Search Results (90)

Background/Objectives: Celiac disease (CD) is an autoimmune disorder characterized by small intestinal enteropathy triggered by gluten ingestion, often associated with gut dysbiosis. The most effective treatment is strict adherence to a gluten-free diet (GFD), which alleviates symptoms. This study uniquely integrates taxonomic, functional, and resistance profiling to evaluate the gut microbiota of women with CD on a GFD. Methods: To evaluate the long-term impact of a GFD, this study analyzed the gut microbiota of 10 women with CD on a GFD for over a year compared to 10 healthy controls with unrestricted diets. Taxonomic diversity (16S rRNA gene sequencing and the analysis of α and β-diversity), metabolic functionality (Biolog EcoPlates^®), and antibiotic resistance profiles (Cenoantibiogram) were assessed. Results: Metagenomic analysis revealed no significant differences in taxonomic diversity but highlighted variations in the abundance of specific bacterial genera. Women with CD showed increased proportions of Bacteroides, Streptococcus, and Clostridium, associated with inflammation, but also elevated levels of beneficial genera such as Roseburia, Oxalobacter, and Paraprevotella. Despite no significant differences in metabolic diversity, higher minimum inhibitory concentrations (MICs) in women in the healthy control group suggest that dietary substrates in unrestricted diets may promote the proliferation of fast-growing bacteria capable of rapidly developing and disseminating antibiotic resistance mechanisms. Conclusions: These findings indicate that prolonged adherence to a GFD in CD supports remission of gut dysbiosis, enhances microbiota functionality, and may reduce the risk of antibiotic resistance, emphasizing the importance of dietary management in CD. Full article

The carbon metabolism activity of rhizosphere soil microbial communities is an essential indicator for assessing soil ecosystem health, as it directly affects soil nutrient cycling and the stability of organic matter. However, there is a limited understanding of the carbon metabolism characteristics of rhizosphere soil microorganisms in alfalfa (Medicago sativa L.) of different ages and their relationships with soil physicochemical properties. This study used Biolog EcoPlates to evaluate the carbon metabolism activity, functional diversity, and carbon-source utilization preferences of rhizosphere soil microbial communities in 5-, 7-, and 9-year-old alfalfa grasslands on the semi-arid Loess Plateau of western China. We analyzed the relationships between soil physicochemical properties and microbial carbon metabolism characteristics, considering their potential covariation. The results showed that, with the extension of alfalfa planting years, the rhizosphere soil water content decreased significantly, pH decreased slightly, but soil organic carbon, total nitrogen, and total phosphorus contents increased significantly. The rhizosphere soil microbial community of 9-year-old alfalfa exhibited the highest carbon metabolism activity, Shannon diversity index, and carbon-source utilization. Rhizosphere soil microorganisms from different-aged alfalfa showed significantly different preferences for carbon-source utilization, with microorganisms from 9-year-old alfalfa preferentially utilizing carbon sources such as N-acetyl-D-glucosamine, D-mannitol, and D-cellobiose. Redundancy analysis revealed that soil water content was among the most important factors influencing the carbon metabolism activity of rhizosphere soil microbial communities while acknowledging that the relative contributions of soil water content, organic carbon, and nitrogen require careful interpretation, owing to their potential collinearity. This study demonstrates that, under rain-fed conditions in the semi-arid Loess Plateau, the continuous cultivation of alfalfa for nine years led to a significant decrease in soil water content but enhanced the rhizosphere soil nutrient status and microbial carbon metabolism activity, with no apparent signs of microbial functional degradation, although soil water depletion was observed. These findings highlight the complex interactions among multiple soil factors in influencing microbial carbon metabolism, providing valuable microbiological insights for understanding the sustainability of alfalfa grasslands and a theoretical basis for the scientific management of alfalfa grasslands in the semi-arid Loess Plateau region. Future research should consider longer planting periods to determine the critical age of alfalfa grassland degradation under semi-arid conditions and its associated microbial mechanisms. Full article

Global warming poses a significant threat to lake ecosystems, with high-mountain lakes being among the earliest and most severely impacted. However, the processes affecting water ecology under climate change remain poorly understood. This study investigates, for the first time, the effects of regional warming on three high-mountain lakes, Sulzata, Okoto and Bubreka, located in the Rila Mountains, Bulgaria, by examining shifts in bacterial metabolic capacity in relation to the rate and range of utilizable carbon sources using the Biolog EcoPlate™ assay. Over the last decade, ice-free water temperatures in the lakes have risen by an average of 2.6 °C, leading to increased nutrient concentrations and enhanced primary productivity, particularly in the shallowest lake. Bacterial communities responded to these changes by increasing their metabolic rates and shifting substrate preferences from carbohydrates to carboxylic acids. While the utilization rates of some carbon sources remained stable, others showed significant changes—some increased (e.g., D-galactonic acid γ-lactone and itaconic acid), while others decreased (e.g., α-D-lactose and D-xylose). The most pronounced effects of warming were observed in June, coinciding with the onset of the growing season. These findings suggest that rising temperatures may substantially alter bacterial metabolic potential, contributing to a long-term positive feedback loop between lake nutrient cycling and climate change. Full article

