Human microbiota research in Africa: a systematic review reveals gaps and priorities for future research

Abstract

Background: The role of the human microbiome in health and disease is an emerging and important area of research; however, there is a concern that African populations are under-represented in human microbiome studies. We, therefore, conducted a systematic survey of African human microbiome studies to provide an overview and identify research gaps. Our secondary objectives were: (i) to determine the number of peer-reviewed publications; (ii) to identify the extent to which the researches focused on diseases identified by the World Health Organization [WHO] State of Health in the African Region Report as being the leading causes of morbidity and mortality in 2018; (iii) to describe the extent and pattern of collaborations between researchers in Africa and the rest of the world; and (iv) to identify leadership and funders of the studies.

Methodology: We systematically searched Medline via PubMed, Scopus, CINAHL, Academic Search Premier, Africa-Wide Information through EBSCOhost, and Web of Science from inception through to 1st April 2020. We included studies that characterized samples from African populations using next-generation sequencing approaches. Two reviewers independently conducted the literature search, title and abstract, and full-text screening, as well as data extraction.

Results: We included 168 studies out of 5515 records retrieved. Most studies were published in PLoS One (13%; 22/168), and samples were collected from 33 of the 54 African countries. The country where most studies were conducted was South Africa (27/168), followed by Kenya (23/168) and Uganda (18/168). 26.8% (45/168) focused on diseases of significant public health concern in Africa. Collaboration between scientists from the United States of America and Africa was most common (96/168). The first and/or last authors of 79.8% of studies were not affiliated with institutions in Africa. Major funders were the United States of America National Institutes of Health (45.2%; 76/168), Bill and Melinda Gates Foundation (17.8%; 30/168), and the European Union (11.9%; 20/168).

Conclusions: There are significant gaps in microbiome research in Africa, especially those focusing on diseases of public health importance. There is a need for local leadership, capacity building, intra-continental collaboration, and national government investment in microbiome research within Africa. Video Abstract.

Keywords: 16S rRNA sequencing; Metagenomics; Microbiome; Next-generation sequencing; Public health; Systematic review.

Fig. 1

Flow diagram showing the selection of studies according to preferred reporting items for systematic reviews and meta-analysis (PRISMA) guidelines

Fig. 2

A line plot showing the number of African Human Microbiome research funded by the top four funding agencies over the past 10 years

Fig. 3

An African map showing the location, frequency, and body sites investigated in human microbiome studies

Fig. 4

Representation of body sites included in microbiome studies conducted in Africa. The most studied diseases are listed for each body site. The total percentage exceeds 100% because eight, three, and one study characterized two, three, and four body sites respectively

Fig. 5

African map with pie charts showing the age categories and the number of participants included in human microbiome studies per country. The size of the divisions within the pie charts corresponds to the proportion of studies that included each age category (young children (0 to 5 years), older children (6 to 17 years), and adults (≥ 18 years)). The size of the pie chart represents the cumulative number of participants from all studies conducted in the country

Fig. 6

African map with pie charts showing the age categories and the number of participants included in human gut microbiome studies per country. The size of the divisions within the pie charts corresponds to the proportion of studies that included each age category (young children (0 to 5 years), older children (6 to 17 years), and adults (≥ 18 years)). The size of the pie chart represents the cumulative number of participants from all studies conducted in the country

Fig. 7

African map with pie charts showing the age categories and the number of participants included in human urogenital microbiome studies per country. The size of the divisions within the pie charts corresponds to the proportion of studies that included each age category (adolescents (13 to 17 years) and adults (≥ 18 years)). The size of the pie chart represents the cumulative number of participants from all studies conducted in the country

Fig. 8

Heatmap of intercontinental collaborations between African countries and non-African countries

Fig. 9

Pie charts showing the percentage of affiliations per country for the first author (A) and for the last author (B)