IRCI Article ID: IRCI-AR-0000000952

Gut microbiome of helminth-infected indigenous Malaysians is context dependent

Journal: Microbiome

Publication: 2022-12-07 · Vol. 10 No. 1

DOI: 10.1186/s40168-022-01385-x

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Abstract

Abstract
Background
While microbiomes in industrialized societies are well characterized, indigenous populations with traditional lifestyles have microbiomes that are more akin to those of ancient humans. However, metagenomic data in these populations remains scarce, and the association with soil-transmitted helminth infection status is unclear. Here, we sequenced 650 metagenomes of indigenous Malaysians from five villages with different prevalence of helminth infections.

Results
Individuals from villages with higher prevalences of helminth infections have more unmapped reads and greater microbial diversity. Microbial community diversity and composition were most strongly associated with different villages and the effects of helminth infection status on the microbiome varies by village. Longitudinal changes in the microbiome in response to albendazole anthelmintic treatment were observed in both helminth infected and uninfected individuals. Inference of bacterial population replication rates from origin of replication analysis identified specific replicating taxa associated with helminth infection.

Conclusions
Our results indicate that helminth effects on the microbiota were highly dependent on context, and effects of albendazole on the microbiota can be confounding for the interpretation of deworming studies. Furthermore, a substantial quantity of the microbiome remains unannotated, and this large dataset from an indigenous population associated with helminth infections is a valuable resource for future studies.

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Authors

Mian Zi Tee

Affiliation: University of Malaya

Yi Xian Er

Affiliation: University of Malaya

ORCID: 0000-0002-3316-4920

Alice V. Easton

Affiliation: New York University

ORCID: 0000-0002-4476-9415

Nan Jiun Yap

Affiliation: University of Malaya

ORCID: 0000-0001-6971-2717

Ii Li Lee

Affiliation: Sultan Abdul Halim Mu'adzam Shah International Islamic University

ORCID: 0000-0002-0153-0527

Joseph Devlin

Affiliation: New York University

ORCID: 0000-0002-0003-4812

Ze Chen

Affiliation: New York University

ORCID: 0000-0001-8236-5764

Kee Seong Ng

Affiliation: University of Malaya

ORCID: 0000-0002-0634-0554

Poorani Subramanian

Affiliation: National Institutes of Health; National Institute of Allergy and Infectious Diseases

ORCID: 0000-0003-4371-7290

Angelina Angelova

Affiliation: National Institutes of Health; National Institute of Allergy and Infectious Diseases

ORCID: 0000-0003-2923-0072

Oyebola Oyesola

Affiliation: National Institute of Allergy and Infectious Diseases

ORCID: 0000-0002-5347-7502

Shushan Sargsian

Affiliation: New York University

ORCID: 0000-0002-2582-022X

Romano Ngui

Affiliation: University of Malaya

ORCID: 0000-0002-3520-579X

Daniel P. Beiting

Affiliation: University of Pennsylvania

ORCID: 0000-0002-2865-4589

Christopher Chiong Meng Boey

Affiliation: University of Malaya

Kek Heng Chua

Affiliation: University of Malaya

ORCID: 0000-0002-0452-9994

Ken Cadwell

Affiliation: NYU Langone Health; New York University

ORCID: 0000-0002-5860-0661

Yvonne Ai Lian Lim

Affiliation: University of Malaya

ORCID: 0000-0003-4050-6332

P’ng Loke

Affiliation: National Institute of Allergy and Infectious Diseases

ORCID: 0000-0002-6211-3292

Soo Ching Lee

Affiliation: National Institute of Allergy and Infectious Diseases

ORCID: 0000-0002-5454-2265

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