Forest fires critically disrupt soil ecosystems by altering physicochemical properties and microbial structure-function dynamics. This study assessed short-term impacts of fire intensities (light/moderate/heavy) on microbial communities in Larix gmelinii forests one year post-fire. Using phospholipid fatty acid (PLFA) and Biolog EcoPlate analyses, we found the following: (1) fire reduced soil organic carbon (SOC), dissolved organic carbon (DOC), total nitrogen (TN), and available nitrogen/potassium (AN/AK) via pyrolytic carbon release, while heavy-intensity fires enriched available phosphorus (AP), AN, and AK through ash deposition. (2) Thermal mortality and nutrient-pH-moisture stress persistently suppressed microbial biomass and metabolic activity. Moderate fires increased taxonomic richness but reduced functional diversity, confirming “functional redundancy.” (3) Neither soil microbial biomass nor metabolic activity at the fire site reached pre-fire levels after one year of recovery. Our findings advance post-fire soil restoration frameworks and advocate multi-omics integration to decode fire-adapted functional gene networks, guiding climate-resilient forest management. Full article

Compost teas (CTs) can be considered natural microbial consortia, able to enhance biostimulation and defense in crops. This study focuses on two plant-derived CTs and their potential use as eco-friendly biofertilizers for chickpeas and peas, with the broader aim to protect soil fertility. Our experiments demonstrated that the two CTs have biostimulatory or inhibitory effects depending on dilution, target plant species, CT microbial load and metabolism, and age of CT preparation. Peas exhibited positive responses to treatments, while chickpeas could be negatively affected depending on CT concentration. The CT microbial load positively affected biostimulation for both plant species. The metabolic profiles of the CT-associated microbial communities were evaluated using the Biolog EcoPlate™ system. Spearman’s correlation analysis allowed us to ascertain a positive interaction between root elongation and the microbial consumption of specific substrates, namely polymers, erythritol, and L-serine. On the contrary, phenolic compound consumption showed a negative correlation. In chickpeas, root and collar necrosis, estimated with the McKinney index, increased after treatment with CTs at the highest concentration, confirming a phytotoxic effect; but diagnostic analyses demonstrated that the necrosis was also partially attributed to pathogenic Fusarium spp. On the other hand, proper dilutions of treatments determined a decrease in necrosis severity, indicating putative CT biocontrol properties. Full article

During an Antarctic expedition that took place in December 2010–January 2011 in the East Antarctic coastal region, soil samples were collected in aseptic conditions and stored for over a decade in freezers at −20 °C. Due to the shortly afterward passing of the Antarctic researcher in charge, Teodor Negoiță, the samples remained unintentionally frozen for a long period and were made available for research 13 years later. A chemical analysis of soil as well as screening for viable microbial presence was performed; soil analysis was conducted via inductively coupled plasma atomic emission spectroscopy (ICP-AES) and Fourier-transform infrared spectroscopy coupled with attenuated total reflection (FTIR-ATR). The presence of aerobic and facultative aerobic microbiotas was evaluated through a Biolog Ecoplates assay, and isolated strains were 16S sequenced for final taxonomic identification. The results obtained new insights into Antarctic soil characteristics from both chemical and microbiological aspects, even after over a decade of conservation. Full article

Microorganisms play a crucial role in purifying aquaculture water bodies. However, there is limited understanding regarding the core species of bacterial communities in aquaculture ponds and their metabolic functions. Using 16S rRNA gene sequencing technology, network analysis, and Biolog EcoPlates, we identified keystone and core taxa of bacterial communities in Litopenaeus vannamei ponds and investigated their correlations with their community’s carbon source utilization abilities based on Biolog EcoPlates. We found that keystone and core taxa in bacterial communities were significantly correlated with the carbon source utilization abilities of bacterial communities. The positively correlated core taxa include (1) Bacillus, Flavobacterium, Brevibacillus, and Paenibacillus, which are used as probiotics in aquaculture, and (2) Candidatus Aquiluna, Dechloromonas, Sulfurifustis, Terrimicrobium, Alsobacter, and Gemmobacter, which have been reported to play a role in nitrogen removal. Furthermore, the positively correlated Tropicimonas (Rhodobacterales: Rhodobacteraceae) in aquaculture has not yet been applied. By nitrogen degradation experiments in aquaculture wastewater, we confirmed the synergistic relationship between the genera Tropicimonas and Bacillus. The co-introduction of Tropicimonas sediminicola SDUM182003 and Priestia aryabhattai HG1802 or Bacillus subtilis XQ1804 into the aquaculture tailwater reduced the time required for the removal rates of nitrite nitrogen and nitrate nitrogen to reach over 90% by 24–48 h. Our research reveals the correlation between core taxa and community carbon source utilization, indicating that the core taxa of bacterial communities play a crucial role in the metabolic functions of the community, and offering a reference for exploring new bacterial genera with probiotic potential. Full article

