Frontiers in microbiomes最新文献

In microbiome studies, addressing the unique characteristics of sequence data-such as compositionality, zero inflation, overdispersion, high dimensionality, and non-normality-is crucial for accurate analysis. In addition, integrating experimental design elements into microbiome data analysis is important for understanding how factors such as treatment, time, and interactions affect microbial abundance. To achieve these objectives, we developed a new method that combines generalized linear models (GLMs) with ANOVA simultaneous component analysis (ASCA), which we term GLM-ASCA. This method aims to improve microbiome analysis by providing a more comprehensive understanding of differential abundance patterns in response to experimental conditions. GLM-ASCA models the unique characteristics of microbiome sequence data with GLMs and uses ASCA to effectively separate the effects of different experimental factors on microbial abundance. We evaluated GLM-ASCA using simulated data and subsequently applied it to real data to analyze the effect of nitrogen deficiency on root microbiome recruitment in tomato. Simulation studies demonstrated the effectiveness of GLM-ASCA in analyzing microbiome data in complex experimental designs, and the real-data application revealed valuable insights into the dynamics of microbial communities under nitrogen starvation, including the identification of beneficial bacterial species that promote tomato (Solanum lycopersicum) growth and health through nitrogen fixation.

Background: Host genetics significantly influence the composition of the gut microbiota, but this relationship remains poorly understood, especially in non-European populations. This study aims to investigate the associations between host genetic variation and gut microbiome composition in the Japanese population and to assess methodological factors affecting reproducibility in microbiome research.

Methods: We performed whole-genome sequencing on 306 Japanese individuals and obtained their gut microbiome profiles using shotgun metagenomic sequencing. Genome-wide association studies (GWAS) were conducted to identify associations between host genetic variants and the relative abundance of microbial taxa and bacterial pathways. Phenome-wide association studies (PheWAS) were performed on predicted high-impact variants. Additionally, we compared methodological approaches to assess their impact on microbiome composition and reproducibility.

Results: We identified significant associations between host genetic variants and the relative abundance of one bacterial family, one genus, one species and eight bacterial pathways (p ≤ 5×10^-8). However, none of these associations surpassed the stringent significance threshold of p ≤ 2.75×10^-11. Notably, we were unable to replicate associations reported in prior studies, including those conducted in Japanese populations, even regarding the direction of effects. Our PheWAS analysis uncovered a frameshift variant in the OR6C1 gene (rs5798345-CA) that was significantly associated with an increased abundance of Bacteroides uniformis. Furthermore, comparative analyses highlighted that methodological differences, particularly in sample processing and DNA extraction protocols, substantially influence the observed gut microbiome composition. This variability may be a key factor contributing to the lack of reproducibility across studies.

Conclusion: Our findings enhance the understanding of how host genetics shape the gut microbiota in the Japanese population and underscore the importance of methodological standardization in microbiome research. The identified associations between host genetic variants and specific microbial taxa provide insights into the complex interplay between genetics and the gut microbiome. Addressing methodological discrepancies is crucial for improving reproducibility and advancing knowledge of host-microbiome interactions.

Selective antimicrobial dry cow therapy (DCT) is implemented as part of mastitis control programs, particularly in dairy cows with recent clinical episodes or elevated somatic cell counts. In this study, we investigated the effects of the use of antimicrobials at drying-off on the milk microbiota and resistome by comparing treated (T, n=18) and untreated (NT, n=13) cows. Milk samples from all animals were analyzed using short-read Illumina shotgun sequencing and a subset of 10 samples were also subjected to long-read Oxford Nanopore Technologies (ONT) sequencing. No significant differences in microbial composition or diversity were observed between treated and untreated groups with either technique, indicating that antimicrobial DCT may not induce long-term shifts in the milk microbiota. However, cows receiving antibiotic treatment showed a higher diversity and abundance of genetic determinants of resistance (GDRs) in their milk resistome. Findings from the two sequencing platforms revealed limited concordance in antimicrobial resistance gene content, highlighting that sequencing platform and bioinformatic pipeline choices substantially influence resistome profiling outcomes. Furthermore, the high proportion of host DNA limited sequencing depth and sensitivity, underscoring the need for improved host DNA depletion or targeted enrichment strategies. This study provides insights into the biological and methodological challenges of milk resistome characterization, particularly in low-biomass, host-DNA-rich samples and demonstrates the lack of standardized analytical approaches in resistome studies. Overall, our findings support the prudent use of antibiotics and highlight the need for further longitudinal studies to clarify the temporal dynamics of antimicrobial DCT effects on the milk resistome and microbiota.

