Differences in Gut Metabolites and Microbial Composition and Functions between Egyptian and U.S. Children Are Consistent with Their Diets

Shankar, Vijay; Gouda, Mostafa; Moncivaiz, Jessica; Gordon, Alex H.; Reo, Nicholas V.; Hussein, Laila; Paliy, Oleg

doi:10.1128/msystems.00169-16

Cited by 119 publications

(138 citation statements)

References 89 publications

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“…To illustrate the advantage of phylogenetic distance based constrained ordination in microbial ecology, we extended the use of a distance-based variant of redundancy analysis (dbRDA) 13, 14 to utilize the phylogenetic UniFrac (UF) distance-based matrix of (dis)similarities among samples in a dataset as has been done in several previous studies 15–18 . UniFrac distance is computed by calculating the fraction of branch lengths of a combined phylogenetic tree that are not shared between two communities 19 .…”

Section: Resultsmentioning

confidence: 99%

Advantages of phylogenetic distance based constrained ordination analyses for the examination of microbial communities

Shankar

Agans

Paliy

2017

Sci Rep

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Recently developed high throughput molecular techniques such as massively parallel sequencing and phylogenetic microarrays generate vast datasets providing insights into microbial community structure and function. Because of the high dimensionality of these datasets, multivariate ordination analyses are often employed to examine such data. Here, we show how the use of phylogenetic distance based redundancy analysis provides ecological interpretation of microbial community differences. We also extend the previously developed method of principal response curves to incorporate phylogenetic distance measure, and we demonstrate the improved ability of this approach to provide ecologically relevant insights into temporal alterations of microbial communities.

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Section: Resultsmentioning

confidence: 99%

Advantages of phylogenetic distance based constrained ordination analyses for the examination of microbial communities

Shankar

Agans

Paliy

2017

Sci Rep

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“…Mitsuokella, like Treponema, showed significant differential abundance only in the lean Bushbuckridge group. Although not a benchmarked traditional taxon, Mitsuokella has repeatedly been associated with non-Western diets and lifestyles 48,62 .…”

Section: Discussionmentioning

confidence: 99%

“…Despite not reaching statistical significance when compared to benchmarked datasets, the large Several studies have identified obesity-associated taxa primarily in non-African populations 23,48,49 despite these reported connections being inconsistent 1,21,2,67 . The differential abundance, prevalence or presence of microbial taxa across populations may require population-specific associations for relevance as universal classifications may not necessarily be generalizable.…”

Section: Algerian Tuaregs Saudi Bedouins and Amazonians From Frenchmentioning

confidence: 99%

“…and Dialister47,48 , as well as Romboutsia, a taxon often associated with a healthy status49,50 , butyrate-producing Anaerostipes, low-fat diet-associated Asteroleplasma33 and Alloprevotella(Figures 5A and 5C). Soweto samples, on the other hand, showed a significant enrichment in Bifidobacterium, the oxalate-metabolizing Oxalobacter 51,52 , Paraprevotella, Turicibacter, Peptococcus and Streptococcus (Figures 5A, 5C and 6B).…”

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confidence: 99%

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Gut Microbiome Profiling of a Rural and Urban South African Cohort Reveals Biomarkers of a Population in Lifestyle Transition

