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Background
Changes to the gut microbiota are associated with an increased incidence of disease in many species. This is particularly important during the process of domestication, where captive animals commonly suffer from gastrointestinal (GI) pathology. Horses are a prime example of a species which suffers from a high incidence of (often life-threatening) GI diseases in domesticated environments. We aimed to indentify the gut microbial changes which occur due to domestication in horses by profiling the faecal microbiota of adult female Exmoor ponies under three management conditions, representing increasing levels of domestication.
Methods
Faecal samples were collected from 29 adult female Exmoor ponies in the South West of the UK; ponies were categorised as Feral (n=10), Semi-Feral (n=10) and Domesticated (n=9), based on their management conditions; thus controlling for age, gender and random effects between groups. Diet and medication were recorded and faecal samples taken to assess parasite infection. Faecal microbial composition was profiled via high-throughput sequencing of the bacterial 16S rRNA gene.
Results
Downstream biostatistical analysis indicated profound step-wise changes in global microbial community structure in the transition from Feral to Semi-Feral to Domesticated groups. A relatively high abundance of members of the phylum Proteobacteria and Tenericutes were associated with the Domesticated group; and higher levels of Methanobacteria were seen in the Feral group. The Semi-Feral group frequently had intermediate levels of these taxa; however, they also exhibited the greatest ‘within group’ variation in bacterial diversity and parasites burdens. Functional predictions revealed increased amino acid and lipid metabolism in the Domesticated group and increased energy metabolism in the Feral group; supporting a hypothesis that differences in diet was the key driver of gut microbial composition.
Conclusions
If assumed the Feral population has a more natural gut microbial phenotype, akin to that with which horses have evolved, these data can potentially be used to provide microbial signitures of balanced gut homeostasis in horses; which, in turn, will aid prevention of GI disease in domesticated horses.
Keywords
Horse, 16S rRNA sequencing, Microbiome, Diet, Domestication, Helminth
Figure 1
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This is a list of supplementary files associated with this preprint. Click to download.
- AdditionalFile1.png
Additional file 1 The rarefaction curve at OTU level generated following in silico subtraction of low-quality and contaminant sequences, indicating that the majority of samples were sequenced at adequate read depth, thus allowing us to undertake further analyses.
- AdditionalFile2.png
Additional file 2 ANOVA plots show there were no significant differences in alpha diversity between farms (evenness P=0.35; Shannon P=0.2; Richness P=0.33). However, greater inter-individual variation in alpha diversity was seen between animals in the Semi-Feral group.
- AdditionalFile3.png
Additional file 3 LEfSe analysis of predicted functional data at KEGG level 2 supported the network analysis; glycan, amino acid, lipid, polyketides and xenobiotics metabolism were increased in the Domesticated group; carbohydrate metabolism, cancers, neurogenerative diseases, excretory system, immune system diseases and metabolic diseases were increased in the Semi-feral group; and energy metabolism, transcription, membrane transporters and genetic information processing were increased in the Domesticated group.
- AdditionalFile4.png
Additional file 4 Box and Whisker plot shows strongyle faecal egg counts (FEC) were significantly lower in the Domesticated group. The average FEC was similar between the Feral and Semi-feral group, however there was much greater variation in parasite burden between animals in the Semi-feral group.
- AdditionalTable1.xlsx
Additional Table 1 Differences in the abundance of specific bacterial taxa between the groups was evaluated using LEfSe (Linear Discriminant Analysis Effect Size) analysis. Significantly differences are seen in relative abundance between Domesticated, Semi-feral and Feral groups; rows highlighted grey are relatively increased in that group. Taxa correlated with faecal egg count (FEC) in regression analysis is also shown; with green indicating a positive association, and orange, a negative.
- AdditionalTable2.csv
Additional Table 2 Individual FEC values for each of the 3 groups show significant different between the groups with the Domesticated having lower FEC on average than the Feral and Semi-feral groups; there was more inter-individual variation in FEC in the Semi-Feral group.
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A new preprint design is coming!
