The commensal human microbiome is estimated to outnumber the amount of human body cells by a factor of ten [1]. These complex microbial communities are normal residents of the skin, the oral cavity, vaginal and intestinal mucosa and carry a broad range of functions indispensable for the wellbe...
It is ideal for the (palaeo)genomic analysis of humans, animals, plants, microbes and even microbiomes. The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial...
Characteristics of metabolic functions of gut microbiome in the calves of two clusters Metagenomic functional analysis showed the distinct features between the cluster1 and cluster2. At the KEGG level2, we observed a significant difference in metabolic functions related to amino acid, energy, vitamins...
Microbiome cores were inferred by Principal Component Analysis. For all statistical tests, p < 0.05 was used. Results The study was performed with 3 projects, involving 245 Amplicon and 164 Shotgun metagenome datasets. All comparisons of variables, according to the type of sequencing, showed ...
The analysis of 16S rRNA gene fragment amplicons provided deeper insight into the indigenous enterobacterial microbiome at OTU-based taxonomic levels. After the sequences were quality-filtered and clustered into OTUs, a network was constructed that links each OTU to the respective sample (Fig. 3)....
Microbiome-microbial metabolome-cancer cell interactions in breast cancer-familiar, but unexplored. Cells. 2019;8:293. Denisenko E, Guo BB, Jones M, Hou R, de Kock L, Lassmann T, Poppe D, Clement O, Simmons RK, Lister R, Forrest ARR. Systematic assessment of tissue dissociation and ...
The average variation degree (AVD) were calculated to examine microbial communities stability according to the method of ref.55. A lower AVD value indicates higher microbiome stability. The “niche breadth index” was calculated using “spaa” R packeage56. One-way analysis of variance (ANOVA) ...
In an era of ecosystem degradation and climate change, maximizing microbial functions in agroecosystems has become a prerequisite for the future of global agriculture. However, managing species-rich communities of plant-associated microbiomes remains a major challenge. Here, we propose interdisciplinary re...
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Principal coordinate analysis (PCoA) and principal component analysis (PCA) based on binary Jaccard distance were performed to obtain principal coordinates and visualize complex, multidimensional data in R (v. 2.15.3). Microbiome similarities were identified using the analysis of similarity (ANOSIM) ...