Additional file 1 of Mono-specific algal diets shape microbial networking in the gut of the sea urchin Tripneustes gratilla elatensis
Creators: name: Masasa, Matan
name: Kushmaro, Ariel
name: Kramarsky-Winter, Esti
name: Shpigel, Muki
name: Barkan, Roy
name: Golberg, Alex
name: Kribus, Abraham
name: Shashar, Nadav
name: Guttman, Lior
Publisher: name: figshare
Year: 2021
Subjects: subject: Microbiology
subject: FOS: Biological sciences

description: Additional file 1. Figure S1. The dissection process of sea urchin T. gratilla elatensis for sampling of the three major regions of the digestive tract. Individual sea urchin (a); circumference cutting presenting upper and lower coelom (b); coelom after removal of the digestive tract (c); (d) Unfolded digestive tract presenting (left to right) the esophagus, stomach, and intestine regions. Red arrow indicates the Aristotle's lantern. Figure S2. Rarefaction curves present the observed OTUs in T. gratilla elatensis GMA from each dietary treatment and gut region (n = 51). Figure S3. Non-metric multidimensional scaling (NMDS) based on Bray-Curtis dissimilarities displaying GMA in different gut regions of T. gratilla elatensis fed with Gracilaria (a), algal-free pellets (b), or Ulva (c). Each dot represents GMA in a specific gut region in an individual sea urchin and is colored in red, green, and blue for esophagus, intestine, and stomach, respectively. The overall area of GMA in each gut region was measured following differences between individuals (inter-niche differences) and indicates overlaps between gut regions (n = 51). Figure S4. (a). A bubble chart of the 17 taxonomic phyla that were identified in the sea urchin digestive tract. The cumulative abundance of all OTUs of each phylum are represented as circles, each representing the sized cumulative abundance of the phylum OTUs in one individual sea urchin under a given treatment of diet and gut region. (b). Abundance of selected phyla with significant variations in the different examined niches of gut region and diet. Differences between individual samples in each specific niche are shown as box plots where middle line in the box indicates mean value, error lines present SD, and whiskers are drawn from the 10th to 90th percentiles (n = 54). Figure S5. Abundance/occurrence ratio of microbes identified as core, core generalists, generalists, specialists, or unique. Ratios of all individuals in group are summarized and presented as box plots with middle line for median, plus sign for mean, error lines for SD, and whiskers drawn from the 10th to 90th percentiles (n = 50). Figure S6. Degrees distribution in GMA networks reveals the different distribution patterns (Poisson or Law-tail) of degrees between nodes in the microbe associations in the following niches: general network (a), under different diets of Gracilaria (b), pellets (c) or Ulva (d); or in different gut regions of esophagus (e), stomach (f), or intestine (g). Figure S7. Topology indices of the GMA association networks examined under different variables of diet (left) or gut region (right). Indices of the general network are shown in graph sets of different diets (left graphs). Figure S8. Schematic diagram of the associations of hub nodes in networks of different diets and gut regions. Type of association (co-occurrence or co-exclusion in blue or red lines, respectively) is also shown in cases of hub-hub association. Nodes are colored as per annotation at phyla level. Figure S9. Pairwise analysis of the association networks in different niches. Each network represents a network pair which was analyzed as control versus case in the respective order for network pairs: Gracilaria vs. pellet (a); Gracilaria vs. Ulva (b); Ulva vs. pellet (c); esophagus vs. stomach (d); esophagus vs. intestine (e); and stomach vs. esophagus (f); Edges in the combined network are colored as per their affiliation as exclusive to the control network (green), exclusive to case network (red), or shared between both (blue). Nodes in networks present only the identified driver microbes as measured by NetShift following their significant increased betweenness in the ‘case’ (red nodes) or control network (black nodes). Nodes diameter indicates NESH score from smaller to higher. Table S1. Ingredients in the formulated algal-free, plant-based pellets for T. gratilla elatensis used in current study. Table S2. Physical characteristics of wet weight and diameter (mean ± SE) of sea urchin individuals after culture under the different diet- types of Ulva, or Gracilaria, or pellets. Values are mean ± SE (n=3). n.d. = not determined. Table S3. OTU count and number of reads for each of the examined samples from a particular gut region and diet regime (n = 54). Table S4. OTU count for the various identified phyla in sea urchin gut samples (n = 54). Table S5. Shared edges between GMA association networks in different diets or gut regions (n = 54) indicating type of relationship (co-occurrence or co-exclusion) and the participating nodes. Table S6. Topology properties of hub microbes in GMA association networks presenting number of degrees, closeness, and betweenness indices in the examined network of the different diets or gut regions (n = 54). Table S7. Topology properties of identified driver nodes in GMA association networks presenting Jaccard Edge Index, NESH score and delta betweenness centrality (normalized to the average path length) indices as measured in pairwise analyses of control versus case networks. Real drivers, i.e. nodes that were identified as driver in a specific niche against each of two other niches, are indicated in bold. Table S8. BLAST (Basic Local Alignment Search Tool) results of the closest phylogenetic species that was identified for each of the OTUs that were identified in current research as core, core-generalist, generalist, specialist, unique, or hub microbes. The bio project number in the NCBI database, where the genome of any of the assigned species is available, is provided. Not found = no genome was available for the closest phylogenetically-related species.