Oduaran

Tamburini

Sahibdeen

et al. 2020

Preprint

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Background: Comparisons of traditional hunter-gatherers and pre-agricultural communities in Africa with urban and suburban Western North American and European cohorts have clearly shown that diet, lifestyle and environment are associated with gut microbiome composition. Yet, little is known about the gut microbiome composition of most African adults. South Africa comprises a richly diverse ethnolinguistic population that is experiencing an ongoing epidemiological transition and concurrent spike in the prevalence of obesity, largely attributed to a shift towards more Westernized diets and increasingly inactive lifestyle practices. To better characterize the microbiome of African adults living in more mainstream lifestyle settings and to investigate associations between the microbiome and obesity, we conducted a pilot study in two South African cohorts that are representative of urban and rural populations. The study was designed collaboratively with community leaders. As the rate of overweight and obesity is particularly high in women, we collected single time-point stool samples from 170 HIV-negative women (51 at Soweto; 119 at Bushbuckridge), performed 16S rRNA gene sequencing on these samples and compared the data to concurrently collected anthropometric data. Results:We found the overall gut microbiome of our cohorts to be reflective of their ongoing epidemiological transition. Specifically, our results show a relatively higher than expected abundance of Western gut-associated taxa such as Barnesiella and the presence of Bifidobacteria and Bacteroides together with the more traditionally non-Western gut-associated Prevotella, Treponema and Succinivibrio. Interestingly, we observed a relatively higher abundance of the Melainabacteria, Vampirovibrio, a predatory bacterium, in the rural cohort. We also found Prevotella, despite its generally high prevalence relative to all taxa present in the cohort, to be associated with obesity. Conclusions:Altogether, this work identifies putative microbial features associated with host health in a historically understudied community. Furthermore, we note the crucial role of community engagement to the success of a study in an African setting, the importance of more population-specific studies to inform targeted interventions as well as present a basic foundation for future research in this regard.

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“…This has broad application across biomedical and environmental science, and in particular, allows for detection of changes in communities or the genes that they carry in the face of biological (Marti et al 2017), chemical (Chambers et al 2015) or environmental (Garner et al 2016) factors. Of particular relevance are studies on antimicrobial resistance (Zhu et al 2013;Su et al 2015;Chambers et al 2015;Chen et al 2016;Garner et al 2016), as well as studies in other areas, such as changes in gut flora in different human communities (Shankar et al 2017) or through the ingestion of probiotics (Unno et al 2015).…”

Section: Introductionmentioning

confidence: 99%

DirtyGenes: significance testing for gene or bacterial population composition changes using the Dirichlet distribution

Shaw

Blanchard

Chen

et al. 2017

Preprint

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High throughput sequencing, and quantitative polymerase chain reaction (qPCR), can detect changes in bacterial communities or the genes that they carry, between different environments or treatments. These methods are applied widely to microbiomes in humans, animals, soil and water; an important application is for changes in antimicrobial resistance genes (ARGs).However, at present, there is no statistical method to determine whether observed changes in the overall composition are significant, or result from random variations between samples. Therefore researchers are limited to graphical descriptions. We describe a novel statistical method to determine whether or not observed differences in bacterial populations or their genes are significant. It can be used with data from shotgun metagenomics, 16SInternational license It is made available under a (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint . http://dx.doi.org/10.1101/204321 doi: bioRxiv preprint first posted online Oct. 16, 2017; characterisation or qPCR. It can also be used for experimental design, to calculate the number of samples needed in future experiments. We show its application to two example data sets. The first is published data on bacterial communities and ARGs in the environment, in which we show that there are significant changes in both ARG and community composition. The second is a new data set on seasonality in bacterial communities and ARGs in hooves from four sheep. While the observed differences are not significant, we show that a minimum group size of eight sheep in a future experiment would provide sufficient power to observe significant changes, should the already observed changes be true. This method has broad uses for statistical testing and experimental design in experiments on changing microbiomes, including for studies on antimicrobial resistance.

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Differences in Gut Metabolites and Microbial Composition and Functions between Egyptian and U.S. Children Are Consistent with Their Diets

Cited by 119 publications

References 89 publications

Advantages of phylogenetic distance based constrained ordination analyses for the examination of microbial communities

Advantages of phylogenetic distance based constrained ordination analyses for the examination of microbial communities

Gut Microbiome Profiling of a Rural and Urban South African Cohort Reveals Biomarkers of a Population in Lifestyle Transition

DirtyGenes: significance testing for gene or bacterial population composition changes using the Dirichlet distribution

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