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Gut microbiome of helminth-infected indigenous Malaysians is context dependent

Tee MZ 1 , Er YX 2 , Easton AV 3 , Yap NJ 2 , Lee IL 4 , Devlin J 3 Show all authors , Chen Z 3 , Ng KS 5 , Subramanian P 6 , Angelova A 6 , Oyesola O 7 , Sargsian S 3 , Ngui R 2 , Beiting DP 8 , Boey CCM 9 , Chua KH 1 , Cadwell K 3 , Lim YAL 10 , Loke P 11 , Lee SC 12

Affiliations 

  • 1 Department of Biomedical Science, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
  • 2 Department of Parasitology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
  • 3 Department of Microbiology, New York University Grossman School of Medicine, New York, NY, USA
  • 4 Kulliyyah of Medicine and Health Sciences, University Islam Antarabangsa Sultan Abdul Halim Mu'adzam Shah, 09300, Kuala Ketil, Kedah, Malaysia
  • 5 Department of Gastroenterology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
  • 6 Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
  • 7 Type 2 Immunity Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, USA
  • 8 Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
  • 9 Department of Paediatrics, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
  • 10 Department of Parasitology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia. limailian@um.edu.my
  • 11 Type 2 Immunity Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, USA. png.loke@nih.gov
  • 12 Type 2 Immunity Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, USA. sooching.lee@nih.gov
Microbiome, 2022 Dec 07;10(1):214.
PMID: 36476263 DOI: 10.1186/s40168-022-01385-x

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. Video Abstract.

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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