Abstract:

Objective To explore the characteristics of the microbiome in the lung including necrosis, granuloma and normal lung areas of patients with pulmonary tuberculosis.Methods A total of 10 matched-pairs formalin-fixed and paraffin-embedded (FFPE) specimens were selected from 10 patients who were diagnosed as pulmonary tuberculosis in Beijing Chest Hospital from 2016 to 2017. The tissues were divided into necrotic, granuloma and normal lung areas using Leica Microsystems. Characteristics of microbiome was investigated using next-generation sequencing (NGS) technology.Results The major phyla in lung samples of pulmonary tuberculosis patients (relative abundance >1%) were Proteobacteria, Actinobacteria, Firmicutes, TM7 and Bacteroidetes. Adonis analysis based on bray_curtis distance showed that microbial communities were not significantly different at the phylum level. In genus level, seven mainly groups were detected (relative abundance >1%): Ochrobactrum (relative abundance of necrosis, granuloma and normal lung areas: (50.70±6.76)%, (56.18±7.50)%, (61.31±7.95)%), Sphingomonas ((7.50±2.07)%, (7.69±1.29)%, (3.81±2.08)%), Corynebacterium ((5.39±2.39)%, (5.23±1.39)%, (7.43±3.56)%), Brevundimonas ((1.67±0.42)%, (1.75±0.67)%, (2.09±0.34)%), Brevibacterium ((2.38±2.23)%, (2.60±2.60)%, (2.29±0.64)%), Sphingobacterium ((0.72±0.31)%, (0.78±0.26)%, (1.20±0.38)%) and Enhydrobacter ((1.25±1.28)%, (0.31±0.19)%, (0.67±0.80)%). Adonis analysis based on Bray-Curtis distance showed that the microbial community in normal area was significantly different from those in necrotic area (F=3.94, P=0.005) and granulomatous area (F=4.76, P=0.002). The relative abundance of Mycobacterium was very low and mainly existed in the necrotic areas ((0.81±1.92)%). Wilcoxon matched-pairs signed-ranks test showed that relative abundances of Mycobacterium were significantly different between necrotic and granulomatous areas ((0.81±1.92)% vs (0.01±0.01)%; Z=2.10, P=0.036), necrotic areas and normal lung areas ((0.81±1.92)% vs (0.01±0.02)%; Z=-2.37, P=0.018).Conclusion The relative abundances of Sphingomonas, Enhydrobacter, Kocuria and Mycobacterium decreased gradually from necrotic area, granuloma area to normal lung area, while the relative abundance of Ochrobactrum and Sphingobacterium showed the reverse trend. The characteristics of microbiome in lungs from pulmonary tuberculosis patients might be related to the changes of histomorphology in pulmonary.

Key words: Tuberculosis, pulmonary, Biopsy, Paraffin embedding, High-throughput nucleotide sequencing, Microbiome