Frontiers in microbiomes最新文献

In recent years, there has been a growing emphasis on the use of plant polysaccharides in animal husbandry, attracting attention for their distinctive benefits and roles. These natural and eco-friendly feed additives not only enhanced livestock performance but also promoted intestinal health and strengthen immunity. This study utilized 16S rRNA high-throughput sequencing to investigate the effects of dietary Codonopsis pilosula polysaccharides on the gut microbiota of Hu sheep. Eighteen 3-month-old Hu sheep with similar body weight (19.60 ± 1.63 kg) and good body condition, were randomly allocated into three groups: a control group (CK) receiving a standard diet, and two trial groups: T1 (supplemented with 0.15% Codonopsis pilosula polysaccharides) and T2 (supplemented with 0.3% Codonopsis pilosula polysaccharides), with six animals in each group. The pre-trial period lasted for 7 days, followed by an experimental period of 90 days. Results demonstrated that incorporating Codonopsis pilosula polysaccharides into the diet markedly increased the acetic acid levels in the ileum. This incorporation was found to enhance the diversity of intestinal flora and influence the species composition and richness of the intestinal microbiota. LEfSe analysis revealed that the genus enriched in the three intestinal segments were primarily Candidatus_Saccharimonas, Christensenellaceae_R_7_group, Romboutsia, and UCG_005. The relative expression levels of Claudin, Occludin, and ZO-1 mRNA in the T1 group were found to be elevated compared to the CK and T2 groups across all three intestinal segments. In conclusion, these findings indicate that dietary supplementation with Codonopsis pilosula polysaccharides not only regulate the intestinal microbial composition of Hu sheep but also enhance their immune capacity by increasing the presence of specific beneficial bacteria, thus fostering the intestinal health of Hu sheep.

Background: Interest in the intestinal microbiota has surged in recent years, leading to the development of various microbiota tests utilizing stool analysis. This study aimed to assess the clinical utility of the TestUrGut.

Results: The abundances of different microbial markers analyzed correlated with various factors and symptoms. While no age differences were observed, an increase in A. muciniphila abundance was noted in women compared to men. Body mass index significantly influenced the abundance of A. muciniphila and M. smithii. Additionally, variations in the abundances of A. muciniphila and M. smithii, as well as a greater presence of Firmicutes or Bacteroidetes based on stool patterns, were linked to diarrhea or constipation. The dysbiosis index was validated, distinguishing between temporary and pathological dysbiosis.

Conclusions: This study revealed significant relationships between the intestinal microbiota and digestive tract symptoms. Microbial markers have emerged as robust indicators of the overall state of the intestinal microbiota, demonstrating that variations are closely associated with patients' clinical symptoms.

Autoimmune diseases arise from the immune system's dysregulated attack on the body's own tissues, influenced by a complex interplay of genetics, environment, and the microbiome. This comprehensive review and meta-analysis examines the dynamic relationship between gut microbiota and autoimmune diseases, highlighting their role in disease onset, progression, and potential therapeutic interventions. Emerging evidence underscores the bidirectional interactions between microbiota and immune pathways, particularly through mechanisms like mucosal immune modulation and regulatory T-cell activity. Microbiota dysbiosis, characterized by altered diversity and function, is consistently associated with autoimmune conditions such as rheumatoid arthritis, multiple sclerosis, and type 1 diabetes. The review identifies critical microbiota-driven factors, including antigenic mimicry and inflammatory signaling pathways that disrupt immune tolerance and exacerbate autoimmunity. Meta-analysis findings reveal a consistent reduction in microbial diversity across autoimmune diseases, emphasizing the role of specific taxa and their metabolites in influencing disease severity and immune responses. Therapeutic strategies, such as probiotics, prebiotics, and microbiome-targeted interventions, offer promising avenues to restore microbiome balance and mitigate autoimmune inflammation. Despite significant advances, challenges in methodology, limited longitudinal studies, and heterogeneity in results highlight the need for standardized research protocols and larger, well-controlled clinical trials. Future studies should prioritize personalized approaches to microbiome modulation, integrating dietary, genetic, and environmental factors to improve disease management and prevention. This work consolidates current knowledge, providing a framework for future research and clinical applications in the field of microbiome-autoimmune interactions.

