Visitors   Views   Downloads

Effects of preservation method on canine (Canis lupus familiaris) fecal microbiota

View preprint
RT @phylogenomics: New paper just accepted on how to store dog poop. Preprint is here: https://t.co/vXgyu36gwW. Final version coming soon.…
RT @phylogenomics: New paper just accepted on how to store dog poop. Preprint is here: https://t.co/vXgyu36gwW. Final version coming soon.…
RT @phylogenomics: New paper just accepted on how to store dog poop. Preprint is here: https://t.co/vXgyu36gwW. Final version coming soon.…
mt @SeqComplete : Effects of preservation method on canine (Canis lupus familia… https://t.co/lMSwTre2N2, see more https://t.co/D9GipwS8tX
Effects of preservation method on canine (Canis lupus familiaris) fecal microbi… https://t.co/lMSwTre2N2, see more https://t.co/UaSzAxtGUD
RT @phylogenomics: New paper just accepted on how to store dog poop. Preprint is here: https://t.co/vXgyu36gwW. Final version coming soon.…
RT @phylogenomics: New paper just accepted on how to store dog poop. Preprint is here: https://t.co/vXgyu36gwW. Final version coming soon.…
RT @phylogenomics: New paper just accepted on how to store dog poop. Preprint is here: https://t.co/vXgyu36gwW. Final version coming soon.…
RT @phylogenomics: New paper just accepted on how to store dog poop. Preprint is here: https://t.co/vXgyu36gwW. Final version coming soon.…
RT @phylogenomics: New paper just accepted on how to store dog poop. Preprint is here: https://t.co/vXgyu36gwW. Final version coming soon.…
RT @phylogenomics: New paper just accepted on how to store dog poop. Preprint is here: https://t.co/vXgyu36gwW. Final version coming soon.…
RT @phylogenomics: New paper just accepted on how to store dog poop. Preprint is here: https://t.co/vXgyu36gwW. Final version coming soon.…
New paper just accepted on how to store dog poop. Preprint is here: https://t.co/vXgyu36gwW. Final version coming soon. Go dog poop.
Effects of preservation method on canine (Canis lupus familiaris) fecal microbiota https://t.co/g4KtjxU423
107 days ago
Effects of preservation method on canine (Canis lupus familiaris) fecal microbiota https://t.co/9izwOY4E7B
Effects of preservation method on canine (Canis lupus familiaris) fecal microbiota https://t.co/b6E0k8f3wh
NOT PEER-REVIEWED
"PeerJ Preprints" is a venue for early communication or feedback before peer review. Data may be preliminary.

A peer-reviewed article of this Preprint also exists.

View peer-reviewed version

Supplemental Information

Fig S1. Average DNA purity (A260/280) by preservation method from Day 0 to 56 at 25°C, 4°C, and -80°C

Across all buffers and temperatures, DNA purity ± standard error did not change significantly over time.

DOI: 10.7287/peerj.preprints.26912v1/supp-1

Fig S2. Shannon diversity index of all samples by buffer, temperature, day, and their interactions

Significant effects were found according to storage buffer (F-value=3.07, DF=3, P=0.03). ***p<0.001, **p<0.01, *p<0.05.

DOI: 10.7287/peerj.preprints.26912v1/supp-2

Fig S3. Species richness of all samples by buffer, temperature, day, and their interactions

Significant effects were found according to storage buffer (F-value=12.4, DF=3, P<0.00001), duration of sample storage (F-value=10.8, DF=1, P=0.0016), the interaction between storage buffer and temperature (F-value=3.443, DF=3, P=0.22), and the interaction between storage buffer and duration of sample storage (F-value=9.67, DF=3, P<0.00001). ***p<0.001, **p<0.01, *p<0.05.

