Frontiers in Microbiology最新文献

Microbial fermentation is an established technology that is becoming increasingly used to produce key food components. Among the various microorganisms used, yeasts play crucial roles due to their efficiency in synthesizing a wide range of industrially important compounds. The growing demand for sustainable, locally sourced, and animal-free food ingredients has increased the focus on yeast biomass and its derivatives. These yeast-based products, such as food emulsifiers, are a promising next-generation of food components, offering advantages like a low risk of allergenicity. Yeast biomass-based fractions have been effectively used as emulsifiers in various food products including in dairy, meat, bakery, meat alternatives, mayonnaises and salad dressing, with effective properties demonstrated in a range of oil-in-water, water-in-oil, and Pickering emulsion models. Both whole cell biomass and yeast cell fractions such as the yeast cell wall, mannoproteins, glucans, exopolysaccharides and other yeast-derived compounds have been demonstrated to function as effective emulsifiers. An increasingly large number of yeasts, beyond just Saccharomyces cerevisiae, have been studied as potential sources of these emulsifiers with the extraction and purification methods employed depending on the specific emulsifier targeted, the required purity, and the intended application. Efficient, cost-effective, and sustainable processes are key to enabling industrial-scale production of these emulsifiers, as such this article reviews the potential yeast-derived food emulsifiers, lists the various yeast species investigated to date, examines the extraction and purification methods, and highlights the potential food applications of these yeast-derived emulsifiers.

Antimicrobial resistance (AMR) is a critical global health threat. This phenomenon involves the diffusion of bacteria and genes among humans, animals and the environment. In particular, the presence of third generation cephalosporin (3GC)-resistant Enterobacteriaceae in natural environments is of high concern as they are classified as critical-priority pathogens of public health importance. In this work we studied the relation among plastic pollution in freshwater ecosystems, the spread of multidrug-resistant (MDR) bacteria and diffusion of antibiotic resistance genes (ARGs). Caged plastic fragments were deliberately introduced in a river of central Italy. Plastic samples were collected and analyzed in parallel with river water samples. Out of 267 cefotaxime (CTX) resistant isolates obtained, 65 CTX-resistant Enterobacteriaceae were selected for further analysis. Most of the isolates (75% of plastic-derived and 84% of water-derived isolates) were MDR with seven being carbapenem-resistant enterobacteria (CRE). Five of them synthesize KPC (Klebsiella pneumoniae carbapenemases) enzymes, and two strains were positive for metallo-β-lactamases (NDM). Among the KPC producers, three isolates were identified as K. pneumoniae sequence type ST1519. Their isolation in a natural ecosystem is alarming because they can potentially re-enter human populations through environmental pathways. Shotgun metagenomic analysis provided a comprehensive snapshot of the microbial communities associated to the plastisphere, revealing dominance of families such as Comamonadaceae, Sphaerotilaceae, and Flavobacteriaceae, which play key roles in environmental biofilm formation and stability. The resistome analysis highlighted the presence of ARGs conferring resistance to clinically important antibiotics, such as beta-lactams, vancomycin, and tetracyclines, alongside mobile genetic elements (MGEs) such as integrons, which facilitate the horizontal transfer of resistance genes. This study provides crucial experimental evidence that riverine plastic debris acts as a genetic reservoir and could act as an efficient vehicle for the accumulation and transfer of clinically relevant resistance determinants.

Background: Clostridioides difficile infection (CDI) is a leading cause of healthcare-associated diarrhea. Although gut microbiota dysbiosis is central to CDI, the specific commensal species that confer protection are not well defined.

Methods: We performed 16S rRNA sequencing on fecal samples from a clinical cohort of 30 CDI patients, 30 non-CDI diarrhea patients, 27 asymptomatic C. difficile carriers, and 30 healthy controls. To functionally validate the clinical finding, an in vitro anaerobic co-culture system was established between the Odoribacter splanchnicus type strain and C. difficile. Toxin protein levels in the supernatant were quantified by ELISA at multiple time points (24, 48, and 72 h). Sporulation was assessed via ethanol resistance assays, and the expression of toxin genes (tcdA/tcdB) was measured by quantitative PCR (qPCR).

