Age‐related differences in gut microbial community composition of captive spotted seals (<scp><i>Phoca largha</i></scp>)

Tian, Jing; Du, Jing; Han, Jingfeng; Song, Xinran; Lu, Zengkui

doi:10.1111/mms.12728

Cited by 17 publications

(25 citation statements)

References 40 publications

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“…We found that gut microbiome alpha-diversity moderately declined with adult age, and that host age predicted 4.3% of the variance in gut microbiome beta-diversity. This is consistent with prior studies conducted in chimpanzees (Pan troglodytes) (108), and spotted seals (Phoca largha) (109), which report a general decline in gut microbiome diversity with host aging, but is not consistent with studies conducted in humans (110), or yaks (Bos grunniens) (111). In spotted hyenas from the Serengeti (112), juveniles have slightly less diverse gut microbiomes than adults, which could be true of the population we studied, but we did not sample juveniles.…”

Section: Gut Microbiomes Are Individualized In Wild Spotted Hyenassupporting

confidence: 93%

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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Section: Gut Microbiomes Are Individualized In Wild Spotted Hyenassupporting

confidence: 93%

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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“…As well as being a common commensal, Escherichia/Shigella are well‐characterized pathogens of humans, and one of the main causes of bacterial diarrhea (Khalil et al, 2018 ) but known to be more common in the young of many mammalian species (Chung et al, 2012 ). This genus is, typically, more prevalent in the microbiota of young mammals or those yet to mature and less abundant in mature mammals with a healthy, stable microbiome (Castaño‐Rodríguez et al, 2018 , Tian et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

A comparative study of the fecal microbiota of gray seal pups and yearlings ‐ a marine mammal sentinel species

et al. 2022

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Gray seals ( Halichoerus grypus ) can act as sentinel species reflecting the condition of the environment they inhabit. Our previous research identified strains of pathogenic Campylobacter and Salmonella , originating from both human and agricultural animal hosts, on rectal swabs from live gray seal ( H. grypus ) pups and yearlings on the Isle of May, Scotland, UK. We examined rectal swabs from the same pup ( n = 90) and yearling ( n = 19) gray seals to gain further understanding into the effects of age‐related changes (pup vs. yearling) and three different natal terrestrial habitats on seal pup fecal microbiota. DNA was extracted from a subset of rectal swabs (pups n = 23, yearlings n = 9) using an optimized procedure, and the V4 region of the 16S ribosomal RNA gene was sequenced to identify each individual's microbiota. Diversity in pup samples was lower (3.92 ± 0.19) than yearlings (4.66 ± 0.39) although not significant at the p = 0.05 level ( p = 0.062) but differences in the composition of the microbiota were ( p < 0.001). Similarly, differences between the composition of the microbiota from pups from three different terrestrial habitats (Pilgrim's Haven [PH], Rona Rocks [RR], and Tarbet Slope [TS]) were highly significant ( p < 0.001). Pairwise tests showed significant differences between all three habitats: PH versus TS ( p = 0.019), PH versus RR ( p = 0.042) and TS versus RR ( p = 0.020). This preliminary study suggests a general trend, that seal microbiomes are modified by both age and, in pups, different terrestrial habitats. Furthermore, knowledge of the microbiota species present has the potential to be used in determining the environmental quality index.

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“…Each ASV was assigned to a taxonomy according to the SILVA database (Yilmaz et al ., 2014), and an ASV abundance table was constructed. Singletons (number of tags in a specific ASV = 1) were discarded to improve data analysis efficiency (Tian et al ., 2020) and ASV tables were normalized using a standard number of tags according to the sample with the least tags (45 128 tags) (Zhao et al ., 2018).…”

Section: Methodsmentioning

confidence: 99%

Exploiting the gut microbiota to predict the origins and quality traits of cultured sea cucumbers

Zhao

Jiang

Zheng

et al. 2022

Environmental Microbiology

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Summary Nowadays, the true economic and nutritional value of food is underpinned by both origin and quality traits, more often expressed as increased quality benefits derived from the origin source. Gut microbiota contribute to food metabolism and host health, therefore, it may be suitable as a qualifying indicator of origin and quality of economic species. Here, we investigated relationships between the gut microbiota of the sea cucumber (Apostichopus japonicus), a valuable aquaculture species in Asia, with their origins and quality metrics. Based on data from 287 intestinal samples, we generated the first biogeographical patterns for A. japonicus gut microbiota from origins across China. Importantly, A. japonicus origins were predicted using the random forest model that was constructed using 20 key gut bacterial genera, with 97.6% accuracy. Furthermore, quality traits such as saponin, fat and taurine were also successfully predicted by random forest models based on gut microbiota, with approximately 80% consistency between predicted and true values. We showed that substantial variations existed in the gut microbiota and quality variables in A. japonicus across different origins, and we also demonstrated the great potential of gut microbiota to track A. japonicus origins and predict their quality traits.

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Age‐related differences in gut microbial community composition of captive spotted seals (Phoca largha)

Cited by 17 publications

References 40 publications

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

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

A comparative study of the fecal microbiota of gray seal pups and yearlings ‐ a marine mammal sentinel species

Exploiting the gut microbiota to predict the origins and quality traits of cultured sea cucumbers

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