Nitrogen (N) and phosphorus (P) are essential nutrients for marine phytoplankton, playing a crucial role in shaping the structure of microbial communities. Nutrients in coastal seawater are influenced by multiple factors, including ocean currents, terrestrial runoff, and anthropogenic activities, leading to region-specific patterns of nutrient limitation. This study investigates nutrient limitation in the transitional waters near Sanmen Island, located at the confluence of the Pearl River Estuary (PRE) and the northern South China Sea. Using 4-hourly in situ time-series observations and nutrient addition experiments, we found that nitrogen limitation persists in this region despite its proximity to the nutrient-rich Pearl River. Urea addition significantly enhanced primary productivity, as evidenced by the increased chlorophyll a concentration and the increased relative abundance of cyanobacteria, whereas phosphate addition alone favored the growth of heterotrophic bacteria, yet limited the growth of cyanobacteria and other primary producers. Combined nitrogen-phosphorus treatments revealed serial co-limitation, where nitrogen relief shifted limitation to phosphorus. In conclusion, these findings highlight the complex nutrient dynamics in transitional coastal waters and underscore the impact of anthropogenic nutrient discharge on ecosystem productivity.

While metagenomics has revolutionized our understanding of microbial diversity and function, the cultivation of microorganisms remains indispensable for elucidating their physiological characteristics and potential biotechnological applications. Cultivation provides context to the vast metagenomic datasets and helps verify metagenome-based hypotheses on microbial interactions. The majority of microorganisms remain uncultivated, and this is particularly prominent from extreme environments such as the Arctic. Here we aimed to contribute to the growing body of work investigating microbial ecology in extreme environments by assessing the efficacy of a variety of cultivation approaches in lake sediment in the High Arctic. To try and capture the full breadth of organisms present, we used standard, in situ, and anoxic cultivation methods. We cultured a total of 1,109 microorganisms which clustered into 155 OTUs (97% rRNA gene sequence similarity), representing organisms from Proteobacteria, Actinobacteria, Bacteroidota, and Firmicutes. Importantly, no single method of cultivation proved to be sufficient to represent the cultivable organisms within the environment. Rather, each method resulted in many unique OTUs. Therefore, multiple approaches should be used in conjunction to access the bulk of microbial taxa in a given environment.

Ocean Alkalinity Enhancement (OAE) is a proposed marine carbon dioxide removal strategy that increases seawater buffering capacity and CO₂ uptake through the addition of alkaline substances. While OAE shows promise as a climate mitigation tool, its ecological implications remain poorly understood, particularly regarding microbial communities. This paper provides a risk assessment of two different OAE strategies: alkalization with olivine and alkalization with addition of dissolved sodium hydroxide (NaOH). With a mesocosm experiment designed to simulate coastal OAE application, European flat oysters (Ostrea edulis) were chronically exposed to alkalinity-enhanced seawater at two concentrations (250 and 500 µmol·L^-¹) derived either from olivine weathering or addition with NaOH. The bacterial community composition of both alkalization types was assessed with amplicon sequencing of the 16S rRNA gene and ecotoxicological impacts were compared to a non-alkalized control. The sampling strategy included samples of the treated waters and the gill microbiome of Ostrea edulis. Our results show that the alkalization type was the primary driver of microbial shifts in the bacterial community of the water samples. Olivine treatments caused distinct taxonomic changes, including an increase in Gammaproteobacteria and Flavobacteriales and a marked decline in Alphaproteobacteria and SAR11 clade. Olivine-treated waters showed reduced richness and evenness. In contrast, dissolved alkalinity treatments produced minimal changes compared to untreated controls. The analysis of the oyster gill microbiome detected a response that was stronger influenced by alkalinity concentration than by alkalization type. Notably, high-alkalinity olivine treatments favored potentially pathogenic Vibrios. Together, these findings highlight that OAE method selection significantly influences bacterial community composition in both marine and host-associated microbiomes. In our experiment, olivine-based OAE posed a greater environmental risk than dissolved OAE. Our study provides insights on the impact of different OAE scenarios, representing a first step toward future field trials and applications.

