Effects of domestication on the gut microbiota parallel those of human industrialization
- Department of Human Evolutionary Biology, Harvard University, United States
- Society of Fellows, Harvard University, United States
- Wildlife Science Center, United States
- Department of Anthropology, University of New Mexico, United States
Figures
Figure 1 with 4 supplements
The mammalian gut microbiota carries a global signature of domestication.
(A) Sampling scheme for cross-species study. (B) Nonmetric multidimensional scaling (NMDS) ordination of Bray–Curtis dissimilarities illustrates a significant signal (p<0.001, R2 = 0.15, F = 6.081, …
Figure 1—figure supplement 1
Alternative factors associated with gut microbiota variation among wild and domesticated mammals.
Diet type (A), digestive physiology (B), and collection locale (C) are significantly associated (permutational MANOVAs) with variation in microbial community composition among wild and domesticated …
Figure 1—figure supplement 2
Microbial parameter comparisons between wild and domesticated mammals and between chimpanzees and humans.
Bray–Curtis nonmetric multidimensional scaling (NMDS) ordination shifts for domestication groups (A) and dyads (B), OTU richness (C), Shannon index (D), bacterial density (E), potential human …
Figure 1—figure supplement 3
Relatedness was correlated with ordination shifts but not dissimilarity within a dyad.
(A) The absolute value of shifts along nonmetric multidimensional scaling (NMDS) axis 1 for individuals relative to their dyad average was higher for dyads with a greater time since divergence …
Figure 1—figure supplement 4
Domestication explained few global gut microbial community characteristics in our cross-species dataset.
Potential pathogen richness (B) but not abundance (A) was significantly higher in wild animals. (C–E) Microbial density (quantified as copies of the 16S rRNA gene per gram feces [C]) and …
Figure 2 with 2 supplements
Gut microbial differences between wild and domesticated mice can be partially overcome by diet swap.
(A) Design scheme for fully factorial host taxon by diet mouse experiment (N = 10 laboratory mice or three wild mice per diet group). (B) Nonmetric multidimensional scaling (NMDS) ordination of …
Figure 2—figure supplement 1
Microbiota composition at all time points during the mouse diet swap experiment.
Nonmetric multidimensional scaling (NMDS) ordination of all time points illustrates significant effects (permutational MANOVA tests) of host taxon and diet on Bray–Curtis dissimilarity.
Figure 2—figure supplement 2
Select microbial and host metabolic parameters under mouse diet swap.
(A) Shannon index by experimental groups over time.(B) OTU richness by experimental groups over time. (C) Microbial load by experimental groups over time. (D) Total fecal production over 1 week …
Figure 3 with 1 supplement
Laboratory mice can be re-wilded through colonization with a wild gut microbial community.
(A) Design scheme for colonization/diet mouse experiment (N = 9–10 mice per treatment group). (B) Nonmetric multidimensional scaling (NMDS) ordination of Bray–Curtis dissimilarities showing changes …
Figure 3—figure supplement 1
Select microbial and host metabolic parameters under wild colonization treatment.
(A) Nonmetric multidimensional scaling (NMDS) ordination of all time points illustrates significant effects (permutational MANOVA tests) of colonization and diet treatment on Bray–Curtis …
Figure 4 with 2 supplements
Microbial differences between wild and domesticated canids can be partially overcome by diet shifts.
(A) Design scheme for fully factorial host taxon by diet canid experiment (N = 9 dogs or N = 10 wolves per diet group). (B) Nonmetric multidimensional scaling (NMDS) ordination of Bray–Curtis …
Figure 4—figure supplement 1
Microbiota composition at all time points during the canid diet swap experiment.
Nonmetric multidimensional scaling (NMDS) ordination of all time points illustrates significant effects (permutational MANOVA tests) of host taxon and diet on Bray–Curtis dissimilarity even after a …
Figure 4—figure supplement 2
Select microbial parameters under canid diet swap.
(A) Microbial loads of experimental groups over time.(B) Shannon index by experimental groups over time. (C) OTU richness differed between genotypes on day 0. * indicates p<0.05, Mann–Whitney U …
Figure 5 with 2 supplements
Differences in gut microbial communities between industrialized humans and wild chimpanzees parallel those observed between domesticated and wild mammals.
