Genome-centered characterization of the microbial communities in llamas’ forestomach via whole-genome shotgun metagenomics

Background The llama is a domesticated South American camelid that inhabits arid and semiarid regions of the Andes, where animals are exposed to high-altitude environments characterized by water scarcity and low-quality grasslands. The forestomach microbiome plays a key role in host nutrition by degrading complex dietary polysaccharides and producing volatile fatty acids. However, its taxonomic composition and functional potential remain poorly characterized. Results In this study, we performed a genome-resolved metagenomic analysis of the llama forestomach microbiome. Digesta samples were collected from five male llamas fed native grasses in Jujuy, Argentina (3,500 m a.s.l.). DNA was extracted and sequenced via a combination of Illumina short reads and Nanopore long reads. Coassembly of both datasets enabled the reconstruction of 165 nonredundant metagenome-assembled genomes spanning 13 phyla, 76% of which could not be assigned to any previously described species, highlighting the high level of unexplored microbial diversity in this environment. Taxonomic profiling revealed that members of the class Bacteroidia were the most abundant group, followed by Bacilli and Clostridia . The functional annotation of the recovered genomes revealed genes encoding enzymes involved in the degradation of major plant polysaccharides present in the llama diet, leading to pyruvate formation and its subsequent conversion into volatile fatty acids. Conclusions In this study, we characterized the microbial communities inhabiting the llama forestomach via genome-resolved metagenomics, reconstructed 165 metagenome-assembled genomes and identified key metabolic pathways involved in plant biomass degradation and fermentation. Despite limitations in sequencing depth that may have prevented a more complete recovery of genomes, our results revealed several dominant community members with the potential to degrade complex polysaccharides and convert them into volatile fatty acids, which are essential energy sources for the host. Our findings expand the current knowledge of microbial diversity in South American camelids and highlight previously undescribed microorganisms potentially involved in lignocellulosic degradation and host nutrition.