Metabolic pathways associated with Firmicutes prevalence in the gut of multiple livestock animals and humans
Abstract Dynamic interspecific interactions and environmental factors deeply impact the composition of microbiotic communities in the gut. These factors intertwined with the host’s genetic background and social habits cooperate synergistically as a hidden force modulating the host’s physiological an...
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BMC
2025-03-01
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| Series: | Animal Microbiome |
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| Online Access: | https://doi.org/10.1186/s42523-025-00379-y |
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| author | Beatriz do Carmo Dias Alessandra Pavan Lamarca Douglas Terra Machado Vinicius Prata Kloh Fabíola Marques de Carvalho Ana Tereza Ribeiro Vasconcelos |
| author_facet | Beatriz do Carmo Dias Alessandra Pavan Lamarca Douglas Terra Machado Vinicius Prata Kloh Fabíola Marques de Carvalho Ana Tereza Ribeiro Vasconcelos |
| author_sort | Beatriz do Carmo Dias |
| collection | DOAJ |
| description | Abstract Dynamic interspecific interactions and environmental factors deeply impact the composition of microbiotic communities in the gut. These factors intertwined with the host’s genetic background and social habits cooperate synergistically as a hidden force modulating the host’s physiological and health determinants, with certain bacterial species being maintained from generation to generation. Firmicutes, one of the dominant bacterial phyla present across vertebrate classes, exhibits a wide range of functional capabilities and colonization strategies. While ecological scenarios involving microbial specialization and metabolic functions have been hypothesized, the specific mechanisms that sustain the persistence of its microbial taxa in a high diversity of hosts remain elusive. This study fills this gap by investigating the Firmicutes metabolic mechanisms contributing to their prevalence and heritability in the host gut on metagenomes-assembled bacterial genomes collected from 351 vertebrate samples, covering 18 food-producing animals and humans, specific breeds and closely-related species. We observed that taxa belonging to Acetivibrionaceae, Clostridiaceae, Lachnospiraceae, Ruminococcaceae, and the not well understood CAG-74 family were evolutionarily shared across all hosts. These prevalent taxa exhibit metabolic pathways significantly correlated with extra-host survival mechanisms, cell adhesion, colonization and host transmission, highlighted by sporulation, glycan biosynthesis, bile acid metabolism, and short-chain fatty acid encoded genes. Our findings provide a deeper understanding of the ecological foundations governing distinct transmission modes, effective colonization establishment, and maintenance of Firmicutes, offering new perspectives on both well-known and poorly characterized species. |
| format | Article |
| id | doaj-art-33b20133a2fc42078ceb341fce576eb0 |
| institution | OA Journals |
| issn | 2524-4671 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | BMC |
| record_format | Article |
| series | Animal Microbiome |
| spelling | doaj-art-33b20133a2fc42078ceb341fce576eb02025-08-20T01:57:48ZengBMCAnimal Microbiome2524-46712025-03-017112210.1186/s42523-025-00379-yMetabolic pathways associated with Firmicutes prevalence in the gut of multiple livestock animals and humansBeatriz do Carmo Dias0Alessandra Pavan Lamarca1Douglas Terra Machado2Vinicius Prata Kloh3Fabíola Marques de Carvalho4Ana Tereza Ribeiro Vasconcelos5Laboratório de Bioinformática, Laboratório Nacional de Computação CientíficaLaboratório de Bioinformática e Evolução Molecular, Universidade Federal do Rio de JaneiroLaboratório de Bioinformática, Laboratório Nacional de Computação CientíficaLaboratório de Bioinformática, Laboratório Nacional de Computação CientíficaLaboratório de Bioinformática, Laboratório Nacional de Computação CientíficaLaboratório de Bioinformática, Laboratório Nacional de Computação CientíficaAbstract Dynamic interspecific interactions and environmental factors deeply impact the composition of microbiotic communities in the gut. These factors intertwined with the host’s genetic background and social habits cooperate synergistically as a hidden force modulating the host’s physiological and health determinants, with certain bacterial species being maintained from generation to generation. Firmicutes, one of the dominant bacterial phyla present across vertebrate classes, exhibits a wide range of functional capabilities and colonization strategies. While ecological scenarios involving microbial specialization and metabolic functions have been hypothesized, the specific mechanisms that sustain the persistence of its microbial taxa in a high diversity of hosts remain elusive. This study fills this gap by investigating the Firmicutes metabolic mechanisms contributing to their prevalence and heritability in the host gut on metagenomes-assembled bacterial genomes collected from 351 vertebrate samples, covering 18 food-producing animals and humans, specific breeds and closely-related species. We observed that taxa belonging to Acetivibrionaceae, Clostridiaceae, Lachnospiraceae, Ruminococcaceae, and the not well understood CAG-74 family were evolutionarily shared across all hosts. These prevalent taxa exhibit metabolic pathways significantly correlated with extra-host survival mechanisms, cell adhesion, colonization and host transmission, highlighted by sporulation, glycan biosynthesis, bile acid metabolism, and short-chain fatty acid encoded genes. Our findings provide a deeper understanding of the ecological foundations governing distinct transmission modes, effective colonization establishment, and maintenance of Firmicutes, offering new perspectives on both well-known and poorly characterized species.https://doi.org/10.1186/s42523-025-00379-yBacterial hereditaryVertebrate gutFirmicutesMetagenome-assembled genomesMetabolic pathway inference |
| spellingShingle | Beatriz do Carmo Dias Alessandra Pavan Lamarca Douglas Terra Machado Vinicius Prata Kloh Fabíola Marques de Carvalho Ana Tereza Ribeiro Vasconcelos Metabolic pathways associated with Firmicutes prevalence in the gut of multiple livestock animals and humans Animal Microbiome Bacterial hereditary Vertebrate gut Firmicutes Metagenome-assembled genomes Metabolic pathway inference |
| title | Metabolic pathways associated with Firmicutes prevalence in the gut of multiple livestock animals and humans |
| title_full | Metabolic pathways associated with Firmicutes prevalence in the gut of multiple livestock animals and humans |
| title_fullStr | Metabolic pathways associated with Firmicutes prevalence in the gut of multiple livestock animals and humans |
| title_full_unstemmed | Metabolic pathways associated with Firmicutes prevalence in the gut of multiple livestock animals and humans |
| title_short | Metabolic pathways associated with Firmicutes prevalence in the gut of multiple livestock animals and humans |
| title_sort | metabolic pathways associated with firmicutes prevalence in the gut of multiple livestock animals and humans |
| topic | Bacterial hereditary Vertebrate gut Firmicutes Metagenome-assembled genomes Metabolic pathway inference |
| url | https://doi.org/10.1186/s42523-025-00379-y |
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