Frontiers in Microbiology最新文献

Introduction: Sarcopenia, which is defined as loss of skeletal muscle mass and strength, affects up to 70% of patients with liver cirrhosis. Since hibernating animals maintain muscle mass through microbial nitrogen recycling, urease-producing bacteria may have a protective role in humans. We hypothesized that altered microbial urease abundance contributes to differences in nitrogen recycling potential between patients with and without sarcopenia, with sex-specific effects.

Methods: Stool samples from 152 patients with (n = 101) and without sarcopenia (n = 51) were analyzed. Functional profiles were predicted from 16S rRNA gene amplicon sequencing data using Tax4Fun2, and predicted abundances of urease subunit alpha were extracted. A systematic literature search identified 120 urease-producing taxa, of which 35 were represented in sequencing data.

Results: Sarcopenia is associated with a lower predicted abundance of urease subunit alpha in patients with cirrhosis (n = 96; p = 0.045, r = 0.20; median = 0.0002 vs. 0.0004), irrespective of sex, and in women (n = 49, p = 0.037, r = 0.30, median = 0.0002 vs. 0.0004), irrespective of cirrhosis. Urease subunit alpha abundance increases with the use of proton pump inhibitors (PPIs) in the entire patient cohort (p = 0.0028, r = 0.24, median = 0.0003 vs. 0.0002), patients with cirrhosis (p = 0.033, r = 0.22, median = 0.0004 vs. 0.0002), and men (n = 103, p = 0.0005, r = 0.34, median = 0.0002 vs. 0.0001). Beta-blockers are associated with higher urease subunit alpha abundance in the entire patient cohort (p = 0.018, r = 0.19, median = 0.0003 vs. 0.0002) and women (p = 0.031, r = 0.31, median = 0.0004 vs. 0.0002). The overall abundance of potentially urease-producing taxa was comparable between the groups.

Discussion: The increased urease subunit alpha abundance in patients with liver cirrhosis and women without sarcopenia, and the influence of medication on abundance, point towards potential additional effects of beta-blockers in sarcopenia.

The rapid expansion of fast-growing plantations in subtropical regions is closely linked to silvicultural practices, however, improper practices often lead to soil acidification and reduced nutrient bioavailability. Phosphorus (P), one of the most critical elements for plantation tree growth, shows complex spatial distribution patterns in soil that are influenced by multiple factors, directly affecting plantation productivity. This study investigated the effects of long-term fertilization and dry-season irrigation on the vertical distribution of phosphorus in an 8-year-old subtropical Eucalyptus plantation. This study employed stratified sampling (0-30 cm topsoil, 30-60 cm subsoil, 60-90 cm substratum) during dry seasons, coupled with metagenomics, metabolomics, and environmental factor analysis, to reveal vertical phosphorus cycling patterns and multiomics regulatory networks. Key findings: (1) Fertilization and dry-season irrigation had a limited influence on labile phosphorus and the diversity of P-cycling microorganisms. The topsoil presented significantly greater P availability than did the subsoil, manifested as elevated acid phosphatase activity (ACP), significant enrichment of the tryptophan metabolic pathway, and greater microbial diversity. (2) pH and the C:P ratio represent critical factors of vertical stratification in soil P cycling. Under acidic conditions, topsoil microorganisms facilitate P release via diverse metabolic pathways, whereas oligotrophic constraints in the substratum limit enzymatic activities. (3) Potential cross-stratum microbial functional coordination exists in acidic soil P cycling, with linkages to tryptophan metabolism and polyphosphate, synthesis/degradation. Our study provides theoretical multiomics insights for optimizing the management of soil P pools in subtropical plantations under fertilization and dry-season irrigation.

Microplastics (MPs) are a global concern due to their persistence in the environment and capacity to carry pollutants and pathogenic microorganisms. Given recent evidence on the co-occurrence of MPs and Campylobacter spp., the leading cause of foodborne gastrointestinal infections worldwide, this study investigates the role of MPs in Campylobacter jejuni contamination and their impact on antimicrobial susceptibility. The potential of five C. jejuni isolates from different origin (poultry, water, and human) to form biofilms on MPs over time (24 h, 48 h, and 72 h) was evaluated using traditional culture-dependent methods, including the reference strain C. jejuni subsp. jejuni strain NCTC 11168. The effect of MPs on the antimicrobial susceptibility of C. jejuni cells detached from MP-associated biofilms was also assessed using Etest strips. To comprehensively understand the interactions between the MPs and the bacteria, whole-genome sequencing was performed to explore the presence of adherence and biofilm-associated genes, as well as antibiotic resistance genes. The strains rapidly colonized the MPs within 24 h, exhibiting varying attachment densities over time ranging from 1.09 to 5.78 log CFU/MP, with strain NCTC 11168 identified as the strongest biofilm former overall. Furthermore, the abundance of adherence and biofilm formation genes was consistent with their abilities to form biofilm on MPs. The gene peb3 played a critical role in determining biofilm formation levels on MPs, while specific combinations of capA, capB, cj1725, and porA were linked to enhanced biofilm development. Similarly, the presence of antibiotic resistance determinants aligned with the phenotypic resistance, and only one strain (ST-6209/CC464) exhibited resistance to ciprofloxacin, nalidixic acid, and tetracycline. Notably, antimicrobial susceptibility of cells detached from MP-biofilms was increased by up to 4.6 log₂-fold compared to planktonic counterparts. The findings indicate that MPs can facilitate the persistence of C. jejuni in the environment while simultaneously increasing their susceptibility to antibiotics. Further research with larger cohorts is needed to validate these preliminary observations in order to support the development of effective policies addressing MP pollution and food safety.

