Frontiers in microbiomes最新文献

Objective: The pathogenesis of exertional heatstroke (EHS) involves substantial contributions from gut microbiota and their metabolites. In this study, we assessed whether cold water immersion (CWI) mitigates EHS-induced intestinal damage via alterations in the microbiome.

Methods: An EHS model was created with 18 Wistar rats divided into three groups, that is, the EHS group comprising rats with exertional heat stroke, the CWI group with rats with heatstroke treated with cold water immersion, and the control (CTRL) group (rats with normothermia control). Pathological changes, core temperature (Tcore), and lactic acid (Lac) and endotoxin lipopolysaccharide (LPS) levels were evaluated. Fecal samples were subjected to metagenomic shotgun sequencing and liquid chromatography-mass spectrometry for microbiota and metabolomic profiling.

Results: Hematoxylin and eosin staining showed that CWI treatment significantly reduced EHS-induced intestinal congestion, edema, and necrosis compared to the EHS group. The EHS group had the highest Tcore, while the CWI group had significantly lower Tcore than the EHS group. The CWI group had significantly reduced LPS and Lac levels, similar to those observed in the CTRL group. Microbiome analysis indicated that EHS disrupted gut bacteria, with an increase in the proportion of pathogens such as Desulfovibrio fairfieldensis, Desulfamplus magnetovallimortis, and Desulfococcus oleovorans (P<0.05). CWI treatment resolved these disturbances and restored the gut microbiota to a level similar to that of the CTRL group. Metagenomic analysis showed that CWI restored gut microbiota diversity (Shannon index, P<0.05), significantly reducing the proportion of pathogenic Desulfovibrio. Metabolomic profiling identified key metabolites, such as inosine, hypoxanthine, guanosine, and taurine (Variable importance in projection>1, P<0.05 with P-values adjusted for multiple comparisons using the Benjamini-Hochberg method, FDR<0.05), differentiating between the CWI and EHS groups.

Conclusion: The metabolites inosine, taurine, hypoxanthine, and guanosine correlated with restored gut microbiota, reduced proportion of Desulfovibrio, and attenuated inflammation (lower LPS/Lac), suggesting that their dual role in mitigating intestinal damage. These findings underscore the therapeutic potential of CWI by modulating microbial-derived metabolites, highlighting its impact on the intestinal health of patients with EHS.

Objective: To establish a gallstone mouse model using a lithogenic diet and investigate changes in the gut microbiota of gallstone mice at different altitudes.

Methods: Sixty mice were randomly assigned to four groups: plain healthy, plain stone, high-altitude healthy, and high-altitude stone. Mice were raised in either plain or high-altitude environments, and a lithogenic diet was used to induce gallstone formation. After 8 weeks, the mice were euthanized, and stone formation was assessed. Blood samples were collected to measure serum total cholesterol (T-CHO), triglycerides (TG), and bile acid (TBA) levels. Fecal samples were also collected for 16S rDNA high-throughput sequencing to analyze the gut microbiota.

Results: TG and T-CHO levels were significantly elevated in gallstone mice in the plain and high-altitude groups. Differential microbiota analysis indicated a decrease in Bacteroidetes and an increase in Firmicutes in the gallstone groups. Several specific bacterial genera showed significant changes in the gallstone mice compared to the healthy controls.

Conclusion: 1) Gut microbiota imbalance likely contributes to gallstone formation in mice, and higher microbiota diversity may reduce the incidence of gallstones. 2) The incidence of gallstones is higher at high altitudes than at lower altitudes, possibly due to hypoxic conditions and elevated inflammation levels.

The human microbiome plays a critical role in shaping physiological processes, immune system function, metabolism, and disease development. Recent research has highlighted the microbiome's profound cancer impact, particularly on lung cancer. This review explores how microbial communities in lung and gut influence tumor progression, immune responses, and treatment outcomes as well as describing the interactions between the microbiome and the host immune system in modulating the efficacy of cancer therapies. Emerging evidence from preclinical and clinical studies investigating the role of the lung and gut microbiome in lung cancer focus on alterations in the microbiota that influence the tumor microenvironment, modulate immune responses, and potentially enhance/hinder treatment effectiveness such as chemotherapy, targeted therapies, and immunotherapy. Microbial diversity plays a significant role in immune regulation, and specific microbial species may activate/suppress immune cells such as T-cells, dendritic cells, and macrophages. Furthermore, this review examines the therapeutic implications of microbiome modulation, including the use of probiotics, antibiotics, and fecal microbiota transplantation in enhancing cancer therapies. Alterations in the lung and gut microbiome and their interaction in the recently described gut-lung axis with its bidirectional communication significantly influence the tumor microenvironment and systemic immune responses. These findings suggest that microbial diversity can regulate immune functions, with specific species capable of activating or suppressing immune cell activity. Furthermore, microbiome-targeted interventions show potential in improving the effectiveness of treatments including chemotherapy, targeted therapies, and immunotherapy, underscoring the importance of the microbiome as a key factor in lung cancer pathogenesis and treatment.

