Host Species and Captivity Distinguish the Microbiome Compositions of a Diverse Zoo-Resident Non-Human Primate Population

Round 1

Reviewer 1 Report

Overview: This manuscript aims to assess the impact of captivity on the NHP gut microbiome using samples collected from a phylogenetically diverse array NHPs housed in a single building at a single urban US zoo. The sampling schema includes multiple samples per individual over a one-month long period, and multiple individuals per species. The authors show that phylogeny is the most important predictor of gut microbial composition despite “shared” environments, but this result could be better supported with a few additional details on animal care to the methods. Additionally, the discussion focuses much more on health than the current study would support, so refocusing on the question of captivity vs. wild microbiomes might be a stronger angle to pursue. The statistics and graphical representations are appropriate and well-suited to the project. Based on my argument summarized above, I think this paper is ready for publication with a few minor revisions to the methods or supplementary text as well as the discussion.    

 

Strengths: This study represents a thorough investigation into the captive NHP gut microbiome at a US zoo. The visualizations are consistent and clean, and care is given to not overstate and results. The statistics and graphical representations are appropriate and well-suited to the project.

 

Weaknesses: The authors should spend more time contextualizing the animal care within either the methods or supplementary text. Supplementary figure 1 was helpful for understanding how the animals are housed, but there is little discussion about other potential shared environmental sources like water, if animals are rotated through different exhibits or if there is shared after hours housing. Further, there are no statements about the individuals themselves (age, sex, reproductive status, etc) – the results appear to be robust to these characteristics, so a brief statement in the methods addressing this would suffice. Additionally, a discussion of the different diets would help support current results. For example, on lines 214-217, the authors state that diet may be an important contributor to alpha diversity and mention that apes receive higher diversity diets. If possible, a plot showing diet diversity and alpha diversity, even at higher taxonomic group levels (apes, non-ape catarrhine, and platyrrhines) for the supplement may support the assertion that phylogeny is the most important contributor to gut microbial diversity and composition. The introduction to the discussion (lines 291-297) and conclusion (lines 422-453) focuses much more on health than the current study could support, so refocusing on the question of captivity vs. wild microbiomes might be a stronger angle to pursue. For example, how might diet changes help “re-wild” an animal’s gut if an animal if being prepared for re-release? Lastly, a supplementary figure a simple phylogeny showing the relatedness of the NHP species could be useful to a broader audience.

 

Other minor comments and questions:

·       Figure 1: Would it be too messy to add ellipses by clade, or outlining the points by broad clade (apes, non-ape catarrhine, and platyrrhines)? This might better illustrate some of the assertions in text (lines 175-177) but isn’t essential.

·       Figure 5: Could this plot’s height be increased? The y axis should match the height of the heatmap.

·       Lines 264-266: Were any animals administered antibiotics during the sampling period? If not, what was the most recent administration prior to the sampling period? This could contribute to the discussion in lines 411-418.

·       Figure 6: Only one individual had a history of multiple antibiotic prescriptions, coloring that point slightly differently could lead to interesting discussion points as above.

Comments for author File: Comments.pdf

Author Response

Please see the attachment. Thank you.

Author Response File: Author Response.pdf

Reviewer 2 Report

The manuscript of Wills et all., characterize the gut microbiome composition of a diverse cohort of NHPs residing in an urban zoo. The main finding of this paper is that the gut microbiome are distinguished between NHP host species. Further, it is not surprising that their wild counterparts and humans display different microbiomes.

 

Overall, the paper is well written and consistent in analyses used for the propose goal.

I am wondering whether the actual data allow the analysis of the microbiome in relation with other factors able to influence the microbiome such as the age or the sex of the animals? This would be especially of interest by the analysis of antibiotic treatment on the microbiome. The conclusion regarding the treatment with antibiotics is due to the low number of samples and not taking in consideration of other confounding factors (age, sex, clinical status, etc.) less sustained and should be “weaker” formulated.

Author Response

Please see the attachment. Thank you.

Author Response File: Author Response.pdf