Results: Clinical analysis revealed a significant negative correlation between the abundance of Odoribacter splanchnicus and CDI severity. In vitro, a high initial ratio of O. splanchnicus significantly suppressed C. difficile toxin production during the stationary phase, without inhibiting bacterial growth. This reduction in vitro levels was accompanied by a concurrent increase in sporulation and was preceded by a downregulation of tcdB gene expression.

Conclusion: This work positions O. splanchnicus as a highly promising candidate for the development of next-generation, defined microbial therapeutics and provides a mechanistic foundation for future anti-virulence approaches to combat CDI.

Introduction: C1 gas bioconversion for single-cell protein (SCP) production offers dual environmental benefits by mitigating greenhouse gases and generating protein resources. This study systematically determined optimal methane-to-air ratios (CH₄:air, v/v) for enhancing methane-oxidizing bacteria (MOB) growth and SCP yield under three distinct nitrogen assimilation modes: nitrate-driven pMMO expression, ammonium-driven sMMO expression, and nitrogen-fixing sMMO expression.

Methods: Experiments were conducted under three nitrogen assimilation regimes: nitrate-fed pMMO expression, ammonium-fed sMMO expression, and nitrogen-fixing sMMO expression systems. By adjusting the volumetric ratio of methane to air, the effects on bacterial growth, biomass accumulation, specific growth rate, and key enzymatic activities were evaluated. Measured parameters included OD₆₀₀, cell dry weight, specific growth rate (μ_max), and nitrogenase activity in the nitrogen-fixing system. Data from repeated measurements were subjected to statistical analysis to clarify the regulatory role of gas ratios on metabolic pathways.

Results: In the nitrate-fed pMMO expression system, a CH₄:air ratio of 1:3 yielded optimal growth, with an OD₆₀₀ of 1.11, cell dry weight of 0.44 ± 0.023 g/L, and μ_max of 0.022 h^-1. Similarly, the ammonium-fed sMMO expression system achieved best performance at the same ratio (OD₆₀₀ 1.19, biomass 0.56 ± 0.014 g/L, μ_max 0.025 h^-1). In contrast, the nitrogen-fixing sMMO expression system performed better at a lower oxygen ratio (CH₄:air = 1:2), reaching an OD₆₀₀ of 0.62, biomass of 0.28 ±0.008 g/L, nitrogenase activity of 1.09 nmol/(min mg protein), and μ_max of 0.016 h^-1).

Discussion: The results reveal oxygen's critical dual role: higher O₂ levels enhance methane oxidation by activating the copper-dependent catalytic site of pMMO but simultaneously and irreversibly damage the oxygen-sensitive nitrogenase ssential for N₂ fixation, suppressing its activity. Conversely, lower O₂ protects nitrogenase but limits pMMO efficiency. This creates a fundamental metabolic trade-off where the optimal CH₄/O₂ ratio balances these opposing effects, strategically partitioning cellular energy either toward efficient methane assimilation (favored by higher O₂) or toward the ATP-intensive process of nitrogen fixation (requiring lower O₂). These identified gas-ratio thresholds provide actionable parameters for designing scaled SCP bioproduction systems, enabling effective coupling of industrial methane mitigation with sustainable protein synthesis through gas-phase engineering.