Introduction: Tilapia (Oreochromis spp.) are among the most widely cultivated freshwater finfish species worldwide. The industry increasingly relies on tilapia strains selected for improved growth and other traits, particularly the Genetically Improved Farmed Tilapia (GIFT) strain. Despite the industry's reliance on tilapia, knowledge of microbiome dynamics in reared tilapia remains limited. Understanding normal successional patterns in the microbiome of farmed tilapia is essential for identifying the characteristics that constitute a healthy microbial community.

Methods: In this study, we assessed the microbiomes of tank and pond-reared GIFT tilapia by analyzing 568 samples, including water, gut, skin, and gill microbiomes of tilapia, from tank systems housing the source GIFT populations in Malaysia. We compared them to those reared in earthen ponds on another farm in Malaysia.

Results: A total of 2,307 amplicon sequence variants (ASVs) were identified, encompassing a broad taxonomic diversity of 39 phyla, 86 classes, 180 orders, 299 families, 501 genera, and 399 species. Our findings elucidated distinct microbial community structures between rearing environments and across fish tissues, shedding light on intricate host-microbe interactions shaped by environmental conditions and management practices. The gut microbiome of tank-reared tilapia was dominated by Fusobacteriota (71.14%), in contrast to pond-reared fish (22%). At the same time, other taxa, such as Bacteroidota, Firmicutes_A, and Cyanobacteria, also varied markedly between environments and sampling periods. Skin and gill samples exhibited notable variability in the relative abundances of Fusobacteriota and Deinococcota between the two rearing sites. Principal Coordinates Analysis (PCoA) highlighted the distinct clustering of samples by rearing environment, particularly within gut microbiomes. Biomarkers such as Cyanobiaceae (pond water) and Sphingomonadaceae (tank water) underscored the impact of rearing conditions on microbial composition.

Discussion: These results establish valuable baseline information on the types of bacteria associated with healthy, genetically defined (GIFT) tilapia strains. This foundational information will help identify specific microbial taxa associated with beneficial or detrimental effects on tilapia health and productivity across varying rearing conditions. Such insights can guide the development of practical microbiome monitoring strategies, such as early-warning tools for farm health, and inform targeted interventions to improve aquaculture performance.

Introduction: Soil microorganisms play a crucial role in plant development, while biopolymers, such as cork and Extracellular Polymeric Substances/Exopolysaccharides (EPS), can enhance soil health. However, these amendments may affect DNA extraction and microbial analysis, necessitating the validation of the extraction method before conducting next-generation sequencing (NGS).

Methods: This study evaluated 48 soil samples from Decatur, Alabama (Silt loam) that underwent four treatments: unamended soil (soil.control), soil with cork (soil.cork), soil with EPS (soil.EPS), and soil with both cork and EPS (soil.cork.EPS). Samples were collected at four time intervals (0-, 24-, 48-, and 72-hours post-treatment), with three biological replicates for each treatment. The FastDNA Spin Kit proved the most effective among the six DNA extraction methods tested.

Results and discussion: Amplicon sequencing of the 16S rRNA gene identified 62,996 amplicon sequence variants (ASVs), with 513 ASVs shared across all time points and 467 ASVs shared among the different treatments. The microbial community was primarily composed of Actinobacteria, Proteobacteria, and Acidobacteria, with Actinobacteria being the most abundant phylum. Actinobacteria, Alphaproteobacteria, Bacilli, and Betaproteobacteria contributed to microbial diversity at the class level. Notable families such as Bacillaceae, Gaiellaceae, Micromonosporaceae, and Streptomycetaceae showed treatment-dependent variations. Core microbiome analysis revealed Bacillus and Gaiella as the dominant genera, which play vital roles in soil ecosystem stability and nutrient cycling. These microbes contribute to carbon sequestration, nitrogen fixation, and phosphorus solubilization, improving soil fertility and plant-microbe interactions. These findings offer valuable insights into microbial dynamics in amended soils, providing information that can improve soil quality and agricultural productivity.

