Dataset Information

Consequences of Domestication on Gut Microbiome: A Comparative Study Between Wild Gaur and Domestic Mithun.

ABSTRACT: Although the gut microbiome benefits the host in several ways, how anthropogenic forces impact the gut microbiome of mammals is not yet completely known. Recent studies have noted reduced gut microbiome diversity in captive mammals due to changes in diet and living environment. However, no studies have been carried out to understand how the gut microbiome of wild mammals responds to domestication. We analyzed the gut microbiome of wild and captive gaur and domestic mithun (domestic form of gaur) to understand whether the gut microbiome exhibits sequential changes from wild to captivity and after domestication. Both captive and domestic populations were characterized by reduced microbial diversity and abundance as compared to their wild counterparts. Notably, two beneficial bacterial families, Ruminococcaceae and Lachnospiraceae, which are known to play vital roles in herbivores' digestion, exhibited lower abundance in captive and domestic populations. Consequently, the predicted bacterial functional pathways especially related to metabolism and immune system showed lower abundance in captive and domestic populations compared to wild population. Therefore, we suggest that domestication can impact the gut microbiome more severely than captivity, which might lead to adverse effects on host health and fitness. However, further investigations are required across a wide range of domesticates in order to understand the general trend of microbiome shifts in domestic animals.

SUBMITTER: Prabhu VR

PROVIDER: S-EPMC7051944 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Consequences of Domestication on Gut Microbiome: A Comparative Study Between Wild Gaur and Domestic Mithun.

Prabhu Vandana R VR Wasimuddin Kamalakkannan Ranganathan R Arjun Moolamkudy Suresh MS Nagarajan Muniyandi M

Frontiers in microbiology 20200225

Although the gut microbiome benefits the host in several ways, how anthropogenic forces impact the gut microbiome of mammals is not yet completely known. Recent studies have noted reduced gut microbiome diversity in captive mammals due to changes in diet and living environment. However, no studies have been carried out to understand how the gut microbiome of wild mammals responds to domestication. We analyzed the gut microbiome of wild and captive gaur and domestic mithun (domestic form of gaur) ...[more]

PMID: 32158434

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Project description:BACKGROUND:Identifying the phenotypic responses to domestication remains a long-standing and important question for researchers studying its early history. The great diversity in domestic animals and plants that exists today bears testament to the profound changes that domestication has induced in their ancestral wild forms over the last millennia. Domestication is a complex evolutionary process in which wild organisms are moved to new anthropogenic environments. Although modern genetics are significantly improving our understanding of domestication and breed formation, little is still known about the associated morphological changes linked to the process itself. In order to explore phenotypic variation induced by different levels of human control, we analysed the diversity of dental size, shape and allometry in modern free-living and captive wild, wild x domestic hybrid, domestic and insular Sus scrofa populations. RESULTS:We show that domestication has created completely new dental phenotypes not found in wild boar (although the amount of variation amongst domestic pigs does not exceed that found in the wild). Wild boar tooth shape also appears to be biogeographically structured, likely the result of post-glacial recolonisation history. Furthermore, distinct dental phenotypes were also observed among domestic breeds, probably the result of differing types and intensity of past and present husbandry practices. Captivity also appears to impact tooth shape. Wild x domestic hybrids possess second molars that are strictly intermediate in shape between wild boar and domestic pigs (third molars, however, showing greater shape similarity with wild boar) while their size is more similar to domestic pigs. The dental phenotypes of insular Sus scrofa populations found on Corsica and Sardinia today (originally introduced by Neolithic settlers to the islands) can be explained either by feralization of the original introduced domestic swine or that the founding population maintained a wild boar phenotype through time. CONCLUSIONS:Domestication has driven significant phenotypic diversification in Sus scrofa. Captivity (environmental control), hybridization (genome admixture), and introduction to islands all correspond to differing levels of human control and may be considered different stages of the domestication process. The relatively well-known genetic evolutionary history of pigs shows a similar complexity at the phenotypic level.

Project description:Adaptation during the domestication from wolves (Canis lupus) to dogs (Canis lupus familiaris) is a debated ecological topic. Changes in food and environment are major divergences in the domestication of dogs. Gut microbes play an important role in animal adaptation to the food and environmental changes. In this study, shotgun sequencing was performed to compare the species diversity and functional diversity of gut microbes in wild wolves (group CLW, n = 3), captive wolves (group CLC, n = 4), and domestic dogs (group CLF, n = 4). The results found that Bacteroidetes, Firmicutes, Fusobacteria, Proteobacteria and Actinobacteria were the most abundant phyla and Bacteroides, Fusobacterium, Prevotella, Megamonas, Paraprevotella, Faecalibacterium, Clostridium were the most abundant genera in the gut of wolves and dogs. Groups CLW, CLC and CLF have shown significant difference in gut microbial species diversity and functional diversity. Bacteroides, Fusobacterium and Faecalibacterium were most abundant genera in groups CLW, CLC and CLF, respectively. Their abundance varied significantly among groups. Compared to the wild wolves, the intestinal microbiol genes of domestic dogs were significantly enriched in the carbohydrate metabolism pathway of KEGG database. One hundred and seventy-seven enzymes were detected with significantly higher abundance in group CLF than that in group CLW, and 49 enzymes showed extremely significant higher abundance in group CLF than that in group CLW (q < 0.01) base on the function abundance annotated in CAZy database. It is noteworthy that there were also significant differences in the abundance of 140 enzymes between groups CLC and CLW (q < 0.05). Clustering analysis based on both the species and the function abundance of intestinal microbiota all found that groups CLC and CLF clustered into one branch, while samples from group CLW clustered into the other branch. This result suggests that captive wolves are more similar to domestic dogs than wild wolves in both species composition and function composition of intestinal microbiota.

