Frontiers in microbiomes最新文献

Arbuscular mycorrhizal (AM) fungi form widespread, ancient, and critically important symbioses with plants, but their functioning and beneficial effects are highly context-dependent. This variability stems from eco-evolutionary dynamics operating across multiple levels of biological organization (e.g., genes to holobionts), making generalizable predictions about mycorrhizal outcomes challenging. Multilevel selection theory (MLST), which posits that selection acts simultaneously on multiple levels of biological organization including in opposite directions, can serve as a powerful framework for interpreting this variability in mycorrhizal functional phenotypes. Here, we outline the key principles of MLST and explore how its application to AM fungal symbioses can improve our understanding of this ubiquitous symbiosis. We highlight how four levels of biological organization important to AM symbioses - genes, nuclei, spores, and holobionts - can serve as one or more units of selection under a tripartite framework for the units of selection. We then examine how ecological contexts, such as stress, spatial structure, and community composition, can modulate the balance of selective forces across levels, ultimately shaping the degree of cooperation among symbiotic partners. We conclude by proposing future research directions using MLST to generate deeper insights into the complexity and adaptability of this globally important symbiosis.

Background: The complex ecosystem on skin comprising tens of thousands of microorganisms plays an important role in health and disease. The last decade in particular has witnessed a surge in microbiome research, which has been elucidating the role of the microbiota in numerous skin pathologies. Of relevance to the current study, are recent evidences implicating the microbiome in skin pigmentary conditions. Melasma is one such refractory, hyperpigmentary condition with a poorly understood pathogenesis. The present study was carried out to characterize the nature of microbial dysbiosis and its impact on microbial community structure in melasma subjects.

Results: The clinical assessment of melasma carried out using biophysical, biochemical and biomarker-based measures confirmed significant changes in melasma lesions, most notably, those linked to redox, inflammation and barrier properties. A deep characterization of the skin microbiome in melasma from human face, indicated significant differences between lesional and peri-lesional areas. Of the 377 genera identified through an agglomeration of all OTUs at the Genus level through 16S rRNA sequencing, 344 were common, while 12 were unique to lesional and 21 unique in peri-lesional areas. A significant decrease was observed in alpha diversity in melasma lesion as compared to peri-lesion areas, with an accompanying decrease in number of interconnections among them. The differences in the microbiome also appeared to correlate with several clinical parameters, notably with the melasma severity measured through modified MASI (mMASI) scoring. The observed changes in both host and microbiome, point to a potential role for the latter in melasma pathogenesis.

Conclusions: Our study indicates that there are significant differences in the microbiome between lesional and peri-lesional areas of melasma subjects, with associated changes in microbial community structures. Additionally, the observed changes were seen to correlate with measured clinical parameters. These findings provide the opportunity to further probe the nature of host and microbiome links that may underlie the phenotypic manifestation, as well as provide effective routes for managing this recalcitrant disorder.

Background: Quality control in metagenomic data analysis is crucial for ensuring the accuracy and reliability of research results. Among the key steps in microbiome research, DNA extraction plays a critical role, as it directly determines DNA yield, integrity, and representation of microbial taxa.

Results: We compared three commercial DNA extraction kits and our protocol specifically developed for the recovery of high molecular weight (HMW) DNA from complex microbial communities, using the ZymoBIOMICS Gut Microbiome Standard. The PureLin^™ Microbiome DNA Purification Kit and our custom protocol provided superior recovery of DNA from Gram-positive bacteria, while the Wizard^® kit and our protocol yielded HMW DNA suitable for long-read Oxford Nanopore sequencing. Among sequencing approaches, metagenomic sequencing on the Illumina platform provided the most accurate representation of the reference composition. However, all methods showed limited ability to detect taxa below 0.5% of relative abundance. Additionally, taxonomic classification based on 16S rRNA gene amplicon sequencing data misclassified closely related species due to high gene homology, a limitation not observed with metagenomic approaches.

Conclusions: Our study establishes that a customized DNA extraction protocol is optimal for comprehensive microbiome studies utilizing long-read sequencing technologies. We show that metagenomic sequencing outperforms 16S rRNA gene amplicon sequencing for species-level accuracy, providing a validated benchmark for future gut microbiome research.

