Frontiers in microbiomes最新文献

The skin microbiome plays a critical role at the interface between the human epidermis and the environment, providing colonization resistance against pathogenic strains, training host immunity, and supporting epithelial turnover. Inversely, dysbiotic skin microbiome states are associated with skin disease, particularly inflammatory conditions such as atopic dermatitis and psoriasis. Current evaluation of human host and microbiome interactions relies on post hoc studies after disease onset. This limits the ability to evaluate the causal roles of host and microbe during disease progression. One approach to characterizing microbial and host biology in a controlled and reproducible context is to derive in vitro models of sufficient complexity and stability to support perturbation and response. Current tools for studying these processes are focused on testing antagonistic or synergistic relations between two or more strains for short (hours to days) culture durations, thereby precluding studies of relevant complexity and chronic disease states. Here, we present an in vitro model of the human skin microbiome comprising a six strain consortium colonizing primary human keratinocyte-derived tissue in Air-Liquid Interface for up to 7 days. We evaluated readouts of tissue health including histology, gene expression, and transepithelial electrical resistance (TEER), as well as relative strain abundance to characterize microbiome stability over time. Skin cells formed a complex tissue structure over two weeks and maintained stable or increasing TEER after 7 days of co-culture with the microbial consortium. Up to five of the six strains were viable on the skin tissue surface on day 7 as validated by custom qPCR assays, demonstrating a robust and stable testbed for microbiome studies. A remarkable feature of this model is the persistence of Cutibacterium acnes in an aerobic tissue culture environment, since C. acnes growth is typically demonstrated under anaerobic conditions, suggesting that the skin tissue model is conducive to more natural growth states of native skin strains. The addition of cytokines representative of atopic dermatitis elicited a marked decrease in tissue barrier by day 7 compared to healthy controls, irrespective of the microbiome presence. Furthermore, an alteration in relative strain abundance was observed in diseased model tissues, demonstrating capability to study the impact of disease states on the microbiome and vice versa. We envision this model system as a test bed to evaluate the influence of commensals on host biology, the influence of external environment on microbiome stability, and chronic diseases impacted by dysbiosis.

Introduction: Climate change and plant biodiversity loss have large impacts on terrestrial ecosystem function, with the soil microbiome being primary mediators of these effects. The soil microbiome is a complex system, consisting of multiple functional groups with contrasting life histories. Most studies of climate forces and plant biodiversity effects on microbiome consider the perturbations and the microbial functional groups in isolation preventing us from understanding the full picture of the relative and differential impacts of perturbations on microbial functional groups.

Methods: We measured changes in multiple microbial communities with different functionality, including plant mutualists and pathogens, after three growing seasons in a full-factorial experiment manipulating precipitation (50%, 150% of ambient), plant diversity, and plant composition. Using amplicon sequencing to characterize the response of fungi, arbuscular mycorrhizal fungi, bacteria and oomycetes, and we found that composition of all microbial groups differentiated strongly between precipitation treatments.

Results: Oomycete and bacterial diversity increased with 150% precipitation, while AM and saprotroph fungal diversity decreased. Microbial differentiation in response to plant family and plant species composition was stronger after the third growing season than observed after year one. However, microbial response to plant species richness was weaker in year three. Microbiome response to plant composition was largely independent of the response to precipitation, except for oomycetes, which had greater response to plant composition in high precipitation.

Discussion: These findings build upon prior findings that these microbial community members differentially respond to plant community compositional treatments, by measuring the response over 3 years and with the addition of precipitation treatments. We find that both changes in climate and plant composition can drive major differences in soil microbiome composition, which can feed back on plant community structure and alter ecosystem function.

With its constitutive and functional characteristics, the intestinal microbiota plays a crucial role in the health condition of the animals. Variations in the composition and gene expression of the intestinal microbiota are associated with the risk of the onset of various pathologies of the gastrointestinal tract and chronic inflammatory intestinal diseases. The objectives of this study were to evaluate the variability in the composition of the intestinal microbiota of goats of different breeds (Sarda, Maltese, and Alpine) farmed in different flocks of the region of Ogliastra (Sardegna, Italy) and to assess whether the type of feeding (natural pasture grazing-based versus intensive) could affect the intestinal bacterial composition. We also evaluated possible differences in the composition of the intestinal microbiota between healthy and Caprine arthritis encephalitis (CAE)-affected goats. The economic damage caused by this pathology is due to the reduction in milk production, with infected animals having greater susceptibility to contract diseases. The results of our study highlighted a statistically significant difference (P = 0.001-0.005) in the intestinal bacterial composition between the intensively managed flock and the other natural pasture-based flock.g In particular, a significantly greater abundance of Acidoaminococcaceae in the intensive flock was obgserved. Furthermore, a significantly greater abundance of Prevotellaceae was found in two localities in which, out of a total of 29 animals, only four tested negative for CAE. From these data, we deduced that the presence of Prevotellaceae can be an indication of the disease. This difference could be attributed to the farming system, the Cardedu farm being the only intensive one, and to the geographical distance of this location from the other sampling sites. Therefore, the results of the present study suggest that extensive or intensive farm management may affect the intestinal microbiota of goats.