Methylmercury (MeHg), a bioaccumulative neurotoxic heavy metal, substantially threatens environmental and human health. In natural environments, MeHg formation and degradation are primarily mediated by microorganisms containing hgcAB, merA, or merB genes. However, these genes have not been simultaneously analyzed in open-ocean samples. This study aimed to investigate the distribution and phylogeny of functional genes associated with mercury (Hg) methylation (hgcA and hgcB), demethylation (merB), and reduction (merA), as well as dissolved total Hg (THg) and MeHg concentrations in the western North Pacific Subtropical Gyre (WNPSG) using metagenomic analysis. Although THg levels varied across sampling sites, MeHg concentrations consistently increased with depth. A strong correlation between dissolved MeHg and apparent oxygen utilization indicated a link between Hg methylation and microbial respiration. hgcA, merB, and merA were predominantly detected at depths of 500-1,500 m, where MeHg concentrations peaked, indicating active microbial Hg speciation within mesopelagic layers. A higher abundance of hgcA than merB suggests that microbial Hg methylation may surpass demethylation in this region. Phylogenetic analyses of hgcAB identified the Nitrospina lineage as dominant Hg methylators. Metabolic pathway analyses of metagenome-assembled genomes (MAGs) showed that Nitrospina harboring hgcAB possesses the nitrite reductase pathway, suggesting a linkage between Hg methylation and nitrogen cycling. MAGs with hgcA affiliated with Myxococcota (Deltaproteobacteria) exhibited a strong association with sulfur cycling. Diverse lineages harboring merB and merA genes were identified, suggesting that MeHg demethylation and Hg(II) reduction likely co-occur. Methanogenesis pathways in some Alphaproteobacteria with merB or merA suggest a potential connection between methane production and MeHg degradation and Hg(II) reduction. These findings provide novel insights into the intricate interactions between microbial communities, functional gene distributions, and Hg biogeochemical cycling in the WNPSG.

Background: Lycopene, a vital antioxidant, can reduce oxidative damage to cells caused by reactive oxygen, prevent cancer, lower blood cholesterol levels, and mitigate cardiovascular diseases. We screened a lycopene-producing strain of the genus Polymorphospora, designated A560, and discovered that its metabolic pathway lacks the lycopene β-cyclase gene crtY, which is responsible for converting lycopene into β-carotene. The absence of crtY alleviates the challenges associated with the addition of a cyclooxygenase inhibitor, which previously hindered the large-scale accumulation of lycopene in Blakeslea trispora.

Method: This study was conducted to enhance lycopene production in strain A560 through a multi-stage optimization strategy, focusing on improving extraction efficiency and optimizing culture medium components. The extraction conditions were optimized by testing different solvent systems (acetone/n-hexane/ethanol), extraction temperatures, and durations. Subsequently, a uniform design (UD) was applied to systematically optimize the composition of the culture medium to maximize lycopene yield.

Results: The extraction conditions were systematically optimized. A crushing duration of 4 min was identified as optimal for complete cell disruption. The most efficient solvent system was determined to be n-hexane/ethanol (2:1, v/v) at 60 °C, which yielded 62.05 ± 4.68 mg/L of lycopene-a 37.13% increase over extraction with acetone at room temperature (45.25 ± 0.98 mg/L). Subsequent medium optimization through a uniform design revealed that soluble starch and glycerol were critical components. Cultivation in the theoretically optimized medium predicted by the model resulted in a lycopene yield of 142.54 ± 8.58 mg/L. Finally, regulating the oxygen supply by adjusting the flask's volume of air to a medium volume (Va/Vm) ratio proved crucial. The highest lycopene production of 201.44 ± 6.23 mg/L was achieved at a Va/Vm ratio of 1.5, which marks a 224.64% improvement over the yield obtained after the initial extraction optimization (62.05 ± 4.68 mg/L).

Conclusion: The extraction and fermentation processes for lycopene production in Polymorphospora sp. A560 were successfully optimized, resulting in significantly enhanced yields. These results demonstrate that strain A560 is a promising microbial resource for the fermentative production of lycopene.

[This corrects the article DOI: 10.3389/fmicb.2023.1252785.].

Introduction: Microbial additives can improve silage quality in lowland areas. However, Saccharomyces cerevisiae and Lactic Acid Bacteriacan efficacy on whole-plant maize silage under Tibet's hypoxic and cold environment, have not been explored.