Karst regions (KRs) have created significant karst carbon sinks globally through the carbon cycling process involving “water-carbon dioxide-carbonate rock-biota”. Soil organic carbon (SOC) represents a crucial component of these carbon sinks. Microorganisms play a vital role in the soil carbon cycle, influencing the formation and preservation of SOC. Therefore, investigating the carbon metabolism of soil microorganisms in KRs is essential for clarifying the unique biogeochemical cycling mechanisms within these regions. In this paper, soils from karst regions (KRs), mixed regions (MRs) and non-karst regions (NKRs) were collected from citrus orchards in Mao Village, Karst Experimental Field, Guilin City, Guangxi Zhuang Autonomous Region, China. The ability to use different carbon sources was analyzed by Biolog-Eco microtiter plate technique; the number of microorganisms was detected by the plate colony counting method, and the microbial biomass was determined by the chloroform fumigation method. The results showed that the soil bacterial number (5.69 ± 0.39 × 10⁶ CFU/g), microbial biomass carbon (MBC) (608.24 ± 63.80 mg/kg), microbial quotient (SMQ) (3.45 ± 0.18%), and Shannon’s index (H′) (3.28 ± 0.05) of the KR were significantly higher than those of the NKR. The pH showed a significant positive correlation (p < 0.05) with the bacterial number and H′ (p < 0.05); SOC showed a highly significant positive correlation with bacterial number (p < 0.01), and a significant positive correlation with MBC, H′, and average well change development (AWCD) (p < 0.05). Total nitrogen (TN) showed a significant positive correlation with MBC (p < 0.05); available potassium (AK) showed a significant positive correlation with bacterial number and MBC (p < 0.05). Exchangeable calcium (Ca²⁺) demonstrated significant positive correlations with bacterial number, MBC, and H′ (p < 0.05). The above results indicate that soil bacterial number, carbon metabolic ability and diversity were highest in the KR. pH, SOC and exchangeable Ca²⁺ were the main influencing factors for the differentiation of soil microbial carbon metabolic diversity between the KR and NKR. Full article

Dietary patterns, such as the Mediterranean diet (MD) and the Western diet (WD), influence gut microbiota composition and functionality, which play important roles in energy metabolism and nutrient absorption. Objectives: A descriptive cross-sectional study was designed to evaluate the gut microbiota of 19 Spanish adolescents and to investigate the association of MD and ultra-processed food (UPF) intake with microbial diversity and community structure. Methods: Functional diversity of gut microbiota was evaluated using Biolog EcoPlates, taxonomic composition was assessed with 16S rRNA sequencing via MinION, and phenotypic responses to antibiotics were analyzed using the cenoantibiogram technique under aerobic and anaerobic conditions. Results: Adolescents with higher adherence to the MD exhibited greater functional diversity, as per the Shannon–Weaver index. In addition, this group showed higher abundance of bacterial genera previously described as beneficial, such as Paraclostridium, Anaerobutyricum, Romboutsia, and Butyricicoccus. In contrast, adolescents reporting greater UPF intakes had a microbiota composition similar to those with low adherence to the MD, characterized by decreased abundance of beneficial genera. Regarding antibiotic resistance, significant differences were only observed under anaerobic conditions, with individuals with low adherence to the MD showing more sensitivity for most antibiotics tested. Conclusions: These results suggest that the MD promotes a healthier and more balanced gut environment, potentially improving metabolic functions in adolescents. Despite the lack of differences in α-diversity, comparisons of microbial community structure between adolescents following the MD and those with high UPF (characteristic of the WD) showed clear differences in terms of β-diversity. These findings suggest that dietary patterns influence the composition of the gut microbiota in a more complex manner, beyond just taxonomic richness. The outcomes of this exploratory study highlight opportunities for future research to deepen understanding of the long-term health implications of these dietary patterns, as well as the mechanisms regulating the composition, functionality, and phenotypic responses to antibiotics of gut microbial communities. Full article