Background: Staphylococcus aureus is a gram-positive bacterium commonly found in the nares and oropharynx of one in three individuals and has the potential to cause significant health problems. With antibiotic-resistant strains causing 11,000 deaths yearly and ~2% of the population nasally colonized with methicillin-resistant S. aureus, a search for predictive markers and associative relationships between carriage have been long-sought goals. Within our study, we leveraged monozygotic twin participants in concert with multi-site microbiome analyses to characterize the impacts of S. aureus on composition.

Results: We recruited 147 monozygotic twin pairs and characterized three sites, i.e., the nares, oropharynx, and hand microbiomes, using 16S rRNA v3-v4 sequencing in addition to S. aureus carriage status. The prevalence of S. aureus was highest in the oropharynx followed by nares and hand with concordance between twin pairs highest in the nares, followed by oropharynx. The detection of S. aureus was statistically correlated with differences in microbiome composition across sites, as indicated by beta diversity and DESeq2 analyses. Microbiome composition was most similar in twins' nares that were S. aureus culture-positive concordant, whereas twins that were culture-negative concordant had the most similarity in the oropharynx. Of significance, Moraxella nonliquefacians and Capnocytophaga were inversely associated with S. aureus in the nares and oropharynx, respectively.

Conclusions: This improved understanding of S. aureus colonization in nares, oropharynx, and hand microbiomes in monozygotic twin pairs is a further step towards unraveling the degree to which the microbiome is influenced by host genetics and S. aureus carriage.

Oceanic hydrothermal vent systems represent some of the oldest habitats on Earth and serve as analogs for extraterrestrial environments. The Lost City Hydrothermal Field (LCHF) near the Mid-Atlantic Ridge is one such environment, and its large chimneys are unique in hosting actively venting hydrothermal fluids that are primarily controlled by serpentinization reactions in the subseafloor. Microbial communities within LCHF have been studied for insights into their functional adaptations to the warm, alkaline, and dissolved inorganic carbon-limited environment. Metagenomic and mineralogical data collected during a recent expedition to Lost City were analyzed to delineate associations between microbial populations and physical, chemical and biological characteristics of the chimneys. Bacterial 16S rRNA gene sequences show a high degree of putative microdiversity within the relatively dominant genera Desulfotomaculum, Sulfurovum, Thiomicrorhabdus, and Serpentinicella, which represent a large core of the overall LCHF vent bacterial community. This microdiversity relates to the compositional fraction of aragonite, brucite, and calcite minerals within chimney samples rather than just the composition of nearby vent fluids. Although many species are found in both chimneys and venting fluids, the overall microbial community structures in chimney biofilms remain distinct from the hydrothermal fluids that flow through them. Shotgun metagenomic analyses reveal differences among genes predicted to be involved in carbon, methane, nitrogen and sulfur cycling with respect to their correlations to the abundances of specific minerals. These data hint at microenvironmental complexity lost within standard bulk analyses. The findings of this study underscore the need to more closely examine microbe-mineral interactions in natural environments, critically informing not just population-level distributions, but also the functional underpinnings of these extremophile microbial communities.

Introduction: Antimicrobial resistance (AMR) has become a major public health concern and challenge. The transfer of antimicrobial resistance genes (ARG) between bacteria and the movement of antibiotic resistant bacteria (ARB) between human, environmental, and animal reservoirs allows AMR to spread and drive its persistence. Modeling efforts are useful for providing understanding of fate and transport, dynamics, or probabilistic risk, but lack estimates of bacterial conjugation parameters to be used within these frameworks.

Methods: A systematic literature review was conducted to summarize measured rates of conjugation for AMR and other resistances across a variety of settings, experimental media, and donor sources. Results: Across the 113 studies, reported conjugation frequencies and rates were examined in environmental, clinical, and animal/agricultural settings. The findings spanned over 12 orders of magnitude. From all studies, a subset of 25 were able to be analyzed for time-dependent rate estimation, which is most useful in modeling approaches. The highest rates were found in samples originating from wastewater sources or transferred in wastewater matrices, pointing to the significance and role of anthropogenic impacts on the environment in dissemination of AMR.

