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Temporal dynamics of fecal microbiota community succession in broiler chickens, calves, and piglets under aerobic exposure.
- Source :
-
Microbiology spectrum [Microbiol Spectr] 2024 Jun 04; Vol. 12 (6), pp. e0408423. Date of Electronic Publication: 2024 May 08. - Publication Year :
- 2024
-
Abstract
- Researchers have extensively studied the effect of oxygen on the growth and survival of bacteria. However, the impact of oxygen on bacterial community structure, particularly its ability to select for taxa within the context of a complex microbial community, is still unclear. In a 21-day microcosm experiment, we investigated the effect of aerobic exposure on the fecal community structure and succession pattern in broiler, calf, and piglet feces ( n = 10 for each feces type). Bacterial diversity decreased and community structure changed rapidly in the broiler microbiome ( P < 0.001), while the fecal community of calves and piglets, which have higher initial diversity, was stable after initial exposure but decreased in diversity after 3 days ( P < 0.001). The response to aerobic exposure was host animal specific, but in all three animals, the change in community structure was driven by a decrease in anaerobic species, primarily belonging to Firmicutes and Bacteroidetes (except in broilers where Bacteroidetes increased), along with an increase in aerobic species belonging to Proteobacteria and Actinobacteria. Using random forest regression, we identified microbial features that predict aerobic exposure. In all three animals, host-beneficial Prevotella -related ASVs decreased after exposure, while ASVs belonging to Acinetobacter , Corynbacterium, and Tissierella were increased. The decrease of Prevotella was rapid in broilers but delayed in calves and piglets. Knowing when these pathobionts increase in abundance after aerobic exposure could inform farm sanitation practices and could be important in designing animal experiments that modulate the microbiome.IMPORTANCEThe fecal microbial community is contained within a dynamic ecosystem of interacting microbes that varies in biotic and abiotic components across different animal species. Although oxygen affects bacterial growth, its specific impact on the structure of complex communities, such as those found in feces, and how these effects vary between different animal species are poorly understood. In this study, we demonstrate that the effect of aerobic exposure on the fecal microbiota was host-animal-specific, primarily driven by a decrease in Firmicutes and Bacteroidetes, but accompanied by an increase in Actinobacteria, Proteobacteria, and other pathobionts. Interestingly, we observed that more complex communities from pig and cattle exhibited initial resilience, while a less diverse community from broilers displayed a rapid response to aerobic exposure. Our findings offer insights that can inform farm sanitation practices, as well as experimental design, sample collection, and processing protocols for microbiome studies across various animal species.<br />Competing Interests: The authors declare no conflict of interest.
- Subjects :
- Animals
Swine microbiology
Cattle microbiology
Aerobiosis
RNA, Ribosomal, 16S genetics
Bacteroidetes genetics
Bacteroidetes classification
Bacteroidetes isolation & purification
Microbiota
Feces microbiology
Chickens microbiology
Bacteria classification
Bacteria genetics
Bacteria isolation & purification
Gastrointestinal Microbiome
Subjects
Details
- Language :
- English
- ISSN :
- 2165-0497
- Volume :
- 12
- Issue :
- 6
- Database :
- MEDLINE
- Journal :
- Microbiology spectrum
- Publication Type :
- Academic Journal
- Accession number :
- 38717193
- Full Text :
- https://doi.org/10.1128/spectrum.04084-23