The Gut Microbiome of 54 Mammalian Species

Jonge, Nadieh de; Carlsen, Benjamin; Christensen, Mikkel Hostrup; Pertoldi, Cino; Nielsen, Jeppe Lund

doi:10.3389/fmicb.2022.886252

Cited by 34 publications

(21 citation statements)

References 71 publications

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“…Several MAGs were assigned to families (e.g., Clostridiaceae and Peptostreptococcaceae ) that have been reported to be more abundant in carnivores such as lions ( Panthera leo ), cheetahs ( Acinonyx jubatus ), and African wild dogs ( Lycaon picus ) compared to ruminants or other herbivores ( 42 ). In addition, several MAGs came from families (e.g., Clostridiaceae , Erysipelotrichaceae , and Bacteroidaceae ) reported to be highly correlated with protein and fat digestibility in domestic dogs ( Canis familiarus domesticus ) ( 43 ).…”

Section: Resultsmentioning

confidence: 99%

“…A total of 149 high-quality MAGs were recovered from the gut microbiomes of four adult female hyenas; some MAGs were assigned to genera that formed part of the core microbiome in our studied individuals. Other MAGs were classified to bacterial families or genera found in the GI tracts of other carnivores, including those of wild cats, wild dogs, and domestic dogs ( 42 ). Interestingly, 80% of our MAGs were novel, as they were not classified to the species level and were evolutionarily distant from the genomes in GTDB-r202.…”

Section: Discussionmentioning

confidence: 99%

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Taxonomic, Genomic, and Functional Variation in the Gut Microbiomes of Wild Spotted Hyenas Across 2 Decades of Study

et al. 2023

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There is a gap in knowledge regarding the genomic diversity and variation of the gut microbiome across a host’s life span and across multiple generations of hosts in wild mammals. Using two types of sequencing approaches, we found that although gut microbiomes were individualized and temporally variable among hyenas, they correlated similarly to large-scale changes in the ecological conditions experienced by their hosts.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Taxonomic, Genomic, and Functional Variation in the Gut Microbiomes of Wild Spotted Hyenas Across 2 Decades of Study

et al. 2023

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show abstract

“…Several MAGs were assigned to families (e.g., Clostridiaceae and Peptostreptococcaceae ) that have been reported to be more abundant in carnivores such as lions ( Panthera leo ), cheetahs ( Acinonyx jubatus ), and African wild dogs ( Lycaon picus ) compared to ruminants or other herbivores (87). In addition, several MAGs came from families (e.g., Clostridiaceae, Erysipelotrichaceae and Bacteroidaceae ) reported to be highly correlated with protein and fat digestibility in domestic dogs ( Canis familiarus domesticus ) (88).…”

Section: Resultsmentioning

confidence: 99%

“…A total of 149 high-quality metagenome-assembled genomes were recovered from hyena GI tracts; some of which were assigned genera that formed part of the core microbiome in our studied individuals. Other MAGs were classified to bacterial families or genera found in the GI tracts of other carnivores, including those of wild cats, wild dogs, and domestic dogs (87). Interestingly, 80% of our MAGs were novel, as they were not classified to species-level and were evolutionarily distant from the genomes in GTDB-r95.…”

Section: Discussionmentioning

confidence: 99%

Taxonomic, genomic, and functional variation in the gut microbiomes of wild spotted hyenas across two decades of study