This research aims to assess whether sequencing the full length of the 16S rRNA gene using PacBio HiFi sequencing and Oxford Nanopore Technology (ONT) platforms outperform Illumina MiSeq platform in providing detailed specie level insights. Moreover, it aims to compare the similarities in microbial communities detected across the three platforms. The study employed DNA from four rabbit does' soft feces, sequenced using Illumina MiSeq for specific 16S rRNA gene regions V3-V4, and for the complete gene sequencing using PacBio HiFi and ONT MinION. Results highlight different levels of taxonomic resolution. At the species level, PacBio and ONT exhibited the better resolutions with 63% and 76% respectively, while 48% for Illumina. However, across all three platforms, the classification output at species level was mainly labeled as "Uncultured_bacterium" for most of the classified sequences, which does not improve the understanding of the gut microbiota composition in rabbits. Moreover, although high correlations between relative abundances of taxa were observed, diversity analysis showed significant differences between the taxonomic compositions of the three platforms. These findings suggest that while PacBio and ONT offer improvements in species-level resolution compared to Illumina, due to references databases ambiguous annotation, all three platforms still fall short in providing a precise species level characterization of the gut microbiota composition in rabbits. Additionally, the disparities observed across the results from these platforms highlight the significant impact of sequencing platform, especially when different primers are used. This consideration is particularly important when comparing or analyzing sequences derived from different sequencing technologies.

Rumen microbial communities are known to drive methane (CH₄) production, but their dynamics in variable "real-world" farming environments are less understood. This research aims to identify specific microbial taxa linked to CH₄ emission in commercial dairy farms by employing 16S rRNA gene sequencing, thereby providing a more ecologically relevant understanding of CH₄ production in real-world settings.Rumen fluid samples were collected from 212 cows across seventeen Dutch dairy farms. Methane production was measured from these dairy cows using the GreenFeed system and expressed as CH₄ intensity (g fat- and protein-corrected milk yield^-1). Rumen microbiota was analyzed using 16S rRNA gene amplicon sequencing. Analysis was performed to assess association between microbial taxa and CH₄ intensity, using data from individual cattle across the dairy farm. We observed that diet and lactation stage influenced CH₄ intensity, consistent with previous studies. Results showed higher CH₄ intensity in cows during late lactation, and feeding type, particularly fresh grass intake, strongly influenced rumen microbiota. However, after classifying low and high CH₄ emitting cows, only limited differences in microbiota composition could be measured. Few taxa, like Lachnospiraceae, were common across both groups, while Ruminoccocaceae and Rikenellaceae were more abundant in low emitters, and Oscillospiraceae in high emitters. Methanobrevibacter differentiated CH₄ emission groups, but archaeal methanogen abundance may not accurately reflect CH₄ variation due to methodological limitations, including reliance on relative abundance, limited taxonomic resolution, and primer bias. Using a bacterial-biased 16S rRNA approach, we observed a limited number of consistent bacterial taxa associated with CH₄ intensity highlights the challenges of studying dairy farms under practical conditions, where variability in diet, genetics, and management practices complicates the identification of specific rumen microbes associated with CH₄ emission. Even with control over key variables, the inherent variability of on-farm conditions impeded the detection of stable microbial patterns. In conclusion, our study clearly indicates that understanding CH₄ emissions from dairy cattle in real-world settings fundamentally requires a broader ecological perspective where rumen microbes are recognized as key determinants influencing microbiota signals within multi-factorial farm settings.

Introduction: When collecting oral and fecal samples for large epidemiological microbiome studies, optimal storage conditions such as immediate freezing are not always feasible. It is essential to study the impact of temporary room temperature (RT) storage on microbiome diversity.

Methods: We conducted a pilot study to validate a sampling protocol based on the viability of 16S rRNA gene sequencing in microbiome samples. Fecal and oral samples from five participants were collected and preserved under different conditions: a) 70% ethanol; b) FIT tube for stool; and c) chlorhexidine solution for oral wash. Four aliquots per sample were stored at RT and frozen at days 0, 5, 10, and 15.

Results: Alpha diversity showed a maximum average decrease of 0.3%, 1.6%, and 1.7% after 5 days for oral, stool in ethanol, and stool in FIT samples, respectively. The relative abundances of the main phyla and orders remained stable throughout the 15 days.

Discussion: Microbiome diversity appears remarkably resilient. Fecal and oral samples stored at RT in 70% ethanol, chlorhexidine, and FIT tubes exhibited minimal changes over 15 days. These results support the feasibility of large-scale microbiome studies with delayed sample processing.

The human respiratory tract microbiome is a multi-kingdom microbial ecology that inhabits several habitats along the respiratory tract. The respiratory tract microbiome promotes host health by strengthening the immune system and avoiding pathogen infection. The lung microbiome mostly originates in the upper respiratory tract. The balance between microbial immigration and removal determines the nature of the lung microbiome. Identification and characterization of microbial communities from airways have been made much easier by recent developments in amplicon and shotgun metagenomic sequencing and data analysis techniques. In pulmonary medicine, there is a growing interest in the respiratory microbiome, which has been linked to human health and illness. However, the primary causes of bacterial co-occurrence seem to be interactions with fungi and bacteria as well as host and environmental factors. This study focused on identifying techniques and the current understanding of the relationship between the microbiota and various lung diseases.