This preprint is under consideration at Microbiome. A preprint is 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.
Learn more about In Review
A new preprint design is coming!
We have improved readability, clarity, accessibility, and opportunities for engagement.
Research
Michael Doane
Sydney Institute of Marine Science
Corresponding Author
ORCiD: https://orcid.org/0000-0001-9820-2193
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background: The vertebrate clade diverged into Chondrichthyes (sharks, rays, and chimeras) and Osteichthyes fishes (bony fishes) approximately 420 mya, with each group accumulating vast anatomical and physiological differences, including skin properties. The skin of Chondrichthyes fishes is covered in dermal denticles, whereas Osteichthyes fishes are covered in scales and are mucous rich. The divergence time among these two fish groups is hypothesized to result in predictable variation among symbionts. Here, using shotgun metagenomics, we test if patterns of diversity in the skin surface microbiome across the two fish clades match predictions made by phylosymbiosis theory. We hypothesize, 1) the skin microbiome will be species and clade-specific, 2) evolutionary difference in elasmobranch and teleost fishes corresponds with a concomitant increase in host-microbiome dissimilarity and 3) the skin structure of the two groups will affect the taxonomic and functional composition of the microbiomes.
Results: We show that the taxonomic and functional composition of the microbiomes is host species-specific. Teleost fish had lower average microbiome within clade similarity compared to among clade comparison, but their composition is not different among clade in a null based model. Elasmobranch’s average similarity within clade was not different than across clade and not different in a null based model of comparison. In the comparison of host distance with microbiome distance, we found that the taxonomic composition of the microbiome was related to host distance for the elasmobranchs, but not the teleost fishes. In comparison, the gene function composition was not related to the host-organism distance for elasmobranchs but was negatively correlated with host distance for teleost fishes.
Conclusion: Our results show the patterns of phylosymbiosis are not consistent across both fish clades, with the elasmobranchs showing phylosymbiosis, while the teleost fish are not. The discrepancy may be linked to alternative processes underpinning microbiome assemblage, including possible historical host-microbiome evolution of the elasmobranchs and convergent evolution in the teleost which filter specific microbial groups. Our comparison of the microbiomes among fishes represents an investigation into the microbial relationships of the oldest divergence extant vertebrate host and reveals that microbial relationships are not consistent across evolutionary timescales.
Keywords
microbiome, phylosymbiosis, metagenomics, elasmobranch skin, teleost, vertebrate fishes, microbial community, community ecology
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.
Loading...
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Under Review
The most recent version of this article is available here.
No community comments so far
Review #1 received
Received 06 Apr, 2020
Review #2 received
Received 05 Apr, 2020
Reviewer #2 agreed
On 01 Apr, 2020
Editor assigned
On 30 Mar, 2020
Reviewers invited
Invitations sent on 30 Mar, 2020
Reviewer #1 agreed
On 30 Mar, 2020
Submission checks complete
On 29 Mar, 2020
Editor invited
On 29 Mar, 2020
Version 1
Posted 30 Dec, 2019
No comments provided
Review #2 received
Received 02 Mar, 2020
Editorial decision: Revise Before Review
On 02 Mar, 2020
Reviewer #2 agreed
On 11 Feb, 2020
Review #1 received
Received 28 Jan, 2020
Reviewer #1 agreed
On 13 Jan, 2020
Reviewers invited
Invitations sent on 12 Jan, 2020
Editor assigned
On 23 Dec, 2019
Submission checks complete
On 22 Dec, 2019
Editor invited
On 22 Dec, 2019
First submitted
On 18 Dec, 2019
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
General Microbiology
Learn more about our company.
A new preprint design is coming!
We have improved readability, clarity, accessibility, and opportunities for engagement.
This preprint is under consideration at Microbiome. A preprint is 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.
Learn more about In Review
Research
Michael Doane
Sydney Institute of Marine Science
Corresponding Author
ORCiD: https://orcid.org/0000-0001-9820-2193
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Under Review
The most recent version of this article is available here.
No community comments so far
Review #1 received
Received 06 Apr, 2020
Review #2 received
Received 05 Apr, 2020
Reviewer #2 agreed
On 01 Apr, 2020
Editor assigned
On 30 Mar, 2020
Reviewers invited
Invitations sent on 30 Mar, 2020
Reviewer #1 agreed
On 30 Mar, 2020
Submission checks complete
On 29 Mar, 2020
Editor invited
On 29 Mar, 2020
Version 1
Posted 30 Dec, 2019
No comments provided
Review #2 received
Received 02 Mar, 2020
Editorial decision: Revise Before Review
On 02 Mar, 2020
Reviewer #2 agreed
On 11 Feb, 2020
Review #1 received
Received 28 Jan, 2020
Reviewer #1 agreed
On 13 Jan, 2020
Reviewers invited
Invitations sent on 12 Jan, 2020
Editor assigned
On 23 Dec, 2019
Submission checks complete
On 22 Dec, 2019
Editor invited
On 22 Dec, 2019
First submitted
On 18 Dec, 2019
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
General Microbiology
License:
This work is licensed under a CC BY 4.0 License. Read Full License
The most recent version of this article is available here.
Background: The vertebrate clade diverged into Chondrichthyes (sharks, rays, and chimeras) and Osteichthyes fishes (bony fishes) approximately 420 mya, with each group accumulating vast anatomical and physiological differences, including skin properties. The skin of Chondrichthyes fishes is covered in dermal denticles, whereas Osteichthyes fishes are covered in scales and are mucous rich. The divergence time among these two fish groups is hypothesized to result in predictable variation among symbionts. Here, using shotgun metagenomics, we test if patterns of diversity in the skin surface microbiome across the two fish clades match predictions made by phylosymbiosis theory. We hypothesize, 1) the skin microbiome will be species and clade-specific, 2) evolutionary difference in elasmobranch and teleost fishes corresponds with a concomitant increase in host-microbiome dissimilarity and 3) the skin structure of the two groups will affect the taxonomic and functional composition of the microbiomes.
Results: We show that the taxonomic and functional composition of the microbiomes is host species-specific. Teleost fish had lower average microbiome within clade similarity compared to among clade comparison, but their composition is not different among clade in a null based model. Elasmobranch’s average similarity within clade was not different than across clade and not different in a null based model of comparison. In the comparison of host distance with microbiome distance, we found that the taxonomic composition of the microbiome was related to host distance for the elasmobranchs, but not the teleost fishes. In comparison, the gene function composition was not related to the host-organism distance for elasmobranchs but was negatively correlated with host distance for teleost fishes.
Conclusion: Our results show the patterns of phylosymbiosis are not consistent across both fish clades, with the elasmobranchs showing phylosymbiosis, while the teleost fish are not. The discrepancy may be linked to alternative processes underpinning microbiome assemblage, including possible historical host-microbiome evolution of the elasmobranchs and convergent evolution in the teleost which filter specific microbial groups. Our comparison of the microbiomes among fishes represents an investigation into the microbial relationships of the oldest divergence extant vertebrate host and reveals that microbial relationships are not consistent across evolutionary timescales.
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.
Loading...