3.1 Clinical data
In this study, thirty patients with drug-naive first-episode MDD and thirty healthy controls were recruited as patients’ group and controls group, respectively. There were no statistically significant differences between patients’ group and controls group in terms of age, height, weight, and tobacco and alcohol consumption (Table 1). Patients group received a standardized treatment. The average dose of escitalopram was 16.33 ± 3.46 mg / d. Patients improved significantly when the mean time of taking drugs was 34.53 ± 5.18 days and the HAMD score decreased by more than 50%.
Table 1
Demographic characteristics of patients and controls
| Patients (n = 30) | Controls (n = 30) | p-value |
| | M ± SD | | M ± SD | |
Age | | 44.83 ± 11.00 | | 43.97 ± 10.57 | 0.757 |
Height(m) | | 1.68 ± 0.07 | | 1.70 ± 0.05 | 0.171 |
Weight(Kg) | | 67.83 ± 6.86 | | 69.21 ± 7.14 | 0.447 |
BMI (kg/m2) | | 23.99 ± 2.05 | | 23.83 ± 2.08 | 0.761 |
tobacco(%)* | | 46.67% | | 30.00% | 0.288 |
alcohol(%)* | | 53.33% | | 33.33% | 0.192 |
*Chi-square test; compared with HCs, P < 0.05; BMI: body mass index |
3.2 Sequencing Data And Bacterial Taxonomic Composition
Total 4,790,651 original sequences were obtained from 60 samples. After double-end Reads splicing and filtering, a total of 4,444,748 Clean tags were generated. Each sample generated at least 12,039 Clean tags, and an average value were 49,386 Clean tags. Taxonomic annotation of OTUs based on Silva (bacterial) and UNITE (fungi) taxonomic databases. At phylum level, the dominated gut microbiota were Bacteroidetes, Firmicutes, Protebacteria, and Actinobacteria in three groups. Bacteroidetes and Firmicutes accounted for nearly 90% of the total gut microbiota. The Firmicutes / Bacteroides ratio of Patients group, Follows group, and Controls group were 0.64, 0.46, and 0.70, respectively. The ratio in Follows group was significantly lower than other two groups. (Fig. 1)
At the genus level, the relative abundance of Parasutterella, Prevotella_9, Fusobacterium, Prevotella_2, Christensenellaceae_R-7_group, Odoribacter, and [Eubacterium] _ruminantium_group in Patients group was significantly lower than that in Controls group,and Parabacteroides、Lactobacillus、Anaerostipes、Ruminococcaceae_UCG-014、Dialister was significantely increased in Patients group.
After treatment with escitalopram, gut microbiota with low abundance in Patients group were significantly increased in Follows group, such as: Christensenellaceae_R-7_group, [Eubacterium] _ruminantium_group and Fusobacterium. The higher abundance of gut microbiota in Patients group was also found to decrease in Follows group, such as Lactobacillus. The mainly change of gut microbiota abundance in Follows group was Bacteroides. (Fig. 2)
In addition, there are also several differences in the gut microbiota between Follows group and Controls group. In Follows group, the relative abundance of Parabacteroides, Prevotellaceae, Ruminiclostridium_6, Flavonifractor were increased significantly, and Prevotella_2, Lachnospira, Collinsella, and Clostridium_sensu_stricto_1 were decreased significantly. Among them, the abundance of Faecalibacterium and Lachnoclostridium in Follows group and Patients group were significantly lower than those in Controls group. (Supplementary Table S1)
3.3 Diversity Analysis
Alpha diversity mainly reflects the richness and diversity of the species in samples. As shown in Fig. 3, the Chaos1, Ace, and Shannon indices of Patients group were significantly higher than those of Follows group and Controls group, and the Simpson index was significantly lower in Patients group than others. This showed that the number and the diversity of gut microbiota in Patients group were significantly higher than those of Follows group and Contros group, and there were statistically differences. Four indices value of Follows group were between the values of other two groups, which were significantly different from that of Patients group, but not statistically different from that of Controls group. This meant that the Alpha diversity of gut microbiota in patients returned to the normal level. The statistics of Alpha diversity index values of each group were showed in Table 2.
Table 2
Richness and diversity index values of patients, follows and controls
| Patients | Follows | Controls | |
ACE | 254.88 ± 2.30 | 187.39 ± 11.09 | 173.43 ± 3.80 | |
Chao1 | 257.38 ± 2.63 | 188.93 ± 11.07 | 172.69 ± 4.46 | |
Shannon | 3.57 ± 0.07 | 3.17 ± 0.11 | 2.99 ± 0.09 | |
Simpson | 0.09 ± 0.01 | 0.12 ± 0.01 | 0.13 ± 0.01 | |
Mothur (version v.1.30) software was used to calculate the Alpha diversity index for samples. The larger of the index values of Ace and Chao1shows the greater number of species in the samples. The larger of the Shannon index value and the smaller of the Simpson index value shows more species category of the sample.
Beta diversity was used to compare the similarity of species diversity between different groups. The binary jaccard algorithm was used to calculate β diversity, and there were statistical differences among three groups (R = 0.273, p = 0.001) (Fig. 4). The gut microbiota of Patients group was significantly different from Controls group, and the gut microbiota within Patients group was more similar. Observing the distribution of Follows group, it could be found that the gut microbiota of a part of patients who accepted escitalopram treatment was like that of Controls group, while the others remained like Patients group. The unweighted paired average method (UPGMA) was used in the R language tool to perform hierarchical clustering of each group. It also found that the gut microbiota of Patients group was significantly different from that of Controls group, and Follows group was more like Controls group. This means that the Beta diversity of the patients' gut microbiota tended to return to normal. (Supplementary Figure S2)
3.4 Functional Properties Predicted By Picrust
The study considered that the structure of gut microbiota in Follows group could not completely return to normal. The PICRUSt software was used to compare the species composition information obtained from 16S sequencing data to infer the functional gene composition between two groups. Through the annotation of the KEGG metabolic pathway, it finally found that there were differences in the metabolic pathways of Transport and catabolism, Nervous system, Glycan biosynthesis and metabolism, Cell motility, and Membrane transport between Follows group and Controls group (Fig. 5). In Patients group, the pathways above also had several differences, but it wasn't significantly different from those of Follows group. It thus suggested that the gut microbiota of Follows group might still contribute to the occurrence of depression (Supplementary Table S3).