Allison E. Mann

recent publications

1. PNAS

   The evolution and changing ecology of the African hominid oral microbiome

   Fellows Yates, J.A., Velsko, I.M., Aron, F., Posth, C., Hofman, C.A., Austin, R.M., Parker, C.E., Mann, A.E., Nägele, K., Weedman Arthur, K., Arthur, J.W., Bauer, C.C., Crevecoeur, I., Cupillard, C., Curtis, M.C., Dalén, L., Díaz-Zorita Bonilla, M., Díez Fernández-Lomana, J.C., Drucker, D.G., Escribano Escrivá, E., Francken, M., Gibbon, V.E., Gonzalez Morales, M., Grande Mateu, A., Harvati, K., Henry, A.G., Humphrey, L., Menéndez, M., Mihailović, D., Peresani, M., Rodríguez Moroder, S., Roksandic, M., Rougier, H., Sázelová, S., Stock, J.T., L., Guy Straus, Svoboda, J., Teßmann, B., Walker, M.J., Power, R.C., Lewis, C.M., Sankaranarayanan, K., Guschanski, K., Wrangham, R., Dewhirst, F.E., Salazar-Garcia, D.C., Krause, J., Herbig, A., and Warinner, C.

   Proceedings of the National Academy of Sciences 2021

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   The oral microbiome plays key roles in human biology, health, and disease, but little is known about the global diversity, variation, or evolution of this microbial community. To better understand the evolution and changing ecology of the human oral microbiome, we analysed 124 dental biofilm metagenomes from humans, including Neanderthals and Late Pleistocene to present-day modern humans, chimpanzees, and gorillas, as well as New World howler monkeys for comparison. We find that a core microbiome of primarily biofilm-structural taxa has been maintained throughout African hominid evolution, and these microbial groups are also shared with howler monkeys, suggesting that they have been important oral members since before the catarrhine-platyrrhine split ca. 40 million years ago. However, community structure and individual microbial phylogenies do not closely reflect host relationships, and the dental biofilms of Homoand chimpanzees are distinguished by major taxonomic and functional differences. Reconstructing oral metagenomes up to 100 thousand years ago, we show that the microbial profiles of both Neanderthals and modern humans are highly similar, sharing functional adaptations in nutrient metabolism. These include an apparent Homo-specific acquisition of salivary amylase-binding capability by oral streptococci, suggesting microbial co-adaptation with host diet