Anthropogenic climate change caused by CO₂ emissions forces humanity to reduce the usage of fossil fuels. Along with the task of emission reduction, societies face the task of removing excess CO₂ from the atmosphere by using negative emission technologies (NETs). Ocean alkalinity enhancement (OAE) is a proposed NET, aiming at increasing oceanic CO₂ uptake through the addition of alkaline substances. This is an anthropogenically accelerated version of rock weathering, a natural global process for atmospheric CO₂ regulation. The environmental impacts of OAE remain poorly understood. This study was part of a comprehensive OAE-mesocosm experiment in the North Sea (RETAKE), and focused on the effects of OAE on the pelagic bacterial community during the experiment. We assessed changes in bacterial community structure with 16S rRNA amplicon sequencing and abundance with flow cytometry, to evaluate responses to alkalinity addition. Beta diversity analysis showed that sampling time was the primary driver for community variation, with only marginal structural differences linked to alkalinity treatments. PERMANOVA tests conducted on predictions of functional metabolic pathways of the community revealed significant differences between treatments and baseline controls. A deeper analysis of the identified metabolic pathways revealed little evidence for alkalinity-induced changes. In contrast, total bacterial cell counts were influenced by alkalinity additions, showing delayed abundance peaks at higher concentrations and a non-linear response threshold between 500-750 µmol/L. These dynamics were linked to shifts in chlorophyll concentrations, suggesting an indirect effect of OAE on bacteria mediated by phytoplankton derived resources. This study is one of the first to assess ecological impacts of OAE on bacteria. Our findings highlight a structural resilience of bacterial communities to OAE but also show a quantitative response. By discussing our findings, this study aims to provide focus points, such as a threshold for save levels of alkalinity addition, to direct future research.

The best way to fight harmful microbes may not lie in new antibiotics, but rather in leveraging the power of microbes themselves. Antimicrobial resistance (AMR) is a growing global concern, where the overuse of antibiotics has led to the emergence of resistant strains. This paper explores the potential of increasing diversity in gut microbiomes as natural approaches to fight AMR. The promotion microbial diversity is proposed as a promising strategy to reduce dependency on antibiotics by fostering a resilient microbial community. Strategies are discussed to address the loss of diversity caused by antibiotics including diet, probiotics, fecal transplants (FMT) and fermentation of animal/plant products. Preliminary findings from an experiment with camel milk fermentation suggest that fermentation can increase microbial diversity, potentially affecting resistance to common antibiotics such as tetracycline, streptomycin, penicillin, and chloramphenicol, and enhancing microbiome resilience, allowing it to naturally resist pathogens without additional antibiotic use. The results highlight both the benefits and potential risks fermented products. Additionally, FMT, naturally occurring in the animal world, is a promising method to restore microbiome balance and mitigating the impact of AMR. A mechanistic model is discussed to underscore the importance of maintaining microbial balance as an effective strategy for mitigating AMR and promoting long-term health. Further research are needed to better understand the mechanisms behind these changes and their implications for public health. This perspective paper calls for a shift in the approach to AMR, advocating for microbiome-based solutions as a sustainable alternative to traditional pharmaceutical interventions.

Introduction: Pancreatic ductal adenocarcinoma (PDAC) is an aggressive form of pancreatic cancer, with overall 5-year survival rates of about 8%. Obesity (and underlying metabolic dysfunction) is estimated to account for up to 50% of all PDACs. Microbial communities can be modulated by obesity and exert biological effects on tissues they colonize as well as distant sites. Recent studies showed that tumors, including PDAC, harbor a microbiome that is able to regulate cancer outcomes such as tumor progression, response to therapy and overall survival. Yet, it is not understood whether patient's characteristics impact this relationship.

Methods: We examined the influence of obesity (defined by body weight in mice or body mass index [BMI] in humans) on the normal and cancerous pancreas microbiome in mice and humans using 16S sequencing.

Results: Overall, we observed that diet-induced obesity accelerated PDAC progression in the KC mouse model of PDAC. We also detected an obesity-induced decrease in the microbial abundance of the normal or cancerous pancreas. Obesity modified the bacterial community composition in the normal pancreas and PDAC of both mice and humans. Further, obese animals and humans each had a distinctive pancreatic microbiome signature with specific bacterial phylum, genus and species compared to controls. Notably, both the normal mouse pancreas and human PDAC showed an obesity-induced decrease in Pseudomonadota phylum. We also found that the presence of cancer by itself reduced microbial diversity in both the pancreas as well the intestinal microbiota. This reduction in microbial richness was further exacerbated by obesity. Finally, we observed that obesity increased inflammatory cytokines and altered the tumor immune infiltrate in humans and mice.

Discussion: Further investigation of obesity-driven microbial differences in the pancreas could provide important insights for personalized treatments for PDAC patients.