Mining activities are often severely disruptive to the landscape, and a significant barrier to reclamation following mining operations is the lack of quality topsoil. This project addresses knowledge gaps in the industry by exploring the compositional nature of topsoil stockpiles and their ability to facilitate post-mining revegetation after long-term storage. To do this, we conducted a microbial profiling of two topsoil stockpiles in the interior of British Columbia, Canada. Both stockpiles show depleted soil quality and significant changes compared to reference soils. Notably, there were declines in microbial diversity and significant shifts in community structure with increasing stockpile depths in one of the stockpiles. These results highlight the influence of topsoil-stockpile height on microbial communities in the soil, which ultimately influences the success of restoration. This research can help the industry to optimize restoration and expedite recovery in their mine-closure practices and provides insights into the general structure of the microbiome existing across a gradient in severely disturbed mining soils.

Introduction: Common vetch (Vicia sativa) is an important legume used for forage and green manure. Anthracnose caused by Colletotrichum spinaciae is a significant disease affecting common vetch, resulting in significant damage and yield reductions. Furthermore, there is a lack of effective control methods for this disease.

Methods: This study evaluated the control of anthracnose in V. sativa under greenhouse conditions, focusing on the efficacy of 25% pyraclostrobin, the arbuscular mycorrhizal (AM) fungus Glomus tortuosum, and Trichoderma longibrachiatum, both individually and in combination.

Results: The results showed that 25% pyraclostrobin, G. tortuosum, and T. longibrachiatum both individually and in combination reduced the incidence of anthracnose by 53.85%, 34.62%, 34.62%, and 15.39%, respectively. Correspondingly, the disease index decreased by 68.97%, 34.48%, 32.76%, and 20.69%. Notably, the application of G. tortuosum and T. longibrachiatum alone enhanced common vetch defense enzyme activities of peroxidase, catalase, superoxide dismutase, and polyphenol oxidase by 23.57% and 22.10%, 27.12% and 26.76%, 21.54% and 19.33%, and 35.79% and 34.35%, respectively (P < 0.05). Moreover, the application of AM fungi and Trichoderma led to increased activities of soil urease, catalase, and neutral phosphatase by 12.77% to 111.17%, as well as improved nitrogen and phosphorus uptake by 12.12% to 13.88% and 13.91% to 35.79%, respectively.

Discussiom: Our findings highlight that G. tortuosum and T. longibrachiatum can effectively induce resistance against anthracnose in common vetch, demonstrating significant control efficacy.

Quorum sensing (QS) serves as a regulatory system of virulence factors in the Ralstonia solanacearum species complex (RSSC). The two-component system PhcS-PhcQ recognizes QS signals, subsequently activating the transcriptional regulator PhcA and promoting the expression of QS-dependent virulence factors. In this study, we identified a sensor histidine kinase (Shk) in the R. solanacearum strain GMI1000 and uncovered its essential roles in PhcA-dependent virulence. To investigate the functions of Shk in QS-dependent virulence, we generated an shk-deletion mutant (Δshk) and demonstrated that the deletion of shk leads to a lowered production of cellulase, biofilm, and exopolysaccharide. Moreover, the complementation of native shk in Δshk cell restored the QS-dependent phenotypes. However, the swarming motility of Δshk cells was significantly increased compared to the wild-type GMI1000 strain. The Δshk mutant exhibited impaired colonization of R. solanacearum in the xylem vessels of tomato plants, resulting in attenuated pathogenicity of Δshk to tomato plants. Consistent with the results of the virulence assay, the deletion of the shk gene of R. solanacearum led to the downregulation of the phcA, epsB, and cbhA genes in planta, while the expression of fliC was upregulated in the Δshk mutant relative to the wild-type GMI1000 strain. Pull-down assays suggested that RSc0040 functions as a response regulator for the sensor Shk in vivo and in vitro. Collectively, Shk is implicated in the regulation of these QS-dependent virulent factors, thereby contributing to the virulence of R. solanacearum to tomato plants.