Surveying Gut Microbiome Research in Africans: Toward Improved Diversity and Representation

Brewster, Ryan; Tamburini, Fiona B.; Asiimwe, Edgar; Oduaran, Ovokeraye H.; Hazelhurst, Scott; Bhatt, Ami S.

doi:10.1016/j.tim.2019.05.006

Cited by 60 publications

(66 citation statements)

References 98 publications

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“…Non-Westernized populations follow a traditional lifestyle and typically consume diets rich in fresh unprocessed food (vegetables and fruits). Although Westernization encompasses more factors and lifestyle modifications than diet alone, as discussed previously (Brewster et al., 2019, Pasolli et al., 2019), the association of Prevotella and Westernization may further support the hypothesis of diet being an important factor in selecting and shaping Prevotella populations. Indeed, diet has previously been shown to be important in the overall diversity of intestinal microbial communities (Smits et al., 2017, Sonnenburg and Bäckhed, 2016, Sonnenburg et al., 2016).…”

Section: Introductionsupporting

confidence: 67%

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The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations

Tett

Huang

Asnicar

et al. 2019

Cell Host & Microbe

347

395

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SummaryPrevotella copri is a common human gut microbe that has been both positively and negatively associated with host health. In a cross-continent meta-analysis exploiting >6,500 metagenomes, we obtained >1,000 genomes and explored the genetic and population structure of P. copri. P. copri encompasses four distinct clades (>10% inter-clade genetic divergence) that we propose constitute the P. copri complex, and all clades were confirmed by isolate sequencing. These clades are nearly ubiquitous and co-present in non-Westernized populations. Genomic analysis showed substantial functional diversity in the complex with notable differences in carbohydrate metabolism, suggesting that multi-generational dietary modifications may be driving reduced prevalence in Westernized populations. Analysis of ancient metagenomes highlighted patterns of P. copri presence consistent with modern non-Westernized populations and a clade delineation time pre-dating human migratory waves out of Africa. These findings reveal that P. copri exhibits a high diversity that is underrepresented in Western-lifestyle populations.

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Section: Introductionsupporting

confidence: 67%

“…Most of our understanding of the microbiome has been accumulated from Westernized populations (Brewster et al., 2019). While small in comparison a number of public datasets have been generated from non-Westernized populations, which were included in the above analysis.…”

Section: Resultsmentioning

confidence: 99%

The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations

Tett

Huang

Asnicar

et al. 2019

Cell Host & Microbe

347

395

View full text Add to dashboard Cite

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“…The gut microbiome is influenced by several factors including diet [2], physical activity [3], use of antibiotics [4], and other lifestyle-related conditions. Studies comparing the microbiome of rural and industrialized communities have also shown that dietary and lifestyle changes linked to Westernization have played a pivotal role in the loss of many microbial taxa and in the rise of others [5][6][7][8][9][10][11][12][13][14]. Although it is difficult to establish causality and mechanisms for these links [15,16], recent studies have extended the identifiable members of the human microbiome to now cover > 90% of its overall diversity [11], which is a prerequisite for advancing the understanding of the role of microbes in human physiology and metabolism.…”

Section: Introductionmentioning

confidence: 99%

Microbial genomes from non-human primate gut metagenomes expand the primate-associated bacterial tree of life with over 1000 novel species

et al. 2019

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BackgroundHumans have coevolved with microbial communities to establish a mutually advantageous relationship that is still poorly characterized and can provide a better understanding of the human microbiome. Comparative metagenomic analysis of human and non-human primate (NHP) microbiomes offers a promising approach to study this symbiosis. Very few microbial species have been characterized in NHP microbiomes due to their poor representation in the available cataloged microbial diversity, thus limiting the potential of such comparative approaches.ResultsWe reconstruct over 1000 previously uncharacterized microbial species from 6 available NHP metagenomic cohorts, resulting in an increase of the mappable fraction of metagenomic reads by 600%. These novel species highlight that almost 90% of the microbial diversity associated with NHPs has been overlooked. Comparative analysis of this new catalog of taxa with the collection of over 150,000 genomes from human metagenomes points at a limited species-level overlap, with only 20% of microbial candidate species in NHPs also found in the human microbiome. This overlap occurs mainly between NHPs and non-Westernized human populations and NHPs living in captivity, suggesting that host lifestyle plays a role comparable to host speciation in shaping the primate intestinal microbiome. Several NHP-specific species are phylogenetically related to human-associated microbes, such as Elusimicrobia and Treponema, and could be the consequence of host-dependent evolutionary trajectories.ConclusionsThe newly reconstructed species greatly expand the microbial diversity associated with NHPs, thus enabling better interrogation of the primate microbiome and empowering in-depth human and non-human comparative and co-diversification studies.

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“…Studies on children’s microbiota were performed mostly in ‘Western’ populations in recent years, in countries with similar profiles of lifestyle and industrialization such as Israel, Japan, and China [ 9 , 10 , 11 , 12 ]. Apparently, the extent to which diet and BMI influence the gut microbiota of Asian children is less investigated.…”

Section: Introductionmentioning

confidence: 99%

Gut Microbiota and Dietary Intake of Normal-Weight and Overweight Filipino Children

et al. 2020

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Diet and body mass index (BMI) have been shown to affect the gut microbiota of children, but studies are largely performed in developed countries. Here, we conducted a cross-sectional investigation on the differences in the bacterial gut microbiota between normal-weight and overweight urban Filipino children, and determined the relationship between their energy, macronutrient and dietary fiber intakes, and their gut microbiota composition and diversity. Forty-three children (normal-weight, n = 32; overweight, n = 11) participated in the study. Energy and fiber intakes were collected using a semi-quantitative Food Frequency Questionnaire (FFQ). The gut microbiota was profiled using 16S rRNA gene amplicon sequencing of the V3–V4 region. The diet of the children was a mixture of traditional and Western patterns. There were no significant differences in energy, macronutrients and energy-adjusted fiber intakes between the normal-weight and overweight groups, but there were significantly more children meeting the recommended fiber intake in the overweight group. Alpha and beta bacterial diversities did not significantly differ between weight groups. Relative abundance of Bifidobacterium, Turicibacter and Clostridiaceae 1 were higher in the normal-weight than overweight children, and Lachnospira was higher in overweight children.

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Surveying Gut Microbiome Research in Africans: Toward Improved Diversity and Representation

Cited by 60 publications

References 98 publications

The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations

The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations

Microbial genomes from non-human primate gut metagenomes expand the primate-associated bacterial tree of life with over 1000 novel species

Gut Microbiota and Dietary Intake of Normal-Weight and Overweight Filipino Children

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