Limits...
Patterns of gut bacterial colonization in three primate species.

McKenney EA, Rodrigo A, Yoder AD - PLoS ONE (2015)

Bottom Line: Here, we show that colonization proceeds along different successional trajectories in developing infants from species with differing dietary regimes and ecological profiles: frugivorous (fruit-eating) Varecia variegata, generalist Lemur catta, and folivorous (leaf-eating) Propithecus coquereli.Our analyses reveal community membership and succession patterns consistent with previous studies of human infants, suggesting that lemurs may serve as a useful model of microbial ecology in the primate gut.Each lemur species exhibits distinct species-specific bacterial diversity signatures correlating to life stages and life history traits, implying that gut microbial community assembly primes developing infants at species-specific rates for their respective adult feeding strategies.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Duke University, Durham, North Carolina, United States of America.

ABSTRACT
Host fitness is impacted by trillions of bacteria in the gastrointestinal tract that facilitate development and are inextricably tied to life history. During development, microbial colonization primes the gut metabolism and physiology, thereby setting the stage for adult nutrition and health. However, the ecological rules governing microbial succession are poorly understood. In this study, we examined the relationship between host lineage, captive diet, and life stage and gut microbiota characteristics in three primate species (infraorder, Lemuriformes). Fecal samples were collected from captive lemur mothers and their infants, from birth to weaning. Microbial DNA was extracted and the v4 region of 16S rDNA was sequenced on the Illumina platform using protocols from the Earth Microbiome Project. Here, we show that colonization proceeds along different successional trajectories in developing infants from species with differing dietary regimes and ecological profiles: frugivorous (fruit-eating) Varecia variegata, generalist Lemur catta, and folivorous (leaf-eating) Propithecus coquereli. Our analyses reveal community membership and succession patterns consistent with previous studies of human infants, suggesting that lemurs may serve as a useful model of microbial ecology in the primate gut. Each lemur species exhibits distinct species-specific bacterial diversity signatures correlating to life stages and life history traits, implying that gut microbial community assembly primes developing infants at species-specific rates for their respective adult feeding strategies.

No MeSH data available.


Related in: MedlinePlus

Composition of 16S libraries sequenced in duplicate from 58 fecal samples, collected from 15 lemurs belonging to Varecia variegata, Lemur catta, and Propithecus coquereli.Samples were collected from infants at (i) birth, (ii) nursing, (iii) introduction of solid foods, (iv) regular consumption of solid foods, (v) weaning, (vi) weaned, and from dams at parturition (p). Infants’ ages are listed below each life stage. The samples collected from each species during the introduction of solid foods are also bracketed and indicated with asterisks. Technical duplicates sequenced from each sample are paired and arranged so that infants’ results are repeated in the same order within each life stage and so that dams’ order corresponds to their infants’. Results are shown at the (A) phylum level and (B) genus level.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4430486&req=5

pone.0124618.g002: Composition of 16S libraries sequenced in duplicate from 58 fecal samples, collected from 15 lemurs belonging to Varecia variegata, Lemur catta, and Propithecus coquereli.Samples were collected from infants at (i) birth, (ii) nursing, (iii) introduction of solid foods, (iv) regular consumption of solid foods, (v) weaning, (vi) weaned, and from dams at parturition (p). Infants’ ages are listed below each life stage. The samples collected from each species during the introduction of solid foods are also bracketed and indicated with asterisks. Technical duplicates sequenced from each sample are paired and arranged so that infants’ results are repeated in the same order within each life stage and so that dams’ order corresponds to their infants’. Results are shown at the (A) phylum level and (B) genus level.

Mentions: We performed quality filtering using default settings and demultiplexed reads using 12 bp barcodes. A total of 5,844,416 sequences were retained after quality filtering in QIIME, giving us an average coverage of 50,297 sequences (standard deviation 15,670) per library. Coverage ranged from 1 sequence (in a library sequenced from a sample collected from P. coquereli at birth, discussed below) to 82,473 sequences, with a median of 53,668 sequences per library. Duplicate 16S libraries were generally more similar to each other than to libraries sequenced from other samples (Figs 2 and 3), suggesting that the coverage (>50,000 paired-end reads per library after quality filtering in QIIME) adequately captured the taxonomic diversity recovered in each DNA extraction.