Project description:BackgroundIn contrast to wild species, which have typically evolved phenotypes over long periods of natural selection, domesticates rapidly gained human-preferred agronomic traits in a relatively short-time frame via artificial selection. Under domesticated conditions, many traits can be observed that cannot only be due to environmental alteration. In the case of silkworms, aside from genetic divergence, whether epigenetic divergence played a role in domestication is an unanswered question. The silkworm is still an enigma in that it has two DNA methyltransferases (DNMT1 and DNMT2) but their functionality is unknown. Even in particular the functionality of the widely distributed DNMT1 remains unknown in insects in general.ResultsBy embryonic RNA interference, we reveal that knockdown of silkworm Dnmt1 caused decreased hatchability, providing the first direct experimental evidence of functional significance of insect Dnmt1. In the light of this fact and those that DNA methylation is correlated with gene expression in silkworms and some agronomic traits in domesticated organisms are not stable, we comprehensively compare silk gland methylomes of 3 domesticated (Bombyx mori) and 4 wild (Bombyx mandarina) silkworms to identify differentially methylated genes between the two. We observed 2-fold more differentiated methylated cytosinces (mCs) in domesticated silkworms as compared to their wild counterparts, suggesting a trend of increasing DNA methylation during domestication. Further study of more domesticated and wild silkworms narrowed down the domesticates' epimutations, and we were able to identify a number of differential genes. One such gene showing demethyaltion in domesticates correspondently displays lower gene expression, and more interestingly, has experienced selective sweep. A methylation-increased gene seems to result in higher expression in domesticates and the function of its Drosophila homolog was previously found to be essential for cell volume regulation, indicating a possible correlation with the enlargement of silk glands in domesticated silkworms.ConclusionsOur results imply epigenetic influences at work during domestication, which gives insight into long time historical controversies regarding acquired inheritance.

Project description:BackgroundBombyx mori was domesticated from the Chinese wild silkworm, Bombyx mandarina. Wild and domestic silkworms are good models in which to investigate genes related to silk protein synthesis that may be differentially expressed in silk glands, because their silk productions are very different. Here we used the mRNA deep sequencing (RNA-seq) approach to identify the differentially expressed genes (DEGs) in the transcriptomes of the median/posterior silk glands of two domestic and two wild silkworms.ResultsThe results indicated that about 58% of the total genes were expressed (reads per kilo bases per million reads (RPKM) ≥ 1) in each silkworm. Comparisons of the domestic and wild silkworm transcriptomes revealed 32 DEGs, of which 16 were up-regulated in the domestic silkworms compared with in the wild silkworms, and the other 16 were up-regulated in the wild silkworms compared with in the domestic silkworms. Quantitative real-time polymerase chain reaction (qPCR) was performed for 15 randomly selected DEGs in domestic versus wild silkworms. The qPCR results were mostly consistent with the expression levels determined from the RNA-seq data. Based on a Gene Ontology (GO) enrichment analysis and manual annotation, five of the up-regulated DEGs in the wild silkworms were predicted to be involved in immune response, and seven of the up-regulated DEGs were related to the GO term "oxidoreductase activity", which is associated with antioxidant systems. In the domestic silkworms, the up-regulated DEGs were related mainly to tissue development, secretion of proteins and metabolism.ConclusionsThe up-regulated DEGs in the two domestic silkworms may be involved mainly in the highly efficient biosynthesis and secretion of silk proteins, while the up-regulated DEGs in the two wild silkworms may play more important roles in tolerance to pathogens and environment adaptation. Our results provide a foundation for understanding the molecular mechanisms of the silk production difference between domestic and wild silkworms.

Project description:A number of recent studies have shown the importance of the mammalian gut microbiome in host health. In the context of endangered species, a few studies have examined the relationship between the gut microbiome in wild versus captive populations due to digestive and other health issues. Unfortunately, the results seem to vary across taxa in terms of captive animals having higher, lower, or equivalent microbiome diversity relative to their wild counterparts. Here, we focus on the black rhinoceros as captive animals suffer from a number of potentially dietary related health effects. We compared gut microbiomes of wild and captive black rhinos to test for differences in taxonomic diversity (alpha and beta) and in functional diversity of the microbiome. We incorporated a more powerful metagenomic shotgun sequencing approach rather than a targeted amplification of the 16S gene for taxonomic assignment of the microbiome. Our results showed no significant differences in the alpha diversity levels between wild and captive black rhinos, but significant differences in beta diversity. We found that bacterial taxa traditionally associated with ruminant guts of domesticated animals had higher relative abundances in captive rhinos. Our metagenomic sequencing results suggest that unknown gut microbes of wild rhinos are being replaced by those found in conventional human-domesticated livestock. Wild rhinos have significantly different functional bacterial communities compared to their captive counterparts. Functional profiling results showed greater abundance of glycolysis and amino acid synthesis pathways in captive rhino microbiomes, representing an animal receiving sub-optimal nutrition with a readily available source of glucose but possibly an imbalance of necessary macro and micronutrients. Given the differences observed between wild and captive rhino gut microbiomes, we make a number of recommendations for potentially modifying captive gut microbiome to better reflect their wild counterparts and thereby hopefully improve overall rhino health in captivity.

Dataset Information

Consequences of Domestication on Gut Microbiome: A Comparative Study Between Wild Gaur and Domestic Mithun.

Publications

Consequences of Domestication on Gut Microbiome: A Comparative Study Between Wild Gaur and Domestic Mithun.

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