Microbial diversity investigation using 16S metagenomics in Tunisian patients with systemic lupus erythematosus

Abstract

• Systemic lupus erythematosus (SLE) is an autoimmune disease. • It is characterized by the immune system deregulation damaging multiple organs. • The etiology of SLE is still unclear. • We aim to identify gut bacteria profile in Tunisian SLE subjects. • We found a dysbiosis in SLE patients and a correlation with clinical parameters. Systemic lupus erythematosus (SLE) is a multisystemic autoimmune disease associated with significant morbidity and mortality. It is characterized by a loss of self-immune tolerance and autoantibody production, leading to multiple organ damage. Emerging investigations have confirmed the role of gut microbiota dysbiosis in patients with SLE, although the underlying mechanisms remain unclear to date. In this study, we aim to investigate the bacterial profile of SLE including phylum/class/genus relative abundance and diversity, to compare them with healthy controls and to study the correlation of relative abundance of different patterns with clinical/biological parameters. In this case–control study, the bacterial profile was investigated in 7 SLE patients and 7 healthy controls using 16S metagenomics clustering. The present study reported a low abundance of the class Bacilli (0.58% in SLE vs 1.26% in the controls), the genus Lactobacillus (0.43% vs 0.74%), as well as a higher abundance of the genera Gammaproteobacteria (2.37% vs 0.77%) and Escherichia – Shigella (2.04% vs 0.51%) in SLE samples compared to the controls ( p < 0.05). We also found an association between the class Betaproteobacteria (4.42% vs 1.57%) and the genus Faecalibacterium (11.34% vs 3.35%) and renal manifestations ( p < 0.05). The phylum Actinobacteria (0.21% vs 3.8%, p = 0.036) and the genus Bifidobacterium levels were lower in active SLE compared to the healthy controls. This study is the first report on the gut microbiota of SLE and the first case–control study in Tunisia and North Africa. We obtained a particular profile of bacterial gut microbiota for the SLE group. We found a specific clustering when compared to the healthy controls. El lupus eritematoso sistémico (LES) es una enfermedad autoinmune multisistémica que ocasiona elevada mortalidad y morbilidad. Se caracteriza por la pérdida de la tolerancia autoinmune y la producción de autoanticuerpos, que dañan múltiples órganos. En este trabajo, investigamos el perfil bacteriano del LES determinando las abundancias relativas a nivel de filo/clase/género y la diversidad en 7 pacientes con LES y 7 controles sanos, empleando agrupamiento metagenómico del gen 16S. Además, estudiamos la correlación de la abundancia relativa de diferentes clusters con parámetros clínicos/biológicos. En los pacientes con LES, encontramos baja abundancia relativa de la clase Bacilli (0,58% vs. 1,26% en controles) y del género Lactobacillus (0,43% vs. 0,74%), así como una mayor abundancia relativa de la clase Gammaproteobacteria (2,37% vs. 0,77%) y de los géneros Escherichia-Shigella (2,04% vs. 0,51%), en comparación con los controles ( p < 0,05). También encontramos en el LES asociación de la clase Betaproteobacteria (4,42% vs. 1,57%) y el género Faecalibacterium (11,34% vs. 3,35%) con la manifestación renal ( p < 0,05). Los niveles del filo Actinobacteria y del género Bifidobacterium disminuyeron en el LES activo frente a los controles sanos (0,21% vs. 3,8% y 0,15% vs. 3,7%, p = 0.036, ambos). Este es el primer informe sobre la microbiota intestinal en personas con LES y el primer estudio de casos y controles en Túnez y el norte de África. Observamos un perfil particular de microbiota intestinal bacteriana en el grupo con LES y detectamos un agrupamiento específico al compararlo con el perfil de los controles sanos.