Baseline characteristics of participants
A total of 21 healthy volunteers, 15 ES patients and 32 ESCC patients were enrolled in this study. Demographic characteristics of all included individuals were shown in Table 1. High age was observed in ESCC groups when compared with healthy controls. There was no significant difference in sex, alcohol intake, smoking, diabetic background and family history of cancer.
Table 1 Clinical characteristics of enrolled patients and healthy controls
Characteristics
|
Normal (n=21)
|
ES (n=15)
|
ESCC (n=32)
|
p value
|
Age
|
47.85±12.01
|
55.60±11.53
|
55.97±11.62
|
0.040*
|
BMI (kg/m2)
|
24.06±3.78
|
24.57±2.92
|
25.89±4.06
|
0.200
|
Sex (male)
|
13
|
9
|
20
|
0.986
|
Smoker (Yes)
|
11
|
10
|
18
|
0.684
|
Alcohol consumption (Yes)
|
7
|
6
|
14
|
0.750
|
Diabetes (Yes)
|
4
|
7
|
9
|
0.214
|
Family history of cancer (Yes)
|
3
|
2
|
3
|
0.796
|
Microbial diversity and richness between three groups
After sequencing and quality filtering, more than 3.2 million tags and a total of 2134 OTUs were obtained with the dominant length of tags locating among 400-440bp (Figure 1A). To test the sequencing depth, we created the rarefaction curves and showed a reasonable amount of sampling (Figure 1B).
The microbial α diversity and β diversity were applied to analyze the microbiota biodiversity and composition among groups. We used Chao1 index and Shannon index to describe the community richness and diversity. A higher richness of microbiota was observed in ESC and ES group than in normal group according to the Chao1 index (ESCC VS normal, p=0.0001, ES VS normal, p=0.0012, Figure 2A). Compared with normal group, the Shannon index of the ESCC group decreased significantly, indicating a lower microbial diversity (p=0.0417, Figure 2B). Whereas, the ES group owned significantly higher Shannon index, in comparison with ESCC group (p<0.0001) and normal group (p=0.0022). Moreover, the Venn diagram indicated that 493 of the total 2134 OTUs were shared among the three groups, with 72, 219 and 871 OUTs were unique for normal, ES and ESCC group respectively (Figure 2C). About β diversity, Partial least squares Discriminant Analysis (PLS-DA) at the OTU level revealed a statistically significant clustering (Figure 2D), suggesting different microbial community structures.
The Changes of Esophageal Microbiota Composition between the three groups
As shown in Figrue 3A-C, each group showed different bacterial composition at the phylum, family, class and genus levels. We explored taxa distribution at the phylum, family and genus level to reveal distinctive characteristics of each group. Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria and Fusobacteria were the five dominant bacterial phyla in the three groups.
Normal esophageal was composed mainly by Firmicutes (62.5%), Proteobacteria (18.2%), Bacteroidetes (13.9%), Actinobacteria (2.6%) and Fusobacteria (1.3%), plus another ~1.5% of unidentified bacteria. At the genus level, Streptococcus (24.3%) was the main contributor to the microbiota profile, followed by Faecalibacterium and Bacteroides (6.1% and 4.3%, respectively); other subdominant genera were Lactobacillus, Neisseria, Curvibacter and Blautia, accounting for about 3% each (Figure 3A-C).
ES group showed a significant decrease of Firmicutes (p=0.0370) together with a statistically significant robust increase of Fusobacteria (p=0.0280) and Bacteroidetes (p=0.0060) with its corresponding genus Bacteroides (p=0.0240) as compared to normal groups (Figure 3A-C).
ESCC samples also displayed a striking reduction in its microbial composition, such as in Fusobacteria (p=0.0010) at phylum level and Faecalibacterium (p=0.0010), Bacteroides (p=0.0090), Curvibacter (p=0.0010) and Blautia (p=0.0040) in comparison with normal groups at genus level. We observed an increasing tendency of Streptococcus in ESCC groups. When compared with ES groups, decreased Bacteroidetes (p=0.0010), Faecalibacterium (p=0.0010), Bacteroides (p=0.0010) and Blautia (p=0.0040) with overexpressed Streptococcus (p=0.0070) in ESCC tissues were identified (Figure 3A-C). In addition, Megamonas, Collinsella, Roseburia and Ruminococcus_2 showed a significantly continuous decreasing trend from Normal to ESCC at the genus level (Figure 3D).
Characterized Microbial Taxa Associated With ESCC Patients
We used multi-level LEfSe analysis to explore potential important microbe biomarkers for the groups in all taxa, and the results of LEfSe among the three groups demonstrated that 138 bacterial species abundance had statistically significant differences. There were 41, 45, and 52 taxa that were abundant in normal volunteers, ES patients, and ESCC patients respectively. Given the large number different bacterial species, we focused on the taxa with LAD socres > 4.0. As shown in Figure 4, at the genus level, increased Streptococcus (LDA score=4.9115, p=0.0021), Actinobacillus (LDA score=4.5193, p<0.0001), Peptostreptococcus (LDA score=4.3049, p<0.0001), Fusobacterium (LDA score=4.2109, p=0.0004), Prevotella (LDA score=4.0768, p=0.0020) were detected as powerful markers in ESCC patients. Particularly, Streptococcus anginosus at the species level (LDA score=4.0115, p<0.0001) showed a greater abundance in ESCC groups. Besides, we observed a high level of Roseburia (LDA score=4.0412, p=0.0001), Faecalibacterium (LDA score=4.4607, p<0.0001) and Curvibacter (LDA score=4.0812, p<0.0001) at the genus level, and Alphaproteobacteria (LDA score=4.2618, p=0.0002) at the class level in the normal individuals. Bacteroides (LDA score=4.6561, p=0.0002) and Blautia (LDA score=4.0883, p<0.0001) at genus level were abundant in ES patients (Figure 4).
Functional analysis of esophageal microbiota across groups
Finally, Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) was conducted to predict the metagenomes and identify the KEGG pathways involved in each group.
Patients with ESCC showed a significant upregulation of microbial genes involved in signaling molecules and interaction, excretory system, cellular community, cell growth and death, membrane transport, energy metabolism, metabolism of other amino acids, nucleotide metabolism, folding, sorting and degradation, translation, glycan biosynthesis and metabolism, replication and repair, metabolism of cofactors and vitamins, while lipid metabolism, xenobiotics biodegradation and metabolism, cell motility, amino acid metabolism, carbohydrate metabolism, transcription, signal transduction were consistently down-regulated compared to normal groups (Figure 5A).
Microbiota associated to ES was characterized by a higher potential for excretory system, digestive system, folding, sorting and degradation, energy metabolism, glycan biosynthesis and metabolism, metabolism of cofactors and vitamins, while showed robustly reduced xenobiotics biodegradation and metabolism, lipid metabolism, cell motility, membrane transport, signal transduction in comparison with control-associated microbiota (Figure 5B).
Moreover, when comparing ES and ESCC tissues, ESCC-associated microbiota showed a significantly increased signaling molecules and interaction, infectious disease, cell growth and death, membrane transport, nucleotide metabolism, folding, sorting and degradation, metabolism of other amino acids, translation, metabolism of cofactors and vitamins, and replication and repair. Conversely, it displayed a consistently decreased lipid metabolism, amino acid metabolism, cell motility, carbohydrate metabolism, transcription, biosynthesis of other secondary metabolites, signal transduction pathways (Figure 5C).