Methods: In this experiment, whole corn plants cultivated in Dazi District, Lhasa City, Xizang (Tibet) Autonomous Region, were selected as silage raw materials. The treatment group was added 0.5 kg of microbial additives per ton of silage. The addition levels for both Saccharomyces cerevisiae and Lactic Acid Bacteria were ≥ 1 × 107 CFU·g-1 FM). The quality of silage and its in vitro fermentation characteristics were determined on 0, 30 and 60 days of fermentation, respectively. Subsequently, dairy cows were fed with silage after 60 days of fermentation to evaluate milk production and milk quality.

Results: The results indicated that the lactic acid content in the treatment group was increased significantly on 30 and 60 days of fermentation (p < 0.05). In addition to Simpson's index, alpha diversity was significantly affected by the fermentation day × treatment interaction (p < 0.05). At 60 days of fermentation, the abundance of Firmicutes phylum in the treatment group was significantly higher than that in the control group (p < 0.05). The abundance of genera such as Acetobacter and Latilactobacillus was significantly decreased (p < 0.05), while the abundance of the genus Weissella was significantly increased (p < 0.05). Dairy cows were fed 60-day maize silage, the milk protein content and total solid content in the treatment group were significantly higher than that in the control group (p < 0.05). The levels of dry matter degradation rate, ammonia nitrogen and total volatile fatty acids in the in vitro fermentation of maize silage in the treatment group on the 60th day of fermentation were significantly higher than that in the control group (p < 0.05).

Conclusion: In Xizang (Lhasa, China), the addition of microbial additives has significantly improved the quality and nutritional value of whole corn silage plants and enhanced the milk quality of local dairy cows. This provides a theoretical basis for the application of microbial additives from the Qinghai-Tibet Plateau to agricultural crops.

To evaluate the biocontrol potential of the cell-free fermentation filtrate (CFFF) of Bacillus atrophaeus strain YL84 against Fusarium oxysporum f. sp. vasinfectum (FOV), this study systematically investigated the effects of the CFFF at various dilution ratios on FOV mycelial growth, conidial germination, cellular nucleic acid leakage, and malondialdehyde (MDA) content. Furthermore, the environmental stability of its antifungal activity was assessed. In addition, a dual-culture assay was conducted to evaluate the antagonistic activity of strain YL84 against FOV. The results of the dual-culture assay showed that strain YL84 significantly inhibited the growth of FOV, with an inhibition rate of 81.06%. Subsequently, the YL84 CFFF exerted significant inhibitory effects on FOV mycelial growth and conidial germination across different concentrations, achieving maximum inhibition rates of 75.68% and 77.56%, respectively. Notably, the treated mycelia exhibited a significant increase in cellular nucleic acid leakage and elevated levels of MDA, a product of lipid peroxidation, suggesting that the CFFF may disrupt the integrity of the pathogen's cell membrane. Stability assays revealed that the CFFF possessed substantial tolerance to high temperatures, ultraviolet irradiation, and hypersaline environments, although it remained sensitive to strongly alkaline conditions. Greenhouse pot experiments further confirmed the efficacy of YL84 CFFF in controlling cotton Fusarium wilt, with a maximum control efficacy of 69.21%. Moreover, the treatment induced the upregulation of defense-related enzyme activities in the plants, suggesting that the CFFF may function through both direct antifungal action and the elicitation of host-induced resistance. Component identification via Ultra-Performance Liquid Chromatography-Ion Mobility-Quadrupole Time-of-Flight Mass Spectrometry (UPLC-IMS-Q-TOF-MS) suggested that the filtrate is rich in structurally diverse compounds that were putatively identified as potential antimicrobial substances, predominantly classified as terpenoids and their derivatives. In conclusion, this study provides a systematic evaluation and supporting evidence for the further development of B. atrophaeus YL84 as a biocontrol agent.