The intestinal microbiota is a complex and dynamic community that contributes to digestion and plays a crucial role in regulating immune health. In this study, post-metamorphic bullfrogs (Aquarana catesbeiana) at different ages (1, 2, 3, and 4 months) were investigated. Growth performance assessment, intestinal histomorphological analysis, and 16S rRNA sequencing were employed to systematically examine the dynamics and diversity of microbial communities in the small intestinal segments (duodenum, jejunum, and ileum). Results showed that bullfrog growth indices increased with age, with faster body weight gain during 2-3 months; notably, this was significantly positively correlated with intestinal morphological development (villus height and muscle layer thickness) (p < 0.05). In terms of microbial composition, Firmicutes, Proteobacteria, Bacteroidetes, Fusobacteria, and Actinobacteria were dominant phyla, while different intestinal segments harbored specific dominant genera. Among them, Cetobacterium was consistently detected throughout the growth period, suggesting it is likely the core symbiont in bullfrog intestines. Moreover, microbiota function varied with growth stages: at 1-2 months, Bifidobacterium and Cetobacterium synergistically participated in immune regulation and basic metabolism, whereas at 3-4 months, Weissella, Lactococcus, and Bacteroides became dominant, with their functions shifting toward efficient energy conversion. Additionally, Alpha diversity analysis showed a decreasing trend in the Simpson index with development, while Beta diversity analysis revealed that microbiota composition was similar among different intestinal segments at the same age but that significant differences existed in each segment during 2-3 months. Overall, this study reveals the specific distribution characteristics of probiotic microbiota in bullfrogs at different growth stages, thereby providing a scientific basis for screening growth-promoting frog-derived probiotics that match host physiological traits.

Quorum sensing (QS) is an intercellular communication mechanism employed by the opportunistic bacteria Pseudomonas aeruginosa to regulate processes beneficial to the longevity of the community and related to its pathogenicity. The LasI/Rhl circuits of the quorum-sensing (QS) network operate through N-acyl-L-homoserine lactones (AHL) and appear at the top in the QS hierarchy. In natural habitats and host environments, bacteria exist and transit between different modes of lifestyle: planktonic single cells, suspended multicellular aggregates, and surface-attached biofilm communities. Using P. aeruginosa PA14 as a model, we determined the contribution of the master regulator LasI/RhlI QS system to multicellular community autoaggregation in liquid, ultrastructure and fitness characteristics of the cell envelope, and extracellular proteome responses, employing phenotypic assays, light imaging, high-resolution transmission electron microscopy and quantitative mass spectrometry-based proteomics and bioinformatics. Wild-type bacteria with a functional QS system were more effective in the protease-mediated autoaggregation than the lasI-/rhlI- mutant, lacking the production of AHL molecules and associated virulence traits. AHL-dependent communication impacted cell envelope characteristics, including ultrastuctural curvature and tolerance to membrane-damaging and antimicrobial agents. Moreover, the LasI/RhlI QS system perturbed the extracellular abundance of a total of 545 extracellular proteins during late exponential and early stationary growth phases. We allocated most of these differentially expressed proteins to the following large functional groups: metabolism; transcription and translation; transport and secretion systems; cell envelope integrity; redox processes; invasiveness and toxicity; and motility. Remarkably, approximately 95% of the extracellular proteome was upregulated in the lasI-/rhlI- mutant compared with the wild type, and these levels were restored to wild type-status when AHL was added. We observed a crucial contribution of the LasI/RhlI QS system to the protease-mediated community autoaggregation in P. aeruginosa PA14. Mechanistically, this was accompanied-through a sophisticated and multifactorial process-by differential expression of an array of components in the secreted proteome involved in both pathogenicity-specific and global readjustments in the homeostasis within the population. By fine tuning the LasI/RhlI system, Pseudomonas can regulate its pathogenic potential and long-term survival in different hosts and habitats.

[This corrects the article DOI: 10.3389/fmicb.2024.1522794.].

Introduction: Hop (Humulus lupulus L.), a vital crop in the brewing industry, is increasingly threatened by infections caused by viroids and viruses. The extensive use of vegetative propagation in hop cultivation facilitates the accumulation and dissemination of these pathogens. However, little is known about their prevalence and ecological behavior in non-commercial settings. This study provides a comprehensive overview of viroid and virus infections across Germany, with particular attention to their occurrence and potential transmission across commercial, settlement, and wild hop populations.

