Dataset Information

Fecal Metagenomes and Metagenome-Assembled Genomes from the South American Sea Lion (Otaria flavescens) from the Comau Fjord (42°S), Patagonia.

ABSTRACT: Environmental disturbances can be monitored using sentinel species. We present 30 temporally explicit metagenomes and 166 metagenome-assembled genomes (MAGs) from the gut of the South American sea lion (Otaria flavescens) to further understanding of whether variations in the gut microbiome composition and gene content might reflect environmental disturbances from salmon farming.

SUBMITTER: Guajardo-Leiva S

PROVIDER: S-EPMC10190646 | biostudies-literature | 2023 May

REPOSITORIES: biostudies-literature

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Publications

Fecal Metagenomes and Metagenome-Assembled Genomes from the South American Sea Lion (Otaria flavescens) from the Comau Fjord (42°S), Patagonia.

Guajardo-Leiva Sergio S Berríos-Farías Valentín V Bermúdez Felipe G FG Castro-Nallar Eduardo E

Microbiology resource announcements 20230417 5

Environmental disturbances can be monitored using sentinel species. We present 30 temporally explicit metagenomes and 166 metagenome-assembled genomes (MAGs) from the gut of the South American sea lion (Otaria flavescens) to further understanding of whether variations in the gut microbiome composition and gene content might reflect environmental disturbances from salmon farming. ...[more]

PMID: 37067403

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Project description:BACKGROUND:Mycobacterium pinnipedii, a member of the Mycobacterium tuberculosis Complex (MTBC), is capable of infecting several host species, including humans. Recently, ancient DNA from this organism was recovered from pre-Columbian mummies of Peru, sparking debate over the origin and frequency of tuberculosis in the Americas prior to European colonization. RESULTS:We present the first comparative genomic study of this bacterial species, starting from the genome sequencing of two M. pinnipedii isolates (MP1 and MP2) obtained from different organs of a stranded South American sea lion. Our results indicate that MP1 and MP2 differ by 113 SNPs (single nucleotide polymorphisms) and 46 indels, constituting the first report of a mixed-strain infection in a sea lion. SNP annotation analyses indicate that genes of the VapBC family, a toxin-antitoxin system, and genes related to cell wall remodeling are under evolutionary pressure for protein sequence change in these strains. OrthoMCL analysis with seven modern isolates of M. pinnipedii shows that these strains have highly similar proteomes. Gene variations were only marginally associated with hypothetical proteins and PE/PPE (proline-glutamate and proline-proline-glutamate, respectively) gene families. We also detected large deletions in ancient and modern M. pinnipedii strains, including a few occurring only in modern strains, indicating a process of genome reduction occurring over the past one thousand years. Our phylogenomic analyses suggest the existence of two modern clusters of M. pinnipedii associated with geographic location, and possibly host species, and one basal node associated with the ancient M. pinnipedii strains. Previously described MiD3 and MiD4 deletions may have occurred independently, twice, over the evolutionary course of the MTBC. CONCLUSION:The presence of superinfection (i.e. mixed-strain infection) in this sea lion suggests that M. pinnipedii is highly endemic in this population. Mycobacterium pinnipedii proteomes of the studied isolates showed a high degree of conservation, despite being under genomic decay when compared to M. tuberculosis. This finding indicates that further genomes need to be sequenced and analyzed to increase the chances of finding variably present genes among strains or that M. pinnipedii genome remodeling occurred prior to bacterial speciation.

Dataset Information

Fecal Metagenomes and Metagenome-Assembled Genomes from the South American Sea Lion (Otaria flavescens) from the Comau Fjord (42°S), Patagonia.

Publications

Fecal Metagenomes and Metagenome-Assembled Genomes from the South American Sea Lion (Otaria flavescens) from the Comau Fjord (42°S), Patagonia.

Similar Datasets

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