Microbial diversity in freshwater samples and their contaminating human and bovine hosts
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Abstract
DNA extracted from feces (human and bovine) and water samples was used for the massive pyrosequencing of the hypervariable V3 region of the 16S rRNA gene, revealing 4296 operational taxonomic units (OTUs). The greatest diversity was observed in samples of cattle feces, and the smallest diversity was found in a pristine water sample. Firmicutes was the predominant group in samples of human feces, while in bovine feces the dominant groups were Firmicutes and Bacteroidetes. The interaction network showed that the stool samples had the greatest diversity and, among the water samples, the one with human pollution source had the highest diversity. The LEfSe method was used to identify host biomarkers. Actinobacteria, Betaproteobacteria, and Firmicutes were identified as human biomarkers, while for cattle, the potential markers were Bacteroidetes, Tenericutes, and Spirochaetes. Host-specific markers were identified, but were not found in the water samples, suggesting either that the tools used did not have the resolution to identify markers in environmental samples, or that the contamination in the water bodies was mixed. Additionally, as the host-specific markers were isolated from non-autochthonous microorganisms, they could be affected by adverse environmental effects including physical-chemical factors and competition with native organisms.
Cite this as
2017. Microbial diversity in freshwater samples and their contaminating human and bovine hosts. PeerJ Preprints 5:e2992v1 https://doi.org/10.7287/peerj.preprints.2992v1Author comment
This is a submission to PeerJ for review.
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Competing Interests
The authors declare that they have no competing interests.
Author Contributions
Nancy C Stoppe conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
Tatiana T Torres conceived and designed the experiments, analyzed the data, wrote the paper, reviewed drafts of the paper.
Fabricio C Leotti analyzed the data, prepared figures and/or tables, reviewed drafts of the paper.
Maria Inês Z Sato contributed reagents/materials/analysis tools, reviewed drafts of the paper.
Laura MM Ottoboni conceived and designed the experiments, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.
Human Ethics
The following information was supplied relating to ethical approvals (i.e., approving body and any reference numbers):
The Research Ethics Committee of the State University of Campinas School of Medical Sciences approved the present study (Permission 046/11)
Data Deposition
The following information was supplied regarding data availability:
The raw data has been uploaded as a supplemental file.
Funding
This work was supported by the State Research Foundation (FAPESP). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
