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Microbial Ecology

Influence of Hand Rearing and Bird Age on the Fecal Microbiota of the Critically Endangered Kakapo

David W. Waite, Daryl K. Eason, Michael W. Taylor
H. Goodrich-Blair, Editor
David W. Waite
aCentre for Microbial Innovation, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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Daryl K. Eason
bResearch Development and Improvement Division, Department of Conservation, Nelson, New Zealand
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Michael W. Taylor
aCentre for Microbial Innovation, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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H. Goodrich-Blair
Roles: Editor
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DOI: 10.1128/AEM.00975-14
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  • FIG 1
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    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
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    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
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    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

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  • TABLE 1

    Sample sizes, mean ages of individuals, and additional notes taken at the time of samplinga

    Sample time pointNo. of individualsMean age (days)Sample yrDescription
    Juvenile_First8162011Fecal sample from wild juvenile kakapo
    Juvenile_Second10512011Fecal 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_Third5692011Fecal sample from juvenile kakapo ∼2.5 wk following release
    Juvenile_Fourth85692012Fecal sample from juvenile kakapo during the next round of health screening; at this point, individuals were mature, independent birds
    Adult_First102011Fecal sample from wild adult kakapo collected at the same time as Juvenile_First
    Adult_Second72012Fecal 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 pointIndividuals sampled
    Juvenile_FirstHakatere
    Ian
    Ihi
    Stella
    Taonga
    Tia
    Tutoko
    Waa
    Juvenile_SecondAtareta
    Hakatere*
    Ian*
    Ihi*
    Stella*
    Taonga*
    Tia*
    Tutoko*
    Waa*
    Waikawa
    Juvenile_ThirdAtareta
    Ian
    Taonga
    Tutoko
    Waikawa
    Juvenile_FourthHakatere
    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 groupGood's coverageShannon diversity indexShannon evenness indexSimpson diversity indexChao1 estimatorACE estimatorReads mapped (%)OTUs mapped (%)
    Adult_First0.9950.730.100.6325.23899.446.4
    Adult_Second0.9791.100.150.52100.1228.824.88.9
    Juvenile_First0.9910.900.120.4933.3110.395.439.0
    Juvenile_Second0.9980.880.120.619.817.488.453.9
    Juvenile_Third0.9841.170.160.4242.2224.199.027.7
    Juvenile_Fourth0.9730.910.120.71152.5348.710.97.1
    • ↵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

    OTUOTU taxonomyMean relative abundance (%)
    OverallAdultJuvenile (wild)Juvenile (antibiotics)
    OTU01Escherichia34.4538.1729.030.84
    OTU02Unclassified Proteobacteria OTU42.46
    OTU03Streptococcus16.335.8131.690.89
    OTU04Clostridium5.738.741.33
    OTU05Enterococcus1.040.0537.97
    OTU06Lactobacillus12.249.75
    OTU07Clostridium7.62
    OTU10Pseudomonas1.29
    OTU11Lactobacillus3.20
    Total57.5552.7283.2595.11
    • ↵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

    OTUOTU taxonomyMean relative abundance (%)q value
    Juvenile_FirstAdult_First
    OTU06Lactobacillus11.160.01<0.001
    OTU07Clostridium4.490.00<0.001
    OTU10Pseudomonas1.410.01<0.001
    OTU16Lactobacillus*1.910.00<0.001
    OTU19Lactobacillus2.580.01<0.001
    OTU50Clostridium*1.780.00<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.

Additional Files

  • Figures
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  • 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

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Influence of Hand Rearing and Bird Age on the Fecal Microbiota of the Critically Endangered Kakapo
David W. Waite, Daryl K. Eason, Michael W. Taylor
Applied and Environmental Microbiology Jul 2014, 80 (15) 4650-4658; DOI: 10.1128/AEM.00975-14

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Influence of Hand Rearing and Bird Age on the Fecal Microbiota of the Critically Endangered Kakapo
David W. Waite, Daryl K. Eason, Michael W. Taylor
Applied and Environmental Microbiology Jul 2014, 80 (15) 4650-4658; DOI: 10.1128/AEM.00975-14
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