Bobowik Katalina, Fachrul Muhamad, Crenna Darusallam Chelzie, Kusuma Pradiptajati, Sudoyo Herawati, Febinia Clarissa A, Malik Safarina G, Wells Christine A, Gallego Romero Irene
School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia.
Human Genomics and Evolution, St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia.
PLoS One. 2025 Jul 24;20(7):e0328788. doi: 10.1371/journal.pone.0328788. eCollection 2025.
Pathogens found within local environments are a major cause of morbidity and mortality. This is particularly true in Indonesia, where infectious diseases such as malaria or dengue are a significant part of the disease burden. Unequal investment in medical funding throughout Indonesia, particularly in rural areas, has resulted in under-reporting of cases, making surveillance challenging. Here, we use transcriptome data from 117 healthy individuals living on the islands of Mentawai, Sumba, and the Indonesian side of New Guinea Island to explore which pathogens are present within whole blood. We identified diverse microbial taxa in RNA-sequencing data from whole blood but found no evidence of a consistent core microbiome across the Indonesian cohort. Yet, Flaviviridae and Plasmodium stood out as the most predominantly abundant taxa, particularly in samples from the easternmost island within our Indonesian dataset. The high prevalence of Plasmodium, the pathogen responsible for malaria, aligns with epidemiological data showing that the Indonesian part of New Guinea has the country's highest malaria rates. We also compare the Indonesian data to two other cohorts from Mali and UK and find a distinct microbiome profile for each group. Higher levels of dissimilarity were found between UK cohort (urban) compared to Indonesian and Malian cohorts (rural), where the former also have significantly lower within-population dissimilarity. This study provides a framework for RNA-seq as a possible retrospective surveillance tool and an insight to what makes up the transient human blood microbiome.
在当地环境中发现的病原体是发病和死亡的主要原因。在印度尼西亚尤其如此，在那里，疟疾或登革热等传染病是疾病负担的重要组成部分。印度尼西亚各地，特别是农村地区，在医疗资金投入上的不均衡，导致病例报告不足，使得监测工作面临挑战。在此，我们使用来自明打威群岛、松巴岛以及新几内亚岛印度尼西亚一侧的117名健康个体的转录组数据，来探索全血中存在哪些病原体。我们在全血的RNA测序数据中鉴定出了多样的微生物分类群，但未发现整个印度尼西亚队列中存在一致的核心微生物组的证据。然而，黄病毒科和疟原虫属是最为主要的丰富分类群，特别是在我们印度尼西亚数据集中最东部岛屿的样本中。导致疟疾的病原体疟原虫的高流行率，与流行病学数据相符，该数据表明新几内亚岛的印度尼西亚部分是该国疟疾发病率最高的地区。我们还将印度尼西亚的数据与来自马里和英国的另外两个队列进行了比较，发现每个组都有独特的微生物组特征。与印度尼西亚和马里队列（农村）相比，英国队列（城市）的差异程度更高，而前者在人群内部的差异也显著更低。这项研究为RNA测序作为一种可能的回顾性监测工具提供了框架，并深入了解了构成人类血液中短暂微生物组的成分。