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This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Research Article
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
History
CURRENT STATUS: Posted
Version 1
Posted 08 Feb, 2021
No community comments so far
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Animal Science
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background
Changes to the gut microbiota are associated with an increased incidence of disease in many species. This is particularly important during the process of domestication, where captive animals commonly suffer from gastrointestinal (GI) pathology. Horses are a prime example of a species which suffers from a high incidence of (often life-threatening) GI diseases in domesticated environments. We aimed to indentify the gut microbial changes which occur due to domestication in horses by profiling the faecal microbiota of adult female Exmoor ponies under three management conditions, representing increasing levels of domestication.
Methods
Faecal samples were collected from 29 adult female Exmoor ponies in the South West of the UK; ponies were categorised as Feral (n=10), Semi-Feral (n=10) and Domesticated (n=9), based on their management conditions; thus controlling for age, gender and random effects between groups. Diet and medication were recorded and faecal samples taken to assess parasite infection. Faecal microbial composition was profiled via high-throughput sequencing of the bacterial 16S rRNA gene.
Results
Downstream biostatistical analysis indicated profound step-wise changes in global microbial community structure in the transition from Feral to Semi-Feral to Domesticated groups. A relatively high abundance of members of the phylum Proteobacteria and Tenericutes were associated with the Domesticated group; and higher levels of Methanobacteria were seen in the Feral group. The Semi-Feral group frequently had intermediate levels of these taxa; however, they also exhibited the greatest ‘within group’ variation in bacterial diversity and parasites burdens. Functional predictions revealed increased amino acid and lipid metabolism in the Domesticated group and increased energy metabolism in the Feral group; supporting a hypothesis that differences in diet was the key driver of gut microbial composition.
Conclusions
If assumed the Feral population has a more natural gut microbial phenotype, akin to that with which horses have evolved, these data can potentially be used to provide microbial signitures of balanced gut homeostasis in horses; which, in turn, will aid prevention of GI disease in domesticated horses.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
This is a list of supplementary files associated with this preprint. Click to download.
- AdditionalFile1.png
Additional file 1 The rarefaction curve at OTU level generated following in silico subtraction of low-quality and contaminant sequences, indicating that the majority of samples were sequenced at adequate read depth, thus allowing us to undertake further analyses.
- AdditionalFile2.png
Additional file 2 ANOVA plots show there were no significant differences in alpha diversity between farms (evenness P=0.35; Shannon P=0.2; Richness P=0.33). However, greater inter-individual variation in alpha diversity was seen between animals in the Semi-Feral group.
- AdditionalFile3.png
Additional file 3 LEfSe analysis of predicted functional data at KEGG level 2 supported the network analysis; glycan, amino acid, lipid, polyketides and xenobiotics metabolism were increased in the Domesticated group; carbohydrate metabolism, cancers, neurogenerative diseases, excretory system, immune system diseases and metabolic diseases were increased in the Semi-feral group; and energy metabolism, transcription, membrane transporters and genetic information processing were increased in the Domesticated group.
- AdditionalFile4.png
Additional file 4 Box and Whisker plot shows strongyle faecal egg counts (FEC) were significantly lower in the Domesticated group. The average FEC was similar between the Feral and Semi-feral group, however there was much greater variation in parasite burden between animals in the Semi-feral group.
- AdditionalTable1.xlsx
Additional Table 1 Differences in the abundance of specific bacterial taxa between the groups was evaluated using LEfSe (Linear Discriminant Analysis Effect Size) analysis. Significantly differences are seen in relative abundance between Domesticated, Semi-feral and Feral groups; rows highlighted grey are relatively increased in that group. Taxa correlated with faecal egg count (FEC) in regression analysis is also shown; with green indicating a positive association, and orange, a negative.
- AdditionalTable2.csv
Additional Table 2 Individual FEC values for each of the 3 groups show significant different between the groups with the Domesticated having lower FEC on average than the Feral and Semi-feral groups; there was more inter-individual variation in FEC in the Semi-Feral group.
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