454 data used in the paper 'On the importance of the microbiome and pathobiome in coral health and disease'

Examples of visualisations of microbial networks associated
with Acorpora muricata collected at
four different locations (Australia, Fiji, Maldives and Solomon Islands).
Networks with vertices representing individual OTUs, and edges representing
absolute values of correlation coefficients of greater than 0.6, were derived
from OTU abundances in a) healthy corals and b) diseased corals.  Edges shown in green show positive
correlations, whereas those shown in red represent negative correlations.  Networks were derived using the qgraph
function in the qgraph package (Epskamp et al., 2012).  c) shows the network derived from the healthy
coral arranged according to a community clustering algorithm (fastgreedy.community
from the igraph package; (Csardi and Nepusz, 2006)).  The algorithm tries to identify clusters of
OTUs which show similar patterns of abundance across samples. d) Shows the
relationship between the cut-off correlation value (x-axis) determining which
of the correlations between OTU abundances should be included and the
proportion of all the pair wise edges included in the network. All network
analysis was done using the R statistical programming language (R Core Team,
2016).  Methods: Acropora muricata samples were collected and preserved in 100%
molecular grade ethanol (Sweet and Séré, 2016). All samples were extracted
using the Qiagen DNeasy Extraction kit, amplified with primers 357 and 518 and
sequenced on the 454 platform. All samples were pooled on the same run with
barcodes for a complete list of methods including downstream processing of the
sequencing run please refer to Sweet and Bythell, (2015).