SeSaMe: Metagenome Sequence Classification of Arbuscular Mycorrhizal Fungi-Associated Microorganisms

Abstract

Arbuscular mycorrhizal fungi (AMF) are plant root symbionts that play key roles in plant growth and soil fertility. They are obligate biotrophic fungi that form coenocytic multinucleated hyphae and spores. Numerous studies have shown that diverse microorganisms live on the surface of and inside their mycelia, resulting in a metagenome when whole-genome sequencing (WGS) data are obtained from sequencing AMF cultivated in vivo. The metagenome contains not only the AMF sequences, but also those from associated microorganisms. In this study, we introduce a novel bioinformatics program, Spore-associated Symbiotic Microbes ( SeSaMe ), designed for taxonomic classification of short sequences obtained by next-generation DNA sequencing. A genus-specific usage bias database was created based on amino acid usage and codon usage of a three consecutive codon DNA 9-mer encoding an amino acid trimer in a protein secondary structure. The program distinguishes between coding sequence (CDS) and non-CDS, and classifies a query sequence into a genus group out of 54 genera used as reference. The mean percentages of correct predictions of the CDS and the non-CDS test sets at the genus level were 71% and 50% for bacteria, 68% and 73% for fungi (excluding AMF), and 49% and 72% for AMF ( Rhizophagus irregularis ), respectively. SeSaMe provides not only a means for estimating taxonomic diversity and abundance but also the gene reservoir of the reference taxonomic groups associated with AMF. Therefore, it enables users to study the symbiotic roles of associated microorganisms. It can also be applicable to other microorganisms as well as soil metagenomes. SeSaMe is freely available at www.fungalsesame.org .

MetaTrass: A high‐quality metagenome assembler of the human gut microbiome by cobarcoding sequencing reads

“…Most of the current approaches to analyzing microbial communities are designed to work with economical next‐generation sequencing (NGS or high‐throughput sequencing [HTS]) reads [ 14 ]. Many highly modularized computational tools have been developed, including genome assemblers, genome binners, taxonomic binners, and taxonomic profilers [ 15 – 17 ]. The assembly‐first‐and‐binning‐later strategies have been commonly used to generate MAGs.…”

The endohyphal microbiome: current progress and challenges for scaling down integrative multi-omic microbiome research

“…Tools have recently been developed to selectively identify eukaryotic and viral contigs from shotgun metagenomics data to aid in the separation and subsequent analyses of certain contigs [ 106 – 108 ]. More specific tools have also shown promise for these analyses: the Spore-associated Symbiotic Microbes (SeSaMe) bioinformatics tool was specifically developed for the sequence classification of microbial associates of arbuscular mycorrhizal fungi from metagenomic sequencing data [ 109 ]. For endohyphal microbiome constituents that are not adequately captured in shotgun metagenomic assemblies, more sensitive read-based taxonomic classification analyses can be used to detect their presence; however, the lack of contigs limits the analyses of other omics types to de novo (without a reference) methods.…”

MetaTrass: High-quality metagenome assembly on the human gut microbiome by co-barcoding sequencing reads

“…Most of current approaches to analyze the microbiome communities are based on high-throughput and low-cost next-generation sequencing (NGS) reads. Many highly modularized computational tools have been developed such as genome assemblers, genome binners, taxonomic binners and taxonomic profilers [13–15]. The combinations of assembling first and binning later have been commonly used to generate metagenome-assembled genomes.…”