(1) Background: In recent years, the increasing emergence of multidrug-resistant pathogens in pig farms has begun to pose a severe threat to animal welfare and, by extension, public health. In this study, we aimed to explore the biological characteristics and genomic features of bacteriophages that are capable of lysing porcine multidrug-resistant E. coli, which was isolated from sewage. In doing so, we provided a reference for phage therapies that can be used to treat multidrug-resistant strains. (2) Method: Using the multidrug-resistant E. coli isolate sq-1 as the host bacterium, bacteriophages were isolated and purified from fecal samples using a double-layer agar plate method. The morphology was observed using a transmission electron microscope, and its host range, optimal multiplicity of infection (MOI), one-step growth curve, thermal stability, acid–base tolerance, and in vitro antibacterial ability were tested. Genomic features were analyzed using whole-genome sequencing. (3) Results: A lytic phage named vB_EcoS_Psq-1 (abbreviated as Psq-1) was successfully isolated. Electron microscopy revealed that Psq-1 belongs to the family of long-tailed phages, possessing clear and transparent plaques of approximately 1 mm in diameter. Psq-1 only lyses the host bacterium and does not affect other E. coli strains or other species of bacteria. The optimal MOI for phage Psq-1 was 0.1, with a latent period of 25 min, an exponential growth period of 25 min, and a lysis yield of 44.21 PFU/cell. Its activity remains stable at temperatures between 40 °C and 60 °C and from pH 4.0 to pH 13.0. Psq-1 exhibited a significant inhibitory effect on E. coli in liquid culture medium. The nucleic acid type of phage Psq-1 was dsDNA, with a total genome length of 44,183 bp and a GC content of 52.16%. No known resistance, lysogenic, or virulence-related genes were detected. The whole genome contains 55 open reading frames (ORFs). (4) Conclusions: This study isolated a bacteriophage that is capable of lysing multidrug-resistant E. coli. Characterized by a narrow E. coli lysis range, a long latent period, limited lytic ability, and stable biological properties, this bacteriophage can serve as a reference isolate for E. coli phages and can provide biological materials and data to support research on bacteriophages that are effective against multidrug-resistant porcine E. coli. Full article

There are discrepancies that exist in the effects of different land uses on soil organic carbon (SOC) and soil microbial carbon metabolism functions. However, the impact of land-use type changes on soil microbial carbon metabolism in alpine grassland arid areas is not well understood, hindering our understanding of the carbon cycling processes in these ecosystems. Therefore, we chose three types of land use (continuous reclamation of grassland (RG), abandoned grassland (AG), and natural grazing grassland (GG)) to study the microbial carbon metabolism and its driving factors by the Biolog-ECO method. The results showed that the soil organic carbon content decreased by 16.02% in the RG and by 32.1% in the AG compared to the GG in the 0–20 cm soil layer (p < 0.05). Additionally, microorganisms have the highest utilization efficiency of carbohydrate carbon sources, the average values of average well color development (AWCD) were RG (0.26), AG (0.35), and GG (0.26). In the 0–20 cm soil layer, the Shannon–Wiener and the Simpson indices were 3% and 1% higher in the AG compared to the GG, respectively. The soil TOC/TN and soil available phosphorus (AP) were key factors that affected the diversity of soil microbial and carbon metabolism. They were closely related to land-use types. This study holds that abandoning grasslands accelerates the carbon metabolism of microorganisms, leading to the loss of SOC content. Full article

Soil microorganisms play a significant role in the dynamic regulation of organic matter in soils. To assess the influence of agricultural practices on soil functional profiling, we examined the effect of soil disturbance and plant sequence with different levels of mycotrophy on wheat microbiomes metabolism. Soil samples were analyzed with community-level physiological profiles (CLPP) using Biolog™ Ecoplates. The results of average well color development (AWCD) showed that the degree of mycotrophy of preceding crop and soil disturbance affected the soil microbiome, although no impact on Shannon Evenness Index was observed during the experiment. The Shannon–Wiener Diversity Index showed variations among the different preceding plants, but not in wheat analysis. The pattern of the C sources metabolism also changed differentially regarding plant type and soil disturbance during the experiment, being also different within the highly mycotrophic plants (legume and grass). In the legume, an increase in the metabolism of amine/amides and phenolic acids was observed, whilst in the grass, an increase in the metabolism of phosphate-carbons (P carbon) and carbohydrates was more evident. Principal component analysis showed that a grouping in the distinct phases of the experiment correlated with the widening of the metabolism of amino acids, carboxylic acids, and carbohydrates. The results indicate that soil functional community structure reflects soil agricultural practice conditions. Previous plant types and soil disturbance impacted the soil microbiome metabolic response (AWCD) in wheat, generating different patterns of carbon metabolism related to previous plant mycotrophy. Full article