Microbiome dysbiosis, characterized by an imbalance in the composition of microbial communities, has emerged as a potential risk factor for the development of cervical, head, and neck cancers. While previous studies have predominantly focused on high-income countries, there is a significant gap in understanding the relationship between microbiome alterations and cancer development in sub-Saharan Africa. Considering the unique socio-economic and environmental factors in this region, investigating the role of vaginal and oral microbiota in the progression of these cancers is crucial. This review explores the involvement of microbial dysbiosis in cervical, head, and neck cancers, particularly how it influences Human Papillomavirus-driven immune evasion, and highlights the importance of microbiota profiling in sub-Saharan Africa. The implications of these insights for cancer prevention and treatment strategies in this population are also discussed.

The soilborne fungus Phymatotrichopsis omnivora causes a mid- to late-season disease known as cotton root rot (CRR). In the United States, P. omnivora is primarily found in Arizona, New Mexico, Oklahoma, and Texas in soils that are alkaline, calcareous, and rarely freeze deeply. This fungus has a wide host range, and can cause substantial losses in cotton crops. In Texas, not all cotton-producing soils have widespread CRR despite having the characteristics to support P. omnivora. Considering the lack of CRR in some Texas soils, we hypothesize that this absence could be due to the microbial composition associated with sclerotia of P. omnivora. The objective of this study was to identify the taxa that make up microbial communities associated with P. omnivora sclerotia in different soils during both the cotton-growing and off seasons. The microbiota associated with P. omnivora sclerotia were identified by burying lab-generated sclerotia in cotton-producing soils. These sclerotia were recovered, along with soil samples for metabarcoding targeting the 16S rRNA gene and the internal transcribed spacer region. When compared to bulk soil, microbial communities associated with sclerotia differed in community composition and taxa relative abundance between a soil with widespread CRR and one in which the disease is absent. Within these soil communities, potential bacterial and fungal biomarkers that reduce CRR were identified. Furthermore, microbial communities of P. omnivora sclerotia changed seasonally. This study presents the first detailed characterization of microorganisms associated with P. omnivora sclerotia in different cotton-producing soils. Our findings support the view that P. omnivora sclerotia serve as ecological hubs, shaping microbial communities with possible implications for disease suppression. Several enriched taxa are culturable, offering candidates for future biocontrol studies that could inform disease management strategies that focus on increased microbial competition.

The community of microorganisms occurring in the animal gut, known as the gut microbiota, is closely connected to host health. It is essential for metabolic processes, digestion, and defense against pathogens. Knowledge about the composition of an intact gut microbiota, along with its natural fluctuations and diversity, is a crucial aspect of proper husbandry and breeding of animals in human care. In this study, we analyzed the fecal microbiota of the critically endangered Coquerel's sifaka (Propithecus coquereli), with a special focus on seasonal effects and the impact of dietary variations. As a tropical species, European winters may influence microbiota diversity or composition, highlighting the importance of this assessment. Ninety-seven fecal samples collected from all individuals housed in European zoos revealed high microbial diversity and variation. Some of the core taxa present in every sample included Lachnospiraceae, Erysipelotrichaceae, Clostridiaceae, and Bacillaceae. Microbial α-diversity showed no decline in winter, indicating no seasonal effect caused by dietary changes. However, results suggest compositional differences between seasons, indicated by significant differences in β-diversity. These findings confirm the importance of longitudinal studies to fill knowledge gaps between sampling intervals and to characterize microbiota oscillations throughout the year.

Microbial biofilms can influence corrosion outcomes on metal surfaces. Though past studies have largely focused on microbiologically induced corrosion, we report here that environmentally derived microbial communities can form biofilms that inhibit the corrosion of an aluminum alloy. Our findings point to the importance of complex microbial communities, which are more likely to be found on metals exposed to natural environments, in determining corrosion outcomes and highlight a potential role of microbial interactions in corrosion inhibition.

Introduction: The intensive use of chemical fertilizers and pesticides in modern agriculture has led to severe soil degradation and environmental pollution, which threatens the long-term production of crops. Plant growth-promoting rhizobacteria (PGPR) and arbuscular mycorrhizal fungi (AMF) are promising biofertilizers which can boost plant growth and improve soil quality. However, the combined effects of these factors on medicinal plants such as Isatis indigotica remain unclear.

Methods: This study isolated and identified six plant growth-promoting rhizobacteria (PGPR) strains (Acinetobacter sp. and Bacillus albus) from the rhizosphere of Isatis indigotica. A pot experiment was conducted with control, PGPR inoculation and AMF+PGPR co-inoculation treatments to assess the effects of these treatments on the growth of Isatis indigotica and its soil physicochemical properties. High-throughput sequencing was used to analyse the structure of the rhizosphere microbial community, while non-targeted metabolomics was employed to profile root metabolites. Finally, a redundancy analysis (RDA) was performed to reveal the correlations between the key microbial taxa and the differential metabolites.

