ArticleNature communications2022
Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers, 1 of them a synthesis that pooled it.
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Who cites it
57 citing papers in PubMed, 1 synthesis or guideline pooled it, 84 citations in OpenAlex.
- Effects of Schistosoma haematobium infection and treatment on the systemic and mucosal immune phenotype, gene expression and microbiome: A systematic review.PLoS neglected tropical diseases · 2024Pooled it
- A hybrid and cost-efficient barcoding strategy for full-length 16S rRNA gene nanopore sequencing of environmental samples.BMC genomics · 2026Article
- Interactions at theMicrobiology (Reading, England) · 2026Review
- Select microbial metabolites promote tau aggregation in a murine tauopathy model.Nature communications · 2026Article
- A review of computational approaches for metagenomics by long-read sequencing.Science China. Life sciences · 2026Review
- Grass supplementation to a pellet-based diet fails to enrich gut microbiomes with wild-like functions in captive-bred hares.Microbiology spectrum · 2026Article
- Gut microbiota and parasite dynamics in an Amazonian community undergoing urbanization in Colombia.mSphere · 2026Article
- Microbiota-host interaction in colorectal cancer: emerging computational technology, multi-omics integration, and mechanisms.Cancer biology & medicine · 2026Review
- Interactions Between the Gut Microbiome and Genetic and Clinical Risk Factors for Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD) in Patients with Type 2 Diabetes Mellitus from Different Geographical Regions of Argentina.Life (Basel, Switzerland) · 2026Article
- The gut microbiome and metabolome associate with Schistosoma mansoni infection and cardiovascular disease risk in Uganda.Nature communications · 2026Article
- Gut microbiota and resistome profiles of Swiss expatriates in Africa revealed by Nanopore metagenomics.Scientific reports · 2026Article
- Characterization of the oral microbiome in the diverse South African population by PacBio HiFi sequencing.Applied microbiology and biotechnology · 2026Article
- dbCAN-HGM: CAZyme gene clusters in gut microbiomes of diverse human populations.Nucleic acids research · 2026Article
- Research trends on autoimmune liver diseases and gut microbiota (1989-2025): a bibliometric and visualization analysis based on the web of science core collection database.Frontiers in immunology · 2026Article
- A Review of Global Patterns in Gut Microbiota Composition, Health and Disease: Locating South Africa in the Conversation.Microorganisms · 2025Review
- Assessing live microbial therapeutic transmission.Gut microbes · 2025Review
- Gut microbiota shift in Ghanaian individuals along the migration axis: the RODAM-Pros cohort.Gut microbes · 2025Article
- A genomic atlas of the human gut virome elucidates genetic factors shaping host interactions.bioRxiv : the preprint server for biology · 2025Article
- Human immunodeficiency virus and antiretroviral therapies exert distinct influences across diverse gut microbiomes.Nature microbiology · 2025Article
- Industrialization drives convergent microbial and physiological shifts in the human metaorganism.bioRxiv : the preprint server for biology · 2025Article
Corrections and comments
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Authors and funding
18 authors at 5 institutions in 4 countries.
Funding
Abstract
Human gut microbiome research focuses on populations living in high-income countries and to a lesser extent, non-urban agriculturalist and hunter-gatherer societies. The scarcity of research between these extremes limits our understanding of how the gut microbiota relates to health and disease in the majority of the world's population. Here, we evaluate gut microbiome composition in transitioning South African populations using short- and long-read sequencing. We analyze stool from adult females living in rural Bushbuckridge (n = 118) or urban Soweto (n = 51) and find that these microbiomes are taxonomically intermediate between those of individuals living in high-income countries and traditional communities. We demonstrate that reference collections are incomplete for characterizing microbiomes of individuals living outside high-income countries, yielding artificially low beta diversity measurements, and generate complete genomes of undescribed taxa, including Treponema, Lentisphaerae, and Succinatimonas. Our results suggest that the gut microbiome of South Africans does not conform to a simple "western-nonwestern" axis and contains undescribed microbial diversity.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.