(A) Nonmetric multidimensional scaling (NMDS) ordination of Bray–Curtis dissimilarities in the gut microbiota illustrates that industrialized human populations (US and US Jha) exhibit similar trends …
Figure 5—figure supplement 1
Trends in gut microbial taxa previously linked to differing human lifestyles.
Abundance of gut microbial taxa previously identified as distinguishing among human lifestyles (Smits et al., 2017) trended in similar directions between domesticated and wild animals as between …
Figure 5—figure supplement 2
Dissimilarity in the gut microbiota among chimpanzees and humans.
Bray–Curtis dissimilarity among samples taken from captive zoo chimpanzees, wild chimpanzees, and human populations shows that the gut microbial communities of captive chimpanzees are more similar …
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Tables
Key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Biological sample (Bos taurus) | Feces | This paper | N = 9, sex unknown | |
| Biological sample (Bison bison) | Feces | This paper | N = 20, sex unknown | |
| Biological sample (Ovis aries) | Feces | This paper | N = 13, twelve females | |
| Biological sample (Ovis canadensis) | Feces | This paper | N = 10, sex unknown | |
| Biological sample (Sus scrofa domesticus) | Feces | This paper | N = 9, sex unknown | |
| Biological sample (Sus scrofa) | Feces | This paper | N = 16, five females | |
| Biological sample (Vicugna pacos) | Feces | This paper | N = 8, sex unknown | |
| Biological sample (Vicugna vicugna) | Feces | This paper | N = 5, two females | |
| Biological sample (Canis lupus familiaris) | Feces | This paper | Comparative: N = 7, four females Experiment: N = 9, sex unknown | |
| Biological sample (Canis lupus) | Feces | This paper | Comparative: N = 9, sex unknown Experiment: N = 10, sex unknown | |
| Biological sample (Oryctolagus cuniculus) | Feces | This paper | Domesticated: N = 11, four femalesWild: N = 12, sex unknown | |
| Biological sample (Cavia porcellus) | Feces | This paper | N = 10, zero female | |
| Biological sample (Cavia tschudii) | Feces | This paper | N = 11, sex unknown | |
| Biological sample(Mus musculus) | Feces | This paper | Comparative: N = 9 (domesticated), zero female N = 9 (wild), sex unknown Experiments: N = 49 (domesticated), zero female N = 6 (wild), sex unknown | |
| Biological sample (Rattus norvegicus) | Feces | This paper | Domesticated: N = 6, sex unknown | |
| Biological sample (Rattus norvegicus) | Intestinal sample | This paper | Wild: N = 10, three females | |
| Biological sample (Pan troglodytes) | Feces | This paper | Wild: N = 7, seven females Captive: N = 3, two females | |
| Biological sample (Homo sapiens) | Feces | This paper | N = 7, five females | |
| Sequence-based reagent | 515F | Caporaso et al., 2011 | PCR primers | GTGCCAGCMGCCGCGGTAA |
| Sequenced-based reagent | 806R | Caporaso et al., 2012 | PCR primers | GGACTACNVGGGTWTCTAAT |
| Software, algorithm | R | R Core Team | Version 3.3 | |
| Software, algorithm | QIIME | Caporaso et al., 2010 | Version 1.8 | |
| Software, algorithm | vegan | Oksanen et al., 2017 | ||
| Software, algorithm | lme4 | Bates et al., 2015 | ||
| Software, algorithm | TimeTree | Kumar et al., 2017 | http://timetree.org | |
| Software, algorithm | boot | Canty and Ripley, 2020 | Version 1.3-25 |
Additional files
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Supplementary file 1
Beta-diversity and nonmetric multidimensional scaling (NMDS) shift analyses were generally robust to the distance metric used and to subsetting the dataset.
- https://cdn.elifesciences.org/articles/60197/elife-60197-supp1-v1.xlsx
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Supplementary file 2
Expanded sampling metadata.
- https://cdn.elifesciences.org/articles/60197/elife-60197-supp2-v1.xlsx
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Supplementary file 3
Nutritional information for experimental diets.
- https://cdn.elifesciences.org/articles/60197/elife-60197-supp3-v1.xlsx
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Transparent reporting form
- https://cdn.elifesciences.org/articles/60197/elife-60197-transrepform-v1.docx
