Wildlife fecal microbiota exhibit community stability across a longitudinal semi-controlled non-invasive sampling experiment
Wildlife microbiome studies are being used to assess microbial links with animal health and habitat. The gold standard of sampling microbiomes directly from captured animals is ideal for limiting potential abiotic influences on microbiome composition, yet fails to leverage the many benefits of non-i...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2024-02-01
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| Series: | Frontiers in Microbiomes |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/frmbi.2024.1274277/full |
| _version_ | 1797315986568773632 |
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| author | Samuel B. Pannoni William E. Holben |
| author_facet | Samuel B. Pannoni William E. Holben |
| author_sort | Samuel B. Pannoni |
| collection | DOAJ |
| description | Wildlife microbiome studies are being used to assess microbial links with animal health and habitat. The gold standard of sampling microbiomes directly from captured animals is ideal for limiting potential abiotic influences on microbiome composition, yet fails to leverage the many benefits of non-invasive sampling. Application of microbiome-based monitoring for rare, endangered, or elusive species creates a need to non-invasively collect scat samples shed into the environment. Since controlling sample age is not always possible, the potential influence of time-associated abiotic factors was assessed. To accomplish this, we analyzed partial 16S rRNA genes of fecal metagenomic DNA sampled non-invasively from Rocky Mountain elk (Cervus canadensis) near Yellowstone National Park. We sampled pellet piles from four different elk, then aged them in a natural forest plot for 1, 3, 7, and 14 days, with triplicate samples at each time point (i.e., a blocked, repeat measures (longitudinal) study design). We compared fecal microbiota of each elk through time with point estimates of diversity, bootstrapped hierarchical clustering of samples, and a version of ANOVA–simultaneous components analysis (ASCA) with PCA (LiMM-PCA) to assess the variance contributions of time, individual and sample replication. Our results showed community stability through days 0, 1, 3 and 7, with a modest but detectable change in abundance in only 2 genera (Bacteroides and Sporobacter) at day 14. The total variance explained by time in our LiMM-PCA model across the entire 2-week period was not statistically significant (p>0.195) and the overall effect size was small (<10% variance) compared to the variance explained by the individual animal (p<0.0005; 21% var.). We conclude that non-invasive sampling of elk scat collected within one week during winter/early spring provides a reliable approach to characterize fecal microbiota composition in a 16S rDNA survey and that sampled individuals can be directly compared across unknown time points with minimal bias. Further, point estimates of microbiota diversity were not mechanistically affected by sample age. Our assessment of samples using bootstrap hierarchical clustering produced clustering by animal (branches) but not by sample age (nodes). These results support greater use of non-invasive microbiome sampling to assess ecological patterns in animal systems. |
| first_indexed | 2024-03-08T03:11:48Z |
| format | Article |
| id | doaj.art-764537cdd3774702b7a4a27109d644f5 |
| institution | Directory Open Access Journal |
| issn | 2813-4338 |
| language | English |
| last_indexed | 2024-03-08T03:11:48Z |
| publishDate | 2024-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiomes |
| spelling | doaj.art-764537cdd3774702b7a4a27109d644f52024-02-13T04:37:33ZengFrontiers Media S.A.Frontiers in Microbiomes2813-43382024-02-01310.3389/frmbi.2024.12742771274277Wildlife fecal microbiota exhibit community stability across a longitudinal semi-controlled non-invasive sampling experimentSamuel B. Pannoni0William E. Holben1Franke College of Forestry and Conservation, University of Montana, Missoula, MT, United StatesCellular, Molecular and Microbial Biology Program, University of Montana, Missoula, MT, United StatesWildlife microbiome studies are being used to assess microbial links with animal health and habitat. The gold standard of sampling microbiomes directly from captured animals is ideal for limiting potential abiotic influences on microbiome composition, yet fails to leverage the many benefits of non-invasive sampling. Application of microbiome-based monitoring for rare, endangered, or elusive species creates a need to non-invasively collect scat samples shed into the environment. Since controlling sample age is not always possible, the potential influence of time-associated abiotic factors was assessed. To accomplish this, we analyzed partial 16S rRNA genes of fecal metagenomic DNA sampled non-invasively from Rocky Mountain elk (Cervus canadensis) near Yellowstone National Park. We sampled pellet piles from four different elk, then aged them in a natural forest plot for 1, 3, 7, and 14 days, with triplicate samples at each time point (i.e., a blocked, repeat measures (longitudinal) study design). We compared fecal microbiota of each elk through time with point estimates of diversity, bootstrapped hierarchical clustering of samples, and a version of ANOVA–simultaneous components analysis (ASCA) with PCA (LiMM-PCA) to assess the variance contributions of time, individual and sample replication. Our results showed community stability through days 0, 1, 3 and 7, with a modest but detectable change in abundance in only 2 genera (Bacteroides and Sporobacter) at day 14. The total variance explained by time in our LiMM-PCA model across the entire 2-week period was not statistically significant (p>0.195) and the overall effect size was small (<10% variance) compared to the variance explained by the individual animal (p<0.0005; 21% var.). We conclude that non-invasive sampling of elk scat collected within one week during winter/early spring provides a reliable approach to characterize fecal microbiota composition in a 16S rDNA survey and that sampled individuals can be directly compared across unknown time points with minimal bias. Further, point estimates of microbiota diversity were not mechanistically affected by sample age. Our assessment of samples using bootstrap hierarchical clustering produced clustering by animal (branches) but not by sample age (nodes). These results support greater use of non-invasive microbiome sampling to assess ecological patterns in animal systems.https://www.frontiersin.org/articles/10.3389/frmbi.2024.1274277/fullmicrobiome-stabilitynon-invasivewildlifelongitudinal time-series16s-rDNA sequencingLiMM-PCA |
| spellingShingle | Samuel B. Pannoni William E. Holben Wildlife fecal microbiota exhibit community stability across a longitudinal semi-controlled non-invasive sampling experiment Frontiers in Microbiomes microbiome-stability non-invasive wildlife longitudinal time-series 16s-rDNA sequencing LiMM-PCA |
| title | Wildlife fecal microbiota exhibit community stability across a longitudinal semi-controlled non-invasive sampling experiment |
| title_full | Wildlife fecal microbiota exhibit community stability across a longitudinal semi-controlled non-invasive sampling experiment |
| title_fullStr | Wildlife fecal microbiota exhibit community stability across a longitudinal semi-controlled non-invasive sampling experiment |
| title_full_unstemmed | Wildlife fecal microbiota exhibit community stability across a longitudinal semi-controlled non-invasive sampling experiment |
| title_short | Wildlife fecal microbiota exhibit community stability across a longitudinal semi-controlled non-invasive sampling experiment |
| title_sort | wildlife fecal microbiota exhibit community stability across a longitudinal semi controlled non invasive sampling experiment |
| topic | microbiome-stability non-invasive wildlife longitudinal time-series 16s-rDNA sequencing LiMM-PCA |
| url | https://www.frontiersin.org/articles/10.3389/frmbi.2024.1274277/full |
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