Discussion: The results allowed us to identify knowledge gaps in measuring conjugation rates in key environmental exposure areas, such as biofilms, and in reporting experimental outputs for understanding cell growth and conjugation dynamics, such as donor, recipient and transconjugant densities over time.

Introduction: Increasing the research on the development and utilization of unconventional feed resources is one of the effective ways for the sustainable development of herbivorous animal husbandry. China is one of the countries most severely impacted by the invasion of the alien plant Solanum rostratum Dunal (S. rostratum), but this resource has not been used effectively.

Methods: The aim of this study was to investigate the effects of Lactobacillus plantarum and cellulase on the fermentation quality and microbial community in mixed silage of S. rostratum and alfalfa. Treatments were a control treatment with no additive (CK), Lactobacillus plantarum (LP), cellulase (CE), and Lactobacillus plantarum in combination with cellulase (L+C), all of which were stored at ambient temperature for 7, 15, 30, and 60 days.

Results: The results showed that the mixture could retain dry matter (DM), crude protein (CP), and water soluble carbohydrates (WSC) content, increase lactic acid (LA) content, decrease pH and alkaloid content, and improve fermentation quality during silage. The use of additives increased the abundance of Lactobacillus and Weissella, which was related to the improvement of the quality of mixed silage and the degradation of total alkaloids. Differential microbial functions were mainly carbohydrate metabolism, biosynthesis of secondary metabolites and carbon metabolism.

Conclusion: The application of additives and mixed silage provides a new idea for the feed utilization of S. rostratum.

Chemotherapy-induced cognitive impairment, also called "chemobrain", has been heavily researched as a major side effect of cancer treatment. Although breast cancer has a 91% survival rate in the U.S., this rate is significantly lower in developing countries. Cancer survivors often experience chemobrain which can decrease their quality-of-life post-chemotherapy. The presented study evaluates potential mechanisms for long-term symptoms in cyclophosphamide, methotrexate, and 5-fluorouracil (CMF)-induced cognitive impairments and implications of CMF on the microbiome. Twelve-week-old C57/B6J female mice were treated with a combination of CMF once a week for 4 weeks. Spatial memory was tested with the Morris water maze. Hippocampal tissues were used to probe for immediate-early genes (IEGs) with western blotting techniques. Fecal matter was collected to assess microbial community composition via 16S rRNA gene sequencing. In this study, we showed that chemotherapy impaired spatial memory during the Morris water maze trials and resulted in a significant decrease in immediate early genes (IEGs) c-Fos, Arc, and Zif286 expression. Comparing Alpha diversity, there were no significant differences identified amongst taxa within the CMF group compared to the saline group for Pielou's evenness. However, Beta diversity qualitative metrics, Jaccard and Unweighted Unifrac were significantly different. These results suggest that continual memory deficits may be associated with alterations in synaptic plasticity and long-term potentiation.

Obesity is a global epidemic that has affected the lives of over 14% of adults worldwide and over a third of Americans. Obesity is associated with the increased risk of thirteen obesity-associated cancers and poor cancer outcomes. Bariatric surgery is the most effective method of sustained weight loss and has been steadily increasing in clinical use over the past 4 decades. Importantly, bariatric surgery is established to decrease cancer risk. Vertical sleeve gastrectomy (VSG) is currently the most common bariatric surgery procedure. To evaluate underlying mechanisms of bariatric associated cancer protection, we developed a robust pre-clinical model of bariatric surgery-induced weight loss in mice. Using multiple strains, we established detailed procedures, defined best practices, and noted specific controls to include to examine mediators critical to cancer onset. This VSG protocol includes stringent pre- and post-operational measures to reduce stress-associated weight loss in obese mice to achieve rigorous and reproducible bariatric surgery-associated weight loss. In addition, we describe collection of fecal and intestinal samples as well as Peyer's patches as important mediators of bariatric surgery's impact on cancer risk. In conclusion, as obesity and weight loss approaches including bariatric surgery are increasingly examined in cancer risk and outcomes including immunotherapy, the establishment of robust pre-clinical interventions will allow the field to address critical underlying mechanisms mediating the benefits of weight loss and cancer.

New and noteworthy: Obesity increases cancer risk and leads to poor outcomes and survival. Bariatric surgery is an effective method of sustained weight loss. To best model obesity, weight loss, and impacts on cancer risk or outcomes, we developed a robust pre-clinical model of bariatric surgery in mice. Because bariatric surgery leads to sustained impacts on the gut microbiome, which can inform anti-tumor immunity, this protocol provides rigorous methods for the collection of intestinal microbiota and Peyer's patches.