DataSheet_1_A gut microbiome signature for HIV and metabolic dysfunction-associated steatotic liver disease.docx

IntroductionMetabolic dysfunction-associated steatotic liver disease (MASLD), has emerged as an increasingly recognized problem among people living with HIV (PLWH). The gut-liver axis is considered to be strongly implicated in the pathogenesis of MASLD. We aimed to characterize the gut microbiota composition in PLWH and MASLD and compare it with that of two control groups: PLWH without MASLD and individuals with MASLD without HIV infection.
MethodsWe collected clinical data and stool samples from participants. Bacterial 16S rRNA genes were amplified, sequenced, and clustered into operational taxonomic unit. Alpha diversity was studied by Shannon and Simpson indexes. To study how different the gut microbiota composition is between the different groups, beta diversity estimation was evaluated by principal coordinate analysis (PCoA) using Bray-Curtis dissimilarity. To further analyze differences in microbiome composition we performed a linear discriminant analysis (LDA) effect size (LEfSe).
ResultsWe included 30 HIV+MASLD+, 30 HIV+MASLD- and 20 HIV-MASLD+ participants. Major butyrate producers, including Faecalibacterium, Ruminococcus, and Lachnospira dominated the microbiota in all three groups. Shannon’s and Simpson’s diversity metrics were higher among MASLD+ individuals (Kruskal-Wallis p = 0.047). Beta diversity analysis showed distinct clustering in MASLD-, with MASLD+ participants overlapping regardless of HIV status (ADONIS significance <0.001). MASLD was associated with increased homogeneity across individuals, in contrast to that observed in the HIV+NAFDL- group, in which the dispersion was higher (Permanova test, p value <0.001; ANOSIM, p value <0.001). MASLD but not HIV determined a different microbiota structure (HIV+MASLD- vs. HIV+MASLD+, q-value = 0.002; HIV-MASLD+ vs. HIV+MASLD+, q-value = 0.930; and HIV-MASLD+ vs. HIV+MASLD-, q-value < 0.001). The most abundant genera in MASLD- were Prevotella, Bacteroides, Dialister, Acidaminococcos, Alloprevotella, and Catenibacterium. In contrast, the most enriched genera in MASLD+ were Ruminococcus, Streptococcus, Holdemanella, Blautia, and Lactobacillus.
ConclusionsWe found a microbiome signature linked to MASLD, which had a greater influence on the overall structure of the gut microbiota than HIV status alone.

引言：代谢功能障碍相关脂肪性肝病（Metabolic dysfunction-associated steatotic liver disease, MASLD）已成为人类免疫缺陷病毒感染者（People Living with HIV, PLWH）中日益受到关注的公共健康问题。肠-肝轴（gut-liver axis）被认为与MASLD的发病机制密切相关。本研究旨在明确人类免疫缺陷病毒感染者合并与未合并MASLD人群的肠道菌群组成，并与两个对照组进行比较：未合并MASLD的人类免疫缺陷病毒感染者，以及未合并人类免疫缺陷病毒感染的MASLD患者。

方法：本研究收集了受试者的临床资料与粪便样本。对细菌16S rRNA基因进行扩增、测序，并聚类为操作分类单元（operational taxonomic unit, OTU）。采用香农（Shannon）指数与辛普森（Simpson）指数开展α多样性分析。为探究不同组别间肠道菌群组成的差异，采用基于Bray-Curtis相异度的主坐标分析（principal coordinate analysis, PCoA）进行β多样性评估。为进一步分析菌群组成差异，本研究实施了线性判别分析效应量（linear discriminant analysis effect size, LEfSe）分析。

结果：本研究共纳入30例HIV合并MASLD阳性受试者、30例HIV合并MASLD阴性受试者以及20例MASLD阳性未合并HIV感染者。拟杆菌属（Faecalibacterium）、瘤胃球菌属（Ruminococcus）和毛螺菌属（Lachnospira）等主要丁酸产生菌在三组菌群中均占主导地位。MASLD阳性人群的香农指数与辛普森指数均更高（Kruskal-Wallis检验，p=0.047）。β多样性分析显示，MASLD阴性组呈现显著的聚类特征，而无论是否合并HIV感染，MASLD阳性组受试者的菌群聚类均存在重叠（ADONIS检验，显著性<0.001）。与菌群离散度更高的HIV+NAFDL-组相比，MASLD阳性与受试者间菌群均一性升高相关（置换多元方差分析（Permanova），p<0.001；相似性分析（ANOSIM），p<0.001）。仅MASLD而非HIV感染决定了菌群结构的差异：HIV+MASLD-组与HIV+MASLD+组比较，q值=0.002；HIV-MASLD+组与HIV+MASLD+组比较，q值=0.930；HIV-MASLD+组与HIV+MASLD-组比较，q值<0.001。MASLD阴性组中丰度最高的菌属为普雷沃菌属（Prevotella）、拟杆菌属（Bacteroides）、戴阿利斯特菌属（Dialister）、氨基酸球菌属（Acidaminococcus，原文拼写为Acidaminococcos，疑为笔误）、别样普雷沃菌属（Alloprevotella）以及链状杆菌属（Catenibacterium）。与之相反，MASLD阳性组中富集度最高的菌属为瘤胃球菌属（Ruminococcus）、链球菌属（Streptococcus）、霍尔德曼氏菌属（Holdemanella）、布拉氏菌属（Blautia）以及乳杆菌属（Lactobacillus）。

结论：本研究发现了与MASLD相关的菌群特征，该特征对肠道菌群整体结构的影响大于单纯的HIV感染状态。