Article Figures & Data
Figures
- FIG 1
Phylogenetic distribution of bacterial OTUs in the kakapo fecal microbiota. High-level taxonomic information is provided as per classification. OTUs are defined as groups of 16S rRNA gene sequences that share >97% similarity and are ordered by phylum and then subordered by class. For clarity, only the 50 most abundant OTUs are plotted, representing 98.0% of the total reads, with 477 OTUs comprising the remainder of the reads following removal of singletons. OTU abundances are scaled as a proportion of all sequences in the respective sample. OTU02 (mentioned in the text) is noted with an asterisk.
- FIG 2
Changes in community structure in wild kakapo samples. Shown is nonmetric multidimensional scaling of the weighted UniFrac distances between individual samples obtained from wild kakapos. (Left) Distances calculated based on OTU0.97 (stress = 0.15; r2 = 0.90). (Right) Distances calculated based on OTU0.95 (stress = 0.15; r2 = 0.91).
- FIG 3
Statistically significant changes in relative OTU abundance during captivity. The Captive+AB and Captive−AB groups refer to the cohort Juvenile_Second split by whether or not antibiotics were administered. Excluding changes in OTU abundance that could be attributed to bird age, only OTU03 and OTU05 were significantly different in antibiotic-treated samples compared to all other kakapo samples (including captive kakapos without antibiotic treatment).
Tables
- TABLE 1
Sample sizes, mean ages of individuals, and additional notes taken at the time of samplinga
Sample time point No. of individuals Mean age (days) Sample yr Description Juvenile_First 8 16 2011 Fecal sample from wild juvenile kakapo Juvenile_Second 10 51 2011 Fecal sample from captive juvenile kakapo fed an artificial diet of lactated Ringer's solution and fresh fruit; 8 juveniles were also treated with antibiotics during captivity (amoxicillin-clavulanic acid formulas) Juvenile_Third 5 69 2011 Fecal sample from juvenile kakapo ∼2.5 wk following release Juvenile_Fourth 8 569 2012 Fecal sample from juvenile kakapo during the next round of health screening; at this point, individuals were mature, independent birds Adult_First 10 2011 Fecal sample from wild adult kakapo collected at the same time as Juvenile_First Adult_Second 7 2012 Fecal sample from wild adult kakapo collected at the same time as Juvenile_Fourth ↵a For “adult” kakapos, age data are incomplete, but the youngest adults were ≥6 years old in 2011.
- TABLE 2
List of individuals sampled at each point in the juvenile surveya
Time point Individuals sampled Juvenile_First Hakatere Ian Ihi Stella Taonga Tia Tutoko Waa Juvenile_Second Atareta Hakatere* Ian* Ihi* Stella* Taonga* Tia* Tutoko* Waa* Waikawa Juvenile_Third Atareta Ian Taonga Tutoko Waikawa Juvenile_Fourth Hakatere Ian Ihi Stella Tia Tutoko Waa Waikawa ↵a Individuals marked with an asterisk received antibiotic treatment with the commercially available antibiotic amoxicillin-clavulanic acid formulas.
- TABLE 3
Common diversity and richness estimators calculated by using OTUs of ≥97% sequence similaritya
Sample group Good's coverage Shannon diversity index Shannon evenness index Simpson diversity index Chao1 estimator ACE estimator Reads mapped (%) OTUs mapped (%) Adult_First 0.995 0.73 0.10 0.63 25.2 38 99.4 46.4 Adult_Second 0.979 1.10 0.15 0.52 100.1 228.8 24.8 8.9 Juvenile_First 0.991 0.90 0.12 0.49 33.3 110.3 95.4 39.0 Juvenile_Second 0.998 0.88 0.12 0.61 9.8 17.4 88.4 53.9 Juvenile_Third 0.984 1.17 0.16 0.42 42.2 224.1 99.0 27.7 Juvenile_Fourth 0.973 0.91 0.12 0.71 152.5 348.7 10.9 7.1 ↵a The median value for each sample group is reported. Reads mapped refers to the proportion of amplicon sequences that could be mapped to preexisting clone library data. OTUs mapped refers to the number of representative OTUs that could be mapped to preexisting clone library data.
- TABLE 4
Differences in core kakapo microbiota based on different partitioning of samplesa
OTU OTU taxonomy Mean relative abundance (%) Overall Adult Juvenile (wild) Juvenile (antibiotics) OTU01 Escherichia 34.45 38.17 29.03 0.84 OTU02 Unclassified Proteobacteria OTU 42.46 OTU03 Streptococcus 16.33 5.81 31.69 0.89 OTU04 Clostridium 5.73 8.74 1.33 OTU05 Enterococcus 1.04 0.05 37.97 OTU06 Lactobacillus 12.24 9.75 OTU07 Clostridium 7.62 OTU10 Pseudomonas 1.29 OTU11 Lactobacillus 3.20 Total 57.55 52.72 83.25 95.11 ↵a OTU labels are provided to allow consistency for comparisons with other tables that report OTU abundances and changes. Values report the mean relative abundance (percent) of an OTU in the overall microbiota for its grouping. Values in boldface type denote core OTUs in their group, while values in lightface type indicate that an OTU was variable. The final row reports the total proportion of the microbiota that is accounted for by these OTUs (percent).
- TABLE 5
Statistically significant changes in OTU abundance between sample groups of interesta
OTU OTU taxonomy Mean relative abundance (%) q value Juvenile_First Adult_First OTU06 Lactobacillus 11.16 0.01 <0.001 OTU07 Clostridium 4.49 0.00 <0.001 OTU10 Pseudomonas 1.41 0.01 <0.001 OTU16 Lactobacillus* 1.91 0.00 <0.001 OTU19 Lactobacillus 2.58 0.01 <0.001 OTU50 Clostridium* 1.78 0.00 <0.001 ↵a Statistical testing and q value corrections were performed across the entire OTU table, but only OTUs that accounted for ≥1% of the bacterial community are reported. OTUs marked with an asterisk were observed in ≤2 individuals within the Juvenile_First cohort and thus may reflect random interindividual variation rather than a cohort-related difference. OTU labels are provided to allow consistency for comparisons with other tables that report OTU abundances and changes.
Supplemental material
Files in this Data Supplement:
- Supplemental file 1 -
Visualization of bacterial community structures of the kakapo and hoatzin hindgut microbiota (Fig. S1); relative abundances of OTUs reported in Figure 1 and the remainder of each sample (Table S1).
PDF, 547K
- Supplemental file 1 -
