# Analysis of Gut Microbiome Structure Based on GMPR+Spectrum
## 3 Results
### Network Analysis Core Flora (Genus Level)  
In order to compare the structure with the core flora identified by GMPR+Spectrum, we also use the network analysis method to construct the gut flora interaction network among different OTUs and then take the MCODE method to identify and visualize the core gut microbiome contained in the interaction network for each group. The MCODE method calculates the adjacent subgraphs and graph densities contained in each node in the network graph, and the score value of a node reflects the density of the node and its surrounding nodes. Then the algorithm expands from the node with the maximum score value to the surrounding nodes, and the qualified nodes are added to this module and generate a module with similar clustering coefficients.  
The intra-module connectivity (Zi) value is a measure of the role of a node in its module, and the larger the Zi value is the greater the role played by this node in that module, and then the top 10 OTUs in each module are considered as the core nodes within each key module according to the magnitude of Zi value corresponding to each OTU. Thus, we obtained the core gut microbiome network for modules 1, 2, and 3 (containing many core modules, but we only chose 3 modules to show here) of all samples' group, as shown in Figure 5, where MCODE1 scored 5 and contained 5 nodes with 10 edges, each corresponding to a Zi value of 0.935. MCODE2, with a score of 3, contained 3 nodes and 3 edges, and the Zi values of nodes OTU1430, OTU1111, and OTU535 were 1.402, 1.351, and 1.351 in order. MCODE3 had a score of 5 and contained 5 nodes with 10 edges, and the Zi values of nodes OTU101, OTU183, OTU907, OTU1153, and OTU582 were 2.293, 2.156, 2.020, 1.951, 1.951, etc. The details of the core colonies contained in each module can be found in Table 14.  
The details of core colonies and corresponding Zi values in patients with N, H, and M contained in modules 1, 2, and 3 can be found in Tables A8-A10. The Zi values of nodes OTU6, OTU683, OTU658, OTU944, OTU406, OTU378, and OTU440 in H were 0.933, 0.906, 0.906, 0.701, 0.574, 0.574, 1.232 representing _Coproccus_, _Precotella_, _Lachospira_, _Parabateroides_, _Streptococcus_, and _Clostridium_, respectively. The Zi values of nodes OTU201, OTU1063, OTU861, OTU1425, OTU1237, OTU225, OTU202, OTU238, OTU1440, OTU1250, and OTU1383 in M were 1.145, 1.115, 1.115, 1.054, 1.054, 1.029, 1.029, 0.984, 0.843, 0.843, and 0.843, representing _Ruminococcus_, _Bacteroides_, _Clostridium_, _Lachospira_, _Faecalibacteriumium_, _Actinomyces_, _Coprococcus_, _Faecalibacteriumium_, _Veillonella_, _Sutterella_, _Oscillospira_, respectively.  
In the network analysis, the mean scores of the core gut microbiota of the normal, minimal hepatic encephalopathy and cirrhotic groups were 8.33, 9.33, and 10, respectively, with higher scores indicating more complex networks. In the three networks, we also found many similar bacteria among different groups, but the intestinal flora of the M group was more complex, and _Precotella_, _Lachospira_, and _Veillonella_ were the key bacteria in the intestinal flora of the M group, which were not included in the core flora of normal subjects. _Actinomyces_, _Sutterella_, and _Oscillospira_ are key bacteria in the intestinal flora of patients with mild hepatic encephalopathy, which are not included in the core flora of N and H groups. _Streptococcus_, as critical bacteria in the intestinal flora of patients with cirrhosis, was equally absent in the other two groups.