DOI: 10.7287/peerj.preprints.26912v1/supp-3

Fig S4. Species evenness of all samples by buffer, temperature, day, and their interactions

There were significant effects associated with interactions between storage buffer and storage temperature (F-value=3.98, DF=3, P=0.01), storage buffer and duration of sample storage (F-value=4.9, DF=3, P=0.004), and buffer, storage temperature, and duration of sample storage (F-value=3.1, DF=3, P=0.03). ***p<0.001, **p<0.01, *p<0.05.

DOI: 10.7287/peerj.preprints.26912v1/supp-4

Fig S5. Bray Curtis Dissimilarities of samples stored at 25°C, 4°C, and -80°C

Boxplot of Bray Curtis dissimilarities between sample groups representing median, lower quartile, and upper quartile distances bound between 0 and 1.

DOI: 10.7287/peerj.preprints.26912v1/supp-5

Fig S6. Comparison of DNA concentration yields obtained from QUBIT and Nanodrop

Across all buffers and temperatures, DNA detection by Nanodrop yielded much higher concentrations than that of QUBIT, particularly in that of RNA later samples.

DOI: 10.7287/peerj.preprints.26912v1/supp-6

Table S1. Effects of storage buffer on Shannon Diversity Index based on Tukey’s HSD

The difference between the means (diff), upper and lower levels of the 95% confidence interval around that mean difference, and p-values adjusted using Tukey were determined on R software. Significant interactions (bold) were considered when p<0.05.

DOI: 10.7287/peerj.preprints.26912v1/supp-7

Table S2. Effects of buffer, duration of storage, the interaction between buffer and temperature, and the interaction between buffer and duration of storage on Species Richness based on Tukey’s HSD

The difference between the means (diff), upper and lower levels of the 95% confidence interval around that mean difference, and p-values adjusted using Tukey were determined on R software. Significant interactions (bold) were considered when p<0.05.

DOI: 10.7287/peerj.preprints.26912v1/supp-8

Table S3. Effects of the interaction between buffer and temperature, buffer and duration of storage, and buffer, temperature, and duration on storage on Species Evenness based on Tukey’s HSD

The difference between the means (diff), upper and lower levels of the 95% confidence interval around that mean difference, and p-values adjusted using Tukey were determined on R software. Significant interactions (bold) were considered when p<0.05.

DOI: 10.7287/peerj.preprints.26912v1/supp-9

Table S4. Bray Curtis Dissimilarity distances between groups of samples at 25°C, 4°C, and -80°C

Significance testing of Bray Curtis dissimilarity was performed using a two-sided Student's two-sample t-test. T-statistics and P-values including Bonferonni correction between buffers were evaluated with sample storage at 25°C, 4°C, and -80°C.

DOI: 10.7287/peerj.preprints.26912v1/supp-10

Additional Information

Competing Interests

Jonathan A. Eisen is an Academic Editor for PeerJ. Holly H. Ganz is the CEO of AnimalBiome, Inc., a company developed to improve gut health in companion animals.

Author Contributions

Katti R Horng conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Holly H Ganz conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Jonathan A Eisen conceived and designed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Stanley L Marks conceived and designed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Data Deposition

The following information was supplied regarding data availability:

The metagenome data can be accessed through NCBI BioProject ID PRJNA414515

(https://www.ncbi.nlm.nih.gov/bioproject/PRJNA414515).

Figshare: https://figshare.com/articles/Canine_fecal_samples/5510422.

Funding

The project described was supported by Nestle Purina PetCare Company (St. Louis, MO) through grant number OVCR-201503617 and the Center for Companion Animal Health (CCAH) at the University of California, Davis, School of Veterinary Medicine through a matching fund award. Financial support was provided by the Students Training in Advanced Research (STAR) Program at UC Davis through National Institutes of Health T35 (T35OD010956-17). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


Add your feedback

Before adding feedback, consider if it can be asked as a question instead, and if so then use the Question tab. Pointing out typos is fine, but authors are encouraged to accept only substantially helpful feedback.

Some Markdown syntax is allowed: _italic_ **bold** ^superscript^ ~subscript~ %%blockquote%% [link text](link URL)
 
By posting this you agree to PeerJ's commenting policies