AXIOME3: Automation, eXtension, and Integration Of Microbial Ecology

Abstract

Background Advances in high-throughput sequencing accessibility have democratized small subunit ribosomal RNA gene sequence data collection, coincident with an increasing availability of computational tools for sequence data processing, multivariate statistics, and data visualization. However, existing tools often require programming ability and frequent user intervention that may not be suitable for fast-paced and large-scale data analysis by end user microbiologists who are unfamiliar with the Linux command line environment or who prefer interactions with a GUI. Here we present AXIOME3, which is a completely redeveloped AXIOME pipeline that streamlines small subunit ribosomal RNA data analysis by managing QIIME2, R, and Python-associated analyses through an interactive web interface. Findings AXIOME3 comes with web GUI to improve usability by simplifying configuration processes and task status tracking. Internally, it uses an automated pipeline that is wrapped around QIIME2 to generate a range of outputs including amplicon sequence variant tables, taxonomic classifications, phylogenetic trees, biodiversity metrics, and ordinations. The extension module for AXIOME3 provides advanced data visualization tools such as principal coordinate analysis, bubble plots, and triplot ordinations that can be used to visualize interactions between a distance matrix, amplicon sequence variant taxonomy, and sample metadata. Conclusions Because repeat analysis of small subunit ribosomal RNA amplicon sequence data is challenging for those who have limited experience in command line environments, AXIOME3 now offers rapid and user-friendly options within an automated pipeline, with advanced data visualization tools and the ability for users to incorporate additional analyses easily through extension. AXIOME3 is completely open source (https://github.com/neufeld/AXIOME3, https://github.com/neufeld/AXIOME3-GUI), and researchers are encouraged to modify and redistribute the package.

Archaea Are Rare and Uncommon Members of the Mammalian Skin Microbiome

“…Sequence reads were demultiplexed using the MiSeq Reporter software version 2.5.0.5 (Illumina). Demultiplexed sequences were processed to generate amplicon sequence variants (ASVs) using QIIME2 ( 74 ), managed by Automation, eXtension, and Integration of Microbial Ecology (AXIOME) version 3.0 ( 75 ). Forward and reverse reads were trimmed to a shared nucleotide-515-to-805 V4 region across all data sets using primers 515F-Y and Pro805R (3′- GACTACNVGGGTATCTAATCC -5′) using cut-adapt ( 76 ) version 2019.10.0.…”

Anoxygenic phototroph of the Chloroflexota uses a type I reaction centre

“…Sequence data analysis was performed for V4–V5 region samples using QIIME2 (v2019.10) 72 via the AXIOME3 pipeline 73 , commit 1ec1ea6 ( https://github.com/neufeld/axiome3 ), with default parameters. In brief, paired-end reads were trimmed, merged and denoised using DADA2 (v1.10.0) 74 to generate an amplicon sequence variant (ASV) table.…”

Characterization of skin- and intestine microbial communities in migrating high Arctic lake whitefish and cisco

“…The 16S rRNA gene V4-V5 region was amplified from each water sample and sequenced using the Illumina MiSeq platform (Illumina Inc., San Diego, CA, USA) (Tremblay et al ., 2017; Cobanli et al ., 2022). A total of 564 samples comprising water, intestine, and skin as well as controls were analyzed using Quantitative Insights Into Microbial Ecology 2 (QIIME2) (version 2020.6) (Bolyen et al ., 2019) managed by automated exploration of microbial diversity (AXIOME3) (Min et al ., 2021). DADA2 (version 2020.6; Callahan et al ., 2016) was used to remove primer sequences and chimeras, dereplicate and denoise reads.…”