PMC:7572126 / 43453-45016 JSONTXT

{"target":"http://pubannotation.org/docs/sourcedb/PMC/sourceid/7572126","sourcedb":"PMC","sourceid":"7572126","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7572126","text":"Alpha-diversity is defined as a local measure of average species diversity in a community. (Whittaker, 1972; Jost, 2007). To estimate the species alpha diversity in Mer and Waiben, we examined the microbial composition in each community using the vegan (Oksanen et al., 2018) package in R. (R Development Core Team, 2010) Accordingly, the 'estimate' function was used to calculate Chao1’s measure of richness; a measure of the number of species (or other taxonomic levels) present at a site. The 'diversity' function was used to estimate the Shannon-Wiener Index (H'); a measure of how many different types of species are present in the community. Species diversity takes into account both species richness and the dominance or evenness of the species. Evenness measures homogeneity in a community in terms of species relative abundances. A community in which all species are proportionately common is regarded as stable and has a high degree of evenness. Since vegan does not provide a function for Shannon’s evenness/equitability (E), we used a modified R function to estimated E by dividing the actual diversity (H') with the maximum possible diversity value (Hmax). The reasoning is, H' decreases when the species composition is more uneven and reaches a maximum with the highest evenness. Therefore, when all species are equally common, Hmax=ln⁡S (where S is the total number of species), and E=H'÷Hmax. Differences in species composition within Mer and Waiben were analyzed in GraphPad using the Mann-Whitney U-test the with FDR multiple-testing adjustment.","tracks":[{"project":"MyTest","denotations":[{"id":"33074097-18027744-26739296","span":{"begin":115,"end":119},"obj":"18027744"}],"namespaces":[{"prefix":"_base","uri":"https://www.uniprot.org/uniprot/testbase"},{"prefix":"UniProtKB","uri":"https://www.uniprot.org/uniprot/"},{"prefix":"uniprot","uri":"https://www.uniprot.org/uniprotkb/"}],"attributes":[{"subj":"33074097-18027744-26739296","pred":"source","obj":"MyTest"}]},{"project":"2_test","denotations":[{"id":"33074097-18027744-26739296","span":{"begin":115,"end":119},"obj":"18027744"}],"attributes":[{"subj":"33074097-18027744-26739296","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"MyTest","color":"#b593ec","default":true},{"id":"2_test","color":"#93ec9b"}]}]}}