Patterns of gut bacterial colonization in three primate species.

McKenney EA, Rodrigo A, Yoder AD - PLoS ONE (2015)

Composition of 16S libraries sequenced in duplicate from 58 fecal samples, collected from 15 lemurs belonging to Varecia variegata, Lemur catta, and Propithecus coquereli.Samples were collected from infants at (i) birth, (ii) nursing, (iii) introduction of solid foods, (iv) regular consumption of solid foods, (v) weaning, (vi) weaned, and from dams at parturition (p). Infants’ ages are listed below each life stage. The samples collected from each species during the introduction of solid foods are also bracketed and indicated with asterisks. Technical duplicates sequenced from each sample are paired and arranged so that infants’ results are repeated in the same order within each life stage and so that dams’ order corresponds to their infants’. Results are shown at the (A) phylum level and (B) genus level.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4430486&req=5

pone.0124618.g002: Composition of 16S libraries sequenced in duplicate from 58 fecal samples, collected from 15 lemurs belonging to Varecia variegata, Lemur catta, and Propithecus coquereli.Samples were collected from infants at (i) birth, (ii) nursing, (iii) introduction of solid foods, (iv) regular consumption of solid foods, (v) weaning, (vi) weaned, and from dams at parturition (p). Infants’ ages are listed below each life stage. The samples collected from each species during the introduction of solid foods are also bracketed and indicated with asterisks. Technical duplicates sequenced from each sample are paired and arranged so that infants’ results are repeated in the same order within each life stage and so that dams’ order corresponds to their infants’. Results are shown at the (A) phylum level and (B) genus level.
Mentions: We performed quality filtering using default settings and demultiplexed reads using 12 bp barcodes. A total of 5,844,416 sequences were retained after quality filtering in QIIME, giving us an average coverage of 50,297 sequences (standard deviation 15,670) per library. Coverage ranged from 1 sequence (in a library sequenced from a sample collected from P. coquereli at birth, discussed below) to 82,473 sequences, with a median of 53,668 sequences per library. Duplicate 16S libraries were generally more similar to each other than to libraries sequenced from other samples (Figs 2 and 3), suggesting that the coverage (>50,000 paired-end reads per library after quality filtering in QIIME) adequately captured the taxonomic diversity recovered in each DNA extraction.

Bottom Line: Here, we show that colonization proceeds along different successional trajectories in developing infants from species with differing dietary regimes and ecological profiles: frugivorous (fruit-eating) Varecia variegata, generalist Lemur catta, and folivorous (leaf-eating) Propithecus coquereli.Our analyses reveal community membership and succession patterns consistent with previous studies of human infants, suggesting that lemurs may serve as a useful model of microbial ecology in the primate gut.Each lemur species exhibits distinct species-specific bacterial diversity signatures correlating to life stages and life history traits, implying that gut microbial community assembly primes developing infants at species-specific rates for their respective adult feeding strategies.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Duke University, Durham, North Carolina, United States of America.

ABSTRACT
Host fitness is impacted by trillions of bacteria in the gastrointestinal tract that facilitate development and are inextricably tied to life history. During development, microbial colonization primes the gut metabolism and physiology, thereby setting the stage for adult nutrition and health. However, the ecological rules governing microbial succession are poorly understood. In this study, we examined the relationship between host lineage, captive diet, and life stage and gut microbiota characteristics in three primate species (infraorder, Lemuriformes). Fecal samples were collected from captive lemur mothers and their infants, from birth to weaning. Microbial DNA was extracted and the v4 region of 16S rDNA was sequenced on the Illumina platform using protocols from the Earth Microbiome Project. Here, we show that colonization proceeds along different successional trajectories in developing infants from species with differing dietary regimes and ecological profiles: frugivorous (fruit-eating) Varecia variegata, generalist Lemur catta, and folivorous (leaf-eating) Propithecus coquereli. Our analyses reveal community membership and succession patterns consistent with previous studies of human infants, suggesting that lemurs may serve as a useful model of microbial ecology in the primate gut. Each lemur species exhibits distinct species-specific bacterial diversity signatures correlating to life stages and life history traits, implying that gut microbial community assembly primes developing infants at species-specific rates for their respective adult feeding strategies.

No MeSH data available.


Related in: MedlinePlus