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Whole blood transcriptomics analysis of Indonesians reveals translocated and pathogenic microbiota in blood
Katalina Bobowik1, Muhamad Fachrul1,2, Chelzie Crenna Darusallam3
1School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia.
Abstract:
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.
Insights
This study explored pathogens in Indonesian blood samples, finding Plasmodium and Flaviviridae were most common, especially in New Guinea. RNA sequencing offers a new way to track infectious diseases in remote areas.
Area of Science:
- Microbiology
- Genomics
- Epidemiology
Background:
- Infectious diseases like malaria and dengue pose significant health challenges in Indonesia.
- Under-reporting of cases due to unequal medical funding, especially in rural areas, complicates disease surveillance.
- Understanding the human blood microbiome is crucial for identifying endemic pathogens.
Purpose of the Study:
- To identify pathogens present in whole blood of healthy individuals from diverse Indonesian regions using transcriptome data.
- To investigate the presence and abundance of microbial taxa, including potential disease-causing agents.
- To compare the Indonesian blood microbiome profile with cohorts from Mali and the UK.
Main Methods:
- Analysis of RNA sequencing (RNA-seq) data from 117 healthy Indonesian individuals across Mentawai, Sumba, and New Guinea Island.
- Identification and quantification of microbial taxa within whole blood samples.
- Comparative analysis of microbiome profiles between Indonesian, Malian, and UK cohorts.
Main Results:
- Diverse microbial taxa were detected in Indonesian whole blood samples, but no consistent core microbiome was observed.
- Flaviviridae and Plasmodium were the most abundant taxa, particularly prevalent in samples from New Guinea Island.
- Significant differences in microbiome composition were found between urban (UK) and rural (Indonesia, Mali) cohorts, with lower within-population dissimilarity in the urban group.
Conclusions:
- RNA-sequencing of blood serves as a viable tool for retrospective infectious disease surveillance.
- The study highlights the prevalence of Plasmodium in Indonesian New Guinea, aligning with malaria epidemiological data.
- Distinct blood microbiome profiles exist across different geographical and environmental settings, influenced by urbanization.
