular chaperone proteins Ssb1 and Ssb2 (Ssb1/2) and the cochaperone ribosome-associated complex (Zuo1 and Ssz1) localize around the ribosome tunnel exit, assisting in the maturation of nascent polypeptides. Exogenous expression of the Zuo1 C-terminus or the Ssz1 N-terminus-but not Ssb1/2-independently activates the transcription factor Pdr1 (but not Pdr3), enhances the transcription of the ATP-binding cassette (ABC) transporter genes PDR5, SNQ2, and YOR1, and increases pleiotropic drug resistance. Furthermore, upregulation of ABC transporter genes by ZUO1 and SSZ1 leads to the release of quorum-sensing molecules, which cause cell growth arrest during diauxic shifts. In this study, we examined whether SSB1/2 are required for the expression of ABC transporter genes and the release of quorum-sensing molecules that lead to cell growth arrest during diauxic shifts. Our results show that Ssb1/2 increased the mRNA levels of PDR5, SNQ2, and YOR1 during the late logarithmic growth phase and increased resistance to cycloheximide and fluconazole, possibly via the same pathway as Zuo1 or Ssz1. Furthermore, Ssb1/2 induced PDR5 expression and resistance to cycloheximide and fluconazole, possibly via the same pathway as Pdr3 (but not Pdr1). In addition, it was suggested that Ssb1/2 are involved in the release of quorum-sensing molecules into the culture medium, which could signal cell growth arrest during diauxic shifts. This work provides useful knowledge regarding genetic interactions between the ribosome-associated molecular chaperone and cell growth arrest during diauxic shifts.

Human papillomavirus (HPV) vaccines elicit specific serum antibodies that confer long-lasting protection and may reduce HPV-related cancers. However, helminthic infections such as chronic schistosomiasis infection at the time of HPV vaccination are known to alter immune responses. This study investigated the impact of chronic S. mansoni infection on immune responses to the HPV vaccine in olive baboons. Baboons were assigned to three groups: (1) untreated S. mansoni-infected, (2) S. mansoni-infected and treated with Praziquantel, and (3) uninfected controls. All received two doses of the Cervarix HPV vaccine four weeks apart. Immune responses were measured using flow cytometry and ELISA. Gardasil® quadrivalent HPV vaccine antigen was used in both ELISA and PBMC stimulation for cytokine ELISA supernatants. HPV-specific whole IgG levels significantly increased in all groups except for the untreated S. mansoni-infected group, whose increase was significant after the second dose. Similarly, IgG1 levels increased only after the second dose. There was no significant difference between the treated and untreated infected groups. These findings emphasize the importance of a booster dose for strong antibody production and suggest that a delayed HPV-specific whole IgG response in untreated S. mansoni-infected individuals reinforces the need for booster HPV vaccination in endemic regions. The results affirm the vaccine's effectiveness in S. mansoni endemic areas.

Fish meal (FM) has long been used as a staple protein source in aquafeed owing to its balanced amino acids, excellent feed conversion, and improved palatability and digestibility. However, the use of FM in aquafeed formulation is facing difficulties due to concerns regarding availability, price, overfishing, and sustainability. Thus, there is a growing interest in seeking alternative protein sources from plant and animal by-products to partially or fully replace FM in aquafeed. Challenges such as lower nutrient bioavailability, high antinutritional factors, indigestible materials, microbial contaminants, and lower palatability issues have limited the incorporation of these protein sources into aquafeed. The application of solid-state fermentation (SSF) strategy represents a sustainable method to address these problems by improving aquafeed quality and introducing health-promoting beneficial microbes. Moreover, numerous studies have shown that SSF enhances growth, feed utilization, health status, immune system, and disease resistance in aquaculture species. At present, molecular approaches such as transcriptomics and proteomics techniques are widely used tools for evaluating the impacts of SSF on fish and shrimp. They provide valuable insights into the mRNA transcripts and proteomes related gene expressions associated with growth, immunity, and stress response. In this article, we outline the requirements for SSF and discussed its role in ameliorating growth, health, immunity, and disease resistance in farmed species. We also provide up-to-date information about the utilization of SSF technology to modulate the transcriptomics and proteomics profiles in fish and shrimp. The complied evidence aims to support future research efforts and encourage the development of fermented feed as a functional dietary option for promoting sustainable aquaculture practices.