Advances in DNA sequencing technologies and data analysis have provided drastic improvements in microbiome analyses, for example, in taxonomic resolution, false discovery rate control and other properties, over earlier methods. In this Review, we discuss the best practices for performing a microbiome ...
The microbiota colonizing the root endophytic compartment and surrounding rhizosphere soils contribute to plant growth and health. However, the key members of plant soil and endophytic microbial communities involved in inhibiting or assisting pathogen in
and provide a perspective for further directions in support of the understanding of microbial communities. Key words: microbiome; multi-omics; co-occurrence; network analysis; integrated analysis Summary of microbiome studies As complex biological systems, microbial communities are not merely a legion of...
Doing meta-analysis in R: a hands-on guide; 2019. https://doi.org/10.5281/zenodo.2551802. Book Google Scholar Ma N, Ma X. Dietary amino acids and the gut-microbiome-immune axis: physiological metabolism and therapeutic prospects. Compr Rev Food Sci Food Saf. 2019;18(1):221–42. ...
in migratory birds. Moreover, metagenomic assembly-based host tracking revealed that most of the ARG-carrying contigs originate fromProteobacteria. Co-occurrence patterns revealed by network analysis showed thatemrD,emrY,ANT(6)-Ia, andtetO, the hubs of ARG type network, are indicators of other ...
analysis, classified them according to functional categories (diversity, differential, biomarker, correlation and network analysis, functional prediction, and other), which could help researchers quickly find relevant R packages for microbiome analysis. Furthermore, we systematically sorted the integrated R ...
Moreover, the results of the downstream analysis can also be stored in the MPSE class, which is also different from existing related packages. For example, we used mp_rrarefy to rarefy the primary matrices data and added the results into the assays slot, then used mp_cal_alpha to ...
community structure is consistent with the monitored results (Additional file4: Figure S3) and co-occurrence ofseason-associated OTUswithin the same phylum in network analysis (Additional file5: Figure S4, Fig.1b, d). In each phylum, positive association (red lines) dominates negative association...
Machine learning and statistical analysis workflows implemented in SIAMCAT The SIAMCAT R package is a versatile toolbox for analyzing microbiome data from case-control studies. The default workflows abstract from and combine many of the complex steps that these workflows entail and that can be diffic...
etc. There is still a lack of systematic learning materials both in China and around the world. The purpose of establishing the "Metagenome" Public WeChat Account is to break the barriers to the analysis and interpretation of microbiome data and promote the development of this field. At present...