Network analysis of gut microbial communities reveal key genera for a multiple sclerosis cohort with Mycobacterium avium subspecies paratuberculosis infection.

IF 4.3 3区 医学 Q1 GASTROENTEROLOGY & HEPATOLOGY Gut Pathogens Pub Date : 2024-07-10 DOI:10.1186/s13099-024-00627-7
Hajra Ashraf, Plamena Dikarlo, Aurora Masia, Ignazio R Zarbo, Paolo Solla, Umer Zeeshan Ijaz, Leonardo A Sechi
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Abstract

Background: In gut ecosystems, there is a complex interplay of biotic and abiotic interactions that decide the overall fitness of an individual. Divulging the microbe-microbe and microbe-host interactions may lead to better strategies in disease management, as microbes rarely act in isolation. Network inference for microbial communities is often a challenging task limited by both analytical assumptions as well as experimental approaches. Even after the network topologies are obtained, identification of important nodes within the context of underlying disease aetiology remains a convoluted task. We therefore present a network perspective on complex interactions in gut microbial profiles of individuals who have multiple sclerosis with and without Mycobacterium avium subspecies paratuberculosis (MAP) infection. Our exposé is guided by recent advancements in network-wide statistical measures that identify the keystone nodes. We have utilised several centrality measures, including a recently published metric, Integrated View of Influence (IVI), that is robust against biases.

Results: The ecological networks were generated on microbial abundance data (n = 69 samples) utilising 16 S rRNA amplification. Using SPIEC-EASI, a sparse inverse covariance estimation approach, we have obtained networks separately for MAP positive (+), MAP negative (-) and healthy controls (as a baseline). Using IVI metric, we identified top 20 keystone nodes and regressed them against covariates of interest using a generalised linear latent variable model. Our analyses suggest Eisenbergiella to be of pivotal importance in MS irrespective of MAP infection. For MAP + cohort, Pyarmidobacter, and Peptoclostridium were predominately the most influential genera, also hinting at an infection model similar to those observed in Inflammatory Bowel Diseases (IBDs). In MAP- cohort, on the other hand, Coprostanoligenes group was the most influential genera that reduces cholesterol and supports the intestinal barrier.

Conclusions: The identification of keystone nodes, their co-occurrences, and associations with the exposome (meta data) advances our understanding of biological interactions through which MAP infection shapes the microbiome in MS individuals, suggesting the link to the inflammatory process of IBDs. The associations presented in this study may lead to development of improved diagnostics and effective vaccines for the management of the disease.

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肠道微生物群落网络分析揭示了感染副结核分枝杆菌亚种的多发性硬化症队列中的关键菌属。
背景:在肠道生态系统中,生物与非生物之间存在着复杂的相互作用,决定着个体的总体健康状况。由于微生物很少单独行动,了解微生物-微生物和微生物-宿主之间的相互作用可能有助于制定更好的疾病管理策略。微生物群落的网络推断通常是一项具有挑战性的任务,它受到分析假设和实验方法的限制。即使获得了网络拓扑结构,在潜在疾病病因的背景下识别重要节点仍然是一项复杂的任务。因此,我们从网络的角度来研究多发性硬化症患者肠道微生物谱中复杂的相互作用,包括感染和未感染副结核分枝杆菌(MAP)。我们的论述以最近在网络范围统计测量方面取得的进展为指导,这些统计测量可识别关键节点。我们采用了几种中心性测量方法,包括最近发布的一种能有效消除偏差的测量方法--综合影响视图(IVI):利用 16 S rRNA 扩增技术,在微生物丰度数据(n = 69 个样本)上生成了生态网络。利用 SPIEC-EASI(一种稀疏的逆协方差估计方法),我们分别获得了 MAP 阳性(+)、MAP 阴性(-)和健康对照(作为基线)的网络。利用 IVI 指标,我们确定了前 20 个关键节点,并利用广义线性潜变量模型将它们与相关协变量进行回归。我们的分析表明,无论是否感染 MAP,Eisenbergiella 在多发性硬化症中都具有关键重要性。在MAP+队列中,拟杆菌(Pyarmidobacter)和肽梭菌(Peptoclostridium)是影响最大的菌属,这也暗示了一种类似于在炎症性肠病(IBD)中观察到的感染模式。另一方面,在 MAP-队列中,Coprostanoligenes 属是最有影响力的菌属,它能降低胆固醇并支持肠道屏障:关键节点、它们的共同出现以及与暴露组(元数据)的关联的确定,加深了我们对 MAP 感染影响多发性硬化症患者微生物组的生物交互作用的理解,并表明这与 IBD 的炎症过程有关。本研究提出的关联可能有助于开发出更好的诊断方法和有效的疫苗来治疗该疾病。
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来源期刊
Gut Pathogens
Gut Pathogens GASTROENTEROLOGY & HEPATOLOGY-MICROBIOLOGY
CiteScore
7.70
自引率
2.40%
发文量
43
期刊介绍: Gut Pathogens is a fast publishing, inclusive and prominent international journal which recognizes the need for a publishing platform uniquely tailored to reflect the full breadth of research in the biology and medicine of pathogens, commensals and functional microbiota of the gut. The journal publishes basic, clinical and cutting-edge research on all aspects of the above mentioned organisms including probiotic bacteria and yeasts and their products. The scope also covers the related ecology, molecular genetics, physiology and epidemiology of these microbes. The journal actively invites timely reports on the novel aspects of genomics, metagenomics, microbiota profiling and systems biology. Gut Pathogens will also consider, at the discretion of the editors, descriptive studies identifying a new genome sequence of a gut microbe or a series of related microbes (such as those obtained from new hosts, niches, settings, outbreaks and epidemics) and those obtained from single or multiple hosts at one or different time points (chronological evolution).
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