Studying fascinating microbiomes, working in cooperation with communities, and illuminating study design.

Bacterial Genetics and Genomics book Discussion Topic: Chapter 1, question 14

I recently attended and was an invited speaker, on-line, at a conference that had a topic about short-and long-read sequencing technologies. The various talks and the panel discussion that I participated in looked at the advantages of both short-read sequencing and long-read sequencing for what they can bring to research and to the clinical setting. The conference was Oxford Global NextGen Omics UK, which runs yearly, usually in London.

Following the conference, I decided that I wanted to blog about a study that had used sequencing to do something interesting. I found this paper, by Ovokeraye Achinike-Oduaran and colleagues at the University of the Witwatersrand, which describes a microbiome study from South Africa. Although the paper does not do whole genome sequencing of the microbiome (it is using 16S rRNA microbiome sequencing), it does overturn longstanding assumptions to develop its experimental design to investigate the gut microbiome.

Graphic in pink of the human small and large intestine overlaid with graphics of larger-than-life microbes.
Graphic in pink of the human small and large intestine overlaid with graphics of larger-than-life microbes. CC

Firstly, there is an issue in a lot of our human genomic data, microbial genome data, and metagenomic data. The vast majority of it has come from Western samples and from white patients. Although this may be changing, as with many things, change is slow. We cannot extrapolate information from the data we have to the whole, if we are lacking information from segments of that whole. In bacteriology, we have relied for a long time on extrapolating the knowledge gained by studying E. coli to other bacterial species, only to discover that many of these other species do things differently. We need more data about other bacterial species and about our own.

Secondly, it is important to remember that Africa is vast and varied. It is important to stop thinking of Africa as one homogeneous population and to remember that the people, the cultures, and the ecosystems and environments vary considerably across the continent. People living in different States in the USA have very different cultures, different weather conditions, and often different accents. In addition to that, they share the same continent with people in Canada and Mexico, who also have their own characteristic States and Provinces. The North American continent is diverse and so too is the continent of Africa.

Thirdly, may studies that have previously looked at the microbiome of humans in Africa have focused on those from populations that live in what Western cultures would consider to be “extreme” conditions, living in rural hunter-gatherer societies or agricultural populations. These studies have been vital in understanding traditional African population microbiomes and, in particular, the microbiomes of the populations that were studied. However, there has been a shift in the last 50 years or so to a more industrialized and sedentary lifestyle in sub-Saharan Africa. Therefore, these transition populations warrant investigation as well. There are a growing number of supermarkets and fast food outlets with trends toward Westernized processed and animal-based food products. As seen in other cultures, there are also associated reports of increases in obesity and decreases in physical activity across 24 African countries.   

In this investigation, two South African populations are investigated, one urban and one transitioning rural. No assumptions are made about the ability to extrapolate findings from non-South African populations onto this community. The gut microbiomes here may be very different to elsewhere in the world, therefore necessitating investigation. Here there is an ongoing transition epidemiologically, which makes it a fascinating community to study, as the gut microbiome may be in transition as the dietary lifestyles of the people change.

The microbiota landscape of obese and lean female individuals from South Africa, chosen from diverse ethnolinguistic groups, were chosen for this investigation. It is noteworthy that even within the study, it is recognized that there is a wealth of diversity within South Africa, both in terms of the dietary transitions and also in terms of ethnolinguistic groups. This is a pilot study that is part of the Human Heredity and Health in Africa (H3Africa) initiative.

Although both cohorts in this study are from South Africa, they are 300 miles (483 km) apart and represent different lifestyles and diets. One group of females, ranging in age from 43 to 72 years, was from Bushbuckridge, a rural community. Here the researchers worked extensively with a community advisory group to ensure their research was performed in a sensitive and respectful manner that was clear and engaging with the community it was seeking to understand.

Photograph of Bushbuckridge, South Africa, a rural community.
Photograph of Bushbuckridge in South Africa, a rural community. CC

The other group of females, ranging from age 43 to 64 years, was from the urban Soweto area, where the median BMI was 36.52 compared to 31.17 in the Bushbuckridge cohort.

Photograph of Soweto, South Africa, an urban community.
Photograph of Soweto, South Africa, an urban community. CC

Benefitting from the data of previous microbiome studies, this investigation was able to reveal that their cohorts’ gut microbiomes had features of both taxa that tended to be found in Western microbiomes and in non-Western microbiomes, which has captured the transition state of the human gut during this transition period in the diets of this population. Some of the genera typical of hunter-gatherer societies are present, but so too are genera typical of people who consume a Western diet.

Given the issues of obesity in many Western societies and the growing issues of obesity in parts of Africa, particularly were Western culinary cultures are being adopted, Oduaran et al., (2020) specifically compared the obese and lean females within their study. They determined that there were no statistically significant within site differences for the Soweto cohort. Some differentially abundant taxa were observed in obese samples from Bushbuckridge, including association of Oscillibacter, which has been reported to be associated with obesity in a European cohort.

Photograph of Ovokeraye Achinike-Oduaran, lead author of the research study being discussed in this blog.
Photograph of Ovokeraye Achinike-Oduaran, lead author of the research study being discussed in this blog.

This study is an important pilot investigation. It shows that these intermediate states of human gut microbiomes are present in the current populations in South Africa, both in the urban setting and rural communities. The consequences of this mixed gut microbiome on human health is unknown, however through preliminary sequencing investigations such as this, the groundwork is set to be able to do more with larger cohort groups in cooperation with communities that are under-represented in our current research datasets. Future research will also be able to capture more sequence data information using enhanced sequencing technologies, perhaps in the not too distant future using robust long read sequencing on its own to generate high quality metagenomic data routinely.

This and other studies being conducted by researchers that are looking at under-represented populations of humans and under-studied bacterial species are important. We must not lose sight of the wonderous diversity of our planet that provides us with ever more to learn as biologists.

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