Large scale metagenome assembly reveals novel animal-associated microbial genomes, biosynthetic gene clusters, and other genetic diversity

Abstract

Large-scale metagenome assemblies of human microbiomes have produced a vast catalogue of previously unseen microbial genomes; however, comparatively few microbial genomes derive from other vertebrates. Here, we generated 4374 metagenome assembled genomes (MAGs) from gut samples of 180 predominantly wild animal species representing 5 classes. Combined with existing datasets, we produced 5596 non-redundant, quality MAGs and 1522 species-level genome bins (SGBs). Most SGBs were novel at the species, genus, or family levels, and the majority were enriched in host versus environment metagenomes. Many traits distinguished SGBs enriched in host or environmental biomes, including the number of antimicrobial resistance genes. We identified 1986 diverse and largely novel biosynthetic gene clusters. Gene-based assembly revealed tremendous gene diversity, much of it host or environment specific. Our MAG and gene datasets greatly expand the microbial genome repertoire and provide a broad view of microbial adaptations to life within a living host.

Large-Scale Metagenome Assembly Reveals Novel Animal-Associated Microbial Genomes, Biosynthetic Gene Clusters, and Other Genetic Diversity

“…In total, 289 samples passed our read quality control (QC), with 3.4e6 ± 5e6 (standard deviation [SD]) paired-end reads per sample, resulting in a mean estimated coverage ± SD of 0.54 ± 0.14 (see Fig. S1 in reference 15 ). One hundred eighty animal species were represented, with up to 6 individuals per species (mean of 1.6).…”

“…After quality control and dereplication (see Materials and Methods), 296 MAGs remained, with mean percent completeness and contamination ± SD of 84% ± 14% and 1.5% ± 1.2%, respectively (see Fig. S2 and supplemental results in reference 15 ).…”

“…We applied our assembly pipeline to each individual data set and generated a total of 5,301 nonredundant MAGs (see Fig. S3 and supplemental results in reference 15 ). The substantially higher number of MAGs from these 14 data sets than in our single multispecies data set is likely due to the larger number of samples and the high sequencing depth for many of those samples (e.g., we used 2 billion paired-end reads from the dog gut microbiome data set [ 16 ]).…”

MicrobeAnnotator: a user-friendly, comprehensive functional annotation pipeline for microbial genomes

“…We compared MicrobeAnnotator to other popular genome annotation pipelines, including Prokka v1.14.6 [ 8 ], RAST [ 7 ], EggNOG-mapper v2.0.1b-4-g4c2b55e, InterProScan v5.47-82.0 and DRAM. The first comparison was in terms of database entries used by each tool.…”

“…A crucial step in assessing the metabolic role of community members is the functional gene prediction and metabolic reconstruction [ 5 ]. The functional gene data can also be used to infer the metabolic differences with close relatives, characterize novel potential metabolisms, or detect the presence of antibiotic resistance genes or toxins, among other genes of interest [ 6 , 7 ].…”