Results: All six of the isolated PGPR strains exhibited multiple capacities that promote plant growth. The pot experiment demonstrated that both PGPR inoculation and AMF+PGPR co-inoculation significantly increased the height and root length of Isatis indigotica compared to the control, while also enhancing the soil's SOC, TN and AP content. Analysis of the microbial community revealed that the inoculation treatments enriched the rhizosphere microbiome with beneficial taxa such as Proteobacteria and Ascomycota. Metabolomic analysis revealed that inoculation treatments significantly increased the concentrations of key bioactive compounds, such as flavonoids, lipids and amino acids. Furthermore, the RDA revealed a strong correlation between the accumulation of various root metabolites (e.g., benzenesulfonic acids, carbohydrates and fatty acids) and dominant microbial genera (e.g., Acinetobacter, Paenibacillus and Botryotrichum).

Conclusions: PGPR and AMF improve the uptake of nutrients and the synthesis of secondary metabolites in Isatis indigotica by altering the structure of the rhizosphere microbiome and root metabolomes. These findings support the use of PGPR and AMF as biofertilizers for sustainably cultivating medicinal plants.

Introduction: The function of the respiratory microbiome during an active infection is not well characterized. Studies from the gut microbiome suggest a diverse community can aid in modulating the immune system to control infectious pathogens.

Methods: To determine if there are microbial community compositional changes in the human lung during an infection, we conducted an analysis of both the 16S rDNA and the Internal Transcribed Spacer (ITS) region of DNA from bronchoalveolar lavage fluid (BALF) of patients from Mayo Clinic Arizona. In addition to general classification, we assessed differences in the lung microbiome of patients with different infections including coccidioidomycosis, a common fungal pneumonia in Arizona.

Results: We observed patterns of dysbiosis in the lung microbiome during active fungal infection. Patients with active coccidioidomycosis infections had an overabundance of Malassezia, Epicoccum, and Penicillium species in the fungal communities and bacteria in the classes Bacilli, Bacteroidia, Clostridia, and Gammaproteobacteria. Patients with disseminated coccidioidomycosis showed evidence of extreme dysbiosis in the lung microbiome with a significant overabundance of Malassezia and Bacilli. We also observed differences in the fungal communities of patients with an active Candida albicans infection, with an overabundance of the genera Candida and Nakaseomyces. Additionally, we observed a decrease in diversity in the lung fungal communities in patients with an active Coccidioides or Candida infection but no difference in the bacterial community.

Discussion: These compositional changes in the lung microbiome during an active Coccidioides spp. infection associated with shifts in the fungal community. This is the first study to examine how these fungal pathogens affect the lung microbial community of humans.

Introduction: Bioregenerative life support systems (BLSS) utilizing plants and/or microorganisms to provide the crew of a spacecraft with food, clean water, breathable air, and other amenities are likely to form key components of future long-distance spaceflight missions. Extensive testing and validation of such technologies are necessary before they can be implemented. EDEN ISS was a platform in Antarctica that tested various plant cultivation technologies for a BLSS. To ensure the continued operation of a BLSS, it is vital that plants remain healthy, which necessitates the monitoring of the plant production facility microbiome to ensure that pathogens are detected early and countermeasures can be engaged.

Methods: Swab surface samples collected in the EDEN ISS Mobile Test Facility (MTF) during different campaigns were used to estimate the bioburden of the various surfaces via viable count. Isolates obtained from the cultivation of the surface samples were identified via partial 16S rRNA gene sequencing. Additionally, 16S amplicon sequencing was performed on DNA extracted directly from the swab samples to characterize the microbiome.

Results and discussion: The results revealed that the bioburden of the different sampling positions was not significantly reduced by cleaning, indicating that the employed cleaning regime was unsuited in its current form to adequately lower the bioburden. Identification of the isolates, as well as the full microbiome, revealed mostly environmental genera. However, in both cases, genera containing plant as well as human pathogens, like Pseudomonas and Acinetobacter, were identified and accounted for up to 16.1% of all reads for a sampling condition in the case of Pseudomonas. The two sets of sequencing data had little overlap, with Rhodococcus and Microbacterium being the only genera shared between all sampling conditions and sequencing approaches, and emphasized different aspects of the MTF microbiome, highlighting the advantages of using a combined approach to obtain a more complete picture of the microbiome composition.