In the pursuit of environmental sustainability and food security, biochar has emerged as a promising soil conditioner to mitigate continuous cropping obstacles (CCOs). This study explored the use of engineered biochar (WP400) with high adsorption capacity for phenolic acids in celery cultivation. Using liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QTOF/MS) for both target and suspect analyses, along with Biolog EcoPlate™ to track the functional diversity of soil bacteria, the study examined chemical and microbiological interactions at varying WP400 application rates. WP400 enhanced celery growth, reduced disease severity, and adsorbed p-coumaric acid (COU), a potential autotoxin. Additionally, other potential allelochemicals, predominantly fatty acid-related, were identified, suggesting a broader role for fatty acids in allelopathy. WP400 also influenced soil bacterial carbon utilization and altered microbial communities. However, higher WP400 doses (0.8% w/w) may not be beneficial for celery growth and reduced bacterial metabolic potential, indicating limitations to its effectiveness. Proper application of WP400 provides a sustainable solution for alleviating continuous cropping issues, promoting both environmental sustainability and agricultural development. Full article

To increase biodiversity in tomato cultivation, two herbal aromatic plants, thyme (Thymus vulgaris) and basil (Ocimum basilicum L.), were introduced as companion plants. Their role was to improve crop plant growth and stress resistance. Moreover, the effect of the soil application of Trichoderma microbial preparations on tomato growth parameters and yield, in combination with companion plants, was studied. Ligno-cellulose multi-layer microcapsules with Trichoderma atroviride TRS14 spores (MIC14) and the commercial preparation Trianum G (TG) were used as microbial preparations. This experiment was carried out in a certified organic field. Tomato plants were intercropped with thyme or basil in the arrangement of two tomato rows alternating with one herbal row. In all intercropping arrangements and in the control (tomato plants grown without herbs), subplots were sectioned. The soil in the subplots was amended with the MIC14 and TG preparations used at a concentration of 10⁴ spores g⁻¹ of the soil and planted with tomato transplants. No control measures were applied during tomato growing, and the plants were naturally infected with late blight. Tomato plant growth parameters and yield were assessed, and late blight severity was monitored. The degree of soil colonization by Trichoderma fungi and the effect of these applications on soil microbial activity and biodiversity (dehydrogenases activity, EcoPlates AWCD, and Shannon index) were evaluated. The results clearly showed a significant influence of thyme and basil on tomato growth and yield in organic production. The cultivation of thyme adjacent to tomatoes had a beneficial effect on the development of the root system and the number of flowers and fruits on the crop plants. Basil, on the other hand, clearly decreased tomato yield and adversely affected the effect of Trichoderma applications by reducing root system development. Moreover, basil as a companion plant increased late blight symptoms. Both Trichoderma strains colonized soil, but they had no significant effect on the microbial activity or metabolic potential measured on the EcoPlates with the use of the BIOLOG system. However, a decrease in dehydrogenases activity was noted. In organic cultivation, the Trichoderma preparations used had no significant effect on tomato yield, opposite to its increase in integrated tomato production. Full article

Background: The need for efficient and simplified techniques for seafood traceability is growing. This study proposes the Biolog EcoPlate assay as an innovative method for assessing wild and farmed Sparus aurata traceability, offering advantages over other molecular techniques in terms of technical simplicity. Methods: The Biolog EcoPlate assay, known for its high-throughput capabilities in microbial ecology, was utilized to evaluate the functional diversity of microbial communities from various organs of S. aurata (seabream) from the Mediterranean area. Samples were taken from the anterior and posterior gut, cloaca swabs and gills to distinguish between farmed and wild-caught individuals. The analysis focused on color development in OmniLog Units for specific carbon sources at 48 h. Results: Gills provided the most accurate clusterization of sample origin. The assay monitored the development of color for carbon sources such as α-cyclodextrin, D-cellobiose, glycogen, α-D-lactose, L-threonine and L-phenylalanine. A mock experiment using principal component analysis (PCA) successfully identified the origin of a blind sample. Shannon and Simpson indexes were used to statistically assess the diversity, reflecting the clusterization of different organ samples; Conclusions: The Biolog EcoPlate assay proves to be a quick, cost-effective method for discriminate S. aurata traceability (wild vs. farmed), demonstrating reliable reproducibility and effective differentiation between farmed and wild-caught seabream. Full article