Methods: Between 2020 and 2023, 418 hop leaf samples from commercial (n = 345), settlement (n = 29), and wild (n = 44) populations were collected. Viroid and virus detection was performed using RT-PCR and PCR. To investigate possible cross-species transmission and sequence variation, HSVd-positive samples from hops and nearby grapevines were further analyzed via Sanger sequencing.

Results: Viroid screening revealed that the citrus bark cracking viroid (CBCVd; Cocadviroid rimocitri) was confined to commercial hop cultivation. This study also marks the first confirmed detection of hop stunt viroid (HSVd; Hostuviroid impedihumuli) in commercial hop fields in Germany. Virus screening showed that hop latent virus (HpLV; Carlavirus latenshumuli) and american hop latent virus (AHpLV; Carlavirus americanense) were exclusively found in commercial hops. Hop mosaic virus (HpMV; Carlavirus humuli) was detected across all three groups-commercial, settlement, and wild populations. Arabis mosaic virus (ArMV; Nepovirus arabis) and apple mosaic virus (ApMV; Ilarvirus ApMV) were identified in both commercial and wild hops but were absent from settlement samples. Overall, commercial hop populations exhibited the highest pathogen burden, frequently harboring multiple viroid and virus infections. These findings underscore the importance of using certified, pathogen-free planting material, implementing early detection strategies, and updating plant passport regulations to include high-risk pathogens. While prevalence estimates reflect risk-based sampling from key production regions, the study provides a solid basis for enhancing pathogen surveillance and improving preventive measures in hop cultivation.

Introduction: Microbial succession in fruit wine has been reported, but the ecological mechanisms linking niche competition to aroma formation remain poorly understood. To test the hypothesis that niche competition between microbial communities significantly influences aroma formation in pomelo wine, the flesh of Jinggang honey pomelo was subjected to semi-inoculation fermentation to produce Jinggang honey pomelo wine.

Methods: High-throughput amplicon sequencing technology was used to investigate the evolving microbial community during the fermentation process of pomelo wine. The changes in volatile compounds were measured using headspace solid phase microextraction (HS-SPME) coupled with gas chromatography-mass spectrometry (GC-MS).

Results: The dominant taxa in the wine were Weissella, Pediococcus, Lactiplantibacillus, Saccharomyces, Komagataella, Wickerhamomyces, and Aspergillus. The microbiota shifts were associated with dynamic changes in physicochemical properties, and they altered the pH, alcohol content, total soluble solids, and overall acidity. Principal component analysis (PCA), orthogonal partial least squares-discriminant analysis (OPLS-DA), and relative odor activity value analysis identified 17 key volatiles. A correlation network analysis revealed that Lactiplantibacillus and Aspergillus were strongly associated with various flavor molecules.

Disscussion: The present findings suggested that inter-kingdom niche competition between fungi and bacteria plays a pivotal role in shaping the aroma profile of pomelo wine, offering new insights for targeted aroma regulation.

Introduction: The utilization of agricultural by-products as feed plays a significant role in reducing resource waste and promoting sustainable development of the livestock industry. This study investigated the effects of replacing corn silage with a fermented cotton straw-apple pomace mixture in beef cattle diets.

Methods: Twenty beef cattle were randomly assigned to two groups: a control (CON) group fed a basal diet and a treatment (TRE) group fed a diet in which corn silage was replaced by the fermented mixture. We assessed growth performance, rumen fermentation parameters, fibrolytic enzyme activities, bacteria community structure, and metabolite profiles.

Results: Compared to the CON group, the TRE group showed reductions in average daily gain (ADG) and dry matter intake (DMI) by 25.42 and 18.79%, respectively (p < 0.05). The concentrations of ruminal volatile fatty acids (VFAs) were also significantly lower (ranging from 9.63 to 17.01% reduction; p < 0.05). The activities of cellulase, hemicellulase, and cellobiohydrolase were significantly decreased in the TRE group (by 13.22, 38.80, and 13.66%, respectively; p < 0.05). The fermented mixture also altered the rumen microbial composition: the relative abundances of Anaeroplasma and Pyramidobacter were higher in the TRE group, whereas those of Anseongella, Holdemania, and Acetoanaerobium were lower. Non-targeted metabolomics analysis revealed significant changes in the rumen metabolite profile of cattle fed the fermented mixture; notably, ferulic acid concentrations were significantly higher in the TRE group than in the CON group. Spearman correlation analysis indicated that Anseongella was significantly positively correlated with ADG, while Pyramidobacter was significantly negatively correlated with ADG and with the activities of cellulase, hemicellulase, cellobiohydrolase. Anaeroplasma was negatively correlated with those enzyme activities and was also significantly associated with ferulic acid and many other differential metabolites.

Discussion: In conclusion, replacing corn silage with the fermented cotton straw-apple pomace mixture reduced ADG, VFA concentrations, and ruminal fibrolytic enzyme activities in beef cattle; these effects may be related to changes in specific rumen bacteria and metabolites.