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Clustering of samples based on beta diversity. Non-metric multi-dimensional scaling (NMDS) plot of Bray–Curtis distances between samples at a microbial genera and b microbial genes level. The stress values of < 0.2 above the panels indicate that the two-dimensional plot is a fair representation of the original high-dimensional distances with some acceptable distortion.
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The rumen microbiome is the focus of a growing body of research, mostly based on investigation of rumen fluid samples collected once from each animal. Exploring the temporal stability of rumen microbiome profiles is imperative, as it enables evaluating the reliability of findings obtained through single-timepoint sampling. We explored the temporal...
Citations
... Among these, several key taxa are particularly abundant and functionally significant. For example, Prevotella is a dominant genus, central to carbohydrate and hydrogen metabolism; Ruminococcus is renowned for its cellulolytic and amylolytic activities, which are vital for breaking down plant materials; and Butyrivibrio is crucial for degrading xylans, pectins, and hemicellulose, as well as for protein breakdown and biohydrogenation of fatty acids [3]. Methanogenic archaea, such as Methanobacterium and Methanothermobacter, are also highly prevalent, removing hydrogen to support fermentation and methane production [4]. ...
... Specifically, the values for Chao1 and observed species at D14 and D120 were significantly higher than those at D7 and D60. Additionally, the PD whole tree index at D120 was significantly higher than that at D60. 3 Interaction denotes interaction effect between preservation time and storage time. 4 The P0 value signifies a pairwise comparison between frozen rumen fluid at a specific preservation time and freshly collected rumen fluid (D0); in the same row, identical lowercase letters indicate no significant difference, while different lowercase letters indicate significant differences. ...
... 4 The P0 value signifies a pairwise comparison between frozen rumen fluid at a specific preservation time and freshly collected rumen fluid (D0); in the same row, identical lowercase letters indicate no significant difference, while different lowercase letters indicate significant differences. 3 Interaction denotes interaction effect between preservation time and storage time. 4 The P0 value signifies a pairwise comparison between frozen rumen fluid at a specific preservation time and freshly collected rumen fluid (D0); in the same row, identical lowercase letters indicate no significant difference, while different lowercase letters indicate significant differences. ...
The aim of this study was to investigate the effects of storage temperature and preservation time on the microbial diversity and community composition of rumen fluid. Rumen fluid samples were collected from six Hu sheep fed on a high-forage diet and stored at −80 °C and −20 °C for intervals of 0, 7, 14, 30, 60, 120, and 240 days. DNA was extracted at each time point for 16S rRNA gene sequencing to evaluate the rumen microbial diversity and community composition. The results showed that storage temperature affected only the relative abundance of Proteobacteria, with no substantial impact on alpha-diversity or other microbial groups (p > 0.05), and no significant interaction effects were observed between storage temperature and preservation time (p > 0.05). Alpha-diversity indices such as Chao1, observed species, and PD whole tree showed dynamic changes after 7 days of storage, while the relative abundances of Verrucomicrobiota and Christensenellaceae R-7 group, as well as the energy metabolism metabolic pathway, exhibited significant alterations after 14 days of storage (p < 0.05). Notably, Patescibacteria, Rikenellaceae RC9 gut group, and Veillonellaceae UCG-001 abundances demonstrated significant changes after 240 days of storage (p < 0.05). Both principal coordinates analysis (PCoA) and non-metric multidimensional scaling (NMDS) showed distinct overlaps. This study suggests that storing rumen fluid at −80 °C and −20 °C does not influence rumen microbial diversity and community composition, whereas the storage time significantly impacts these factors, with most differences emerging after 14 days of preservation. Consequently, it is advised that the analysis of microbial diversity and community composition in rumen fluid samples be conducted within 14 days post-collection.