Rojas

Holekamp

Viladomat

et al. 2022

Preprint

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The gut microbiome provides vital functions for mammalian hosts, yet research on the variability and function of the microbiome across adult lifespans and multiple generations is limited in large mammalian carnivores. Here we use 16S rRNA gene and metagenomic sequencing to profile the taxonomic composition, genomic diversity, and metabolic function of the gut microbiome of 12 wild spotted hyenas (Crocuta crocuta) residing in the Masai Mara National Reserve, Kenya over a 23-year period spanning three generations. We determined the extent to which host factors predict variation in the gut microbiome and identify the core microbes present in the guts of hyenas. We also investigate novel genomic diversity in the mammalian gut by reporting the first metagenome-assembled genomes (MAGs) for hyenas. We found that gut microbiome taxonomic composition was highly variable across the two decades of sampling, but despite this, a core set of 22 bacterial genera and 19 amplicon sequence variants were identified. The strongest predictors of microbiome alpha and beta-diversity were host identity and age, suggesting that hyenas possess individualized microbiomes, and that these may change with age during adulthood. Gut microbiome functional profiles were also individual-specific, and were moderately correlated with antelope prey abundance, indicating that the functions of the gut microbiome vary with host diet. We recovered 149 high-quality MAGs from the hyena gut, spanning 25 bacterial orders and 51 genera. Some MAGs were classified as taxa previously reported for other carnivores, but many were novel and lacked species level matches to genomes in existing reference databases, greatly greatly expanding the microbial genome repertoire known for hyenas, carnivores and wild mammals in general.

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“…These complex communities are directly tied to the health and disease of the host. Although numerous studies have been able to provide valuable insights into the GI microbiome in mammals [3][4][5][6], such studies have yet to be done extensively on reptiles, speci cally members of the order Testudines, commonly referred to as turtles and tortoises. Testudines currently contains 357 recognized species, over half (51%) of which are considered globally threatened.…”

Section: Introductionmentioning

confidence: 99%

Microbiome resilience of three-toed box turtles (Terrapene carolina triunguis) in response to rising temperatures

Guan

Ramírez

Eng

et al. 2023

Preprint

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Background The gastrointestinal (GI) microbiome of chelonians plays an important role in their metabolism, nutrition, and overall health but the GI microbiome of three-toed box turtles (Terrapene carolina triunguis) has yet to be characterized. How the GI microbiome responds to rapidly rising environmental temperatures has also not been studied extensively in ectotherms, specifically chelonians. Ambient temperature increases are known to perturb host-associated microbial communities and can result in dysbiosis and possible shedding of pathogens. In this study, twenty (20) T.c.triunguis were split into control and experimental groups. The experimental group experienced 4.5°C increases every two weeks while the control group stayed at a constant ambient temperature (24°C) through the entirety of the experiment. Before each temperature increase, all turtles had cloacal swab samples taken. These samples underwent DNA extraction followed by 16S rRNA gene sequencing and microbial community analyses. Results Community composition of both groups were primarily composed of members of the classes Alphaproteobacteria, Gammaproteobacteria, Bacteroidia, Clostridia, and Bacilli. Differences in diversity at the community level in the controls compared to the experimental groups were not significant, indicating microbiome resilience to rapid temperature changes in T.c.triunguis, although some differentially abundant genera were identified. Interestingly, an amplicon sequence variant belonging to the Erysipelothrix spp. was exclusively enriched in the highest temperature group relative to controls. Conclusions Although there were significant differences in both ambient and body temperature in the experimental group, there was not a significant change in diversity of the microbiome. This suggests that there may be an innate robustness to rapid temperature swings in the microbiome of T.c.triunguis which are native to temperate North America. Despite this resilience, a sequence type of Erysipelothrix spp. was enriched at the highest temperature. Phylogenetic analysis of this amplicon variant showed that it is a close relative of Erysipelothrix rhusiopathiae, a pathogen of zoonotic importance associated with both wildlife and livestock.

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The Gut Microbiome of 54 Mammalian Species

Cited by 34 publications

References 71 publications

Taxonomic, Genomic, and Functional Variation in the Gut Microbiomes of Wild Spotted Hyenas Across 2 Decades of Study

Taxonomic, Genomic, and Functional Variation in the Gut Microbiomes of Wild Spotted Hyenas Across 2 Decades of Study

Taxonomic, genomic, and functional variation in the gut microbiomes of wild spotted hyenas across two decades of study

Microbiome resilience of three-toed box turtles (Terrapene carolina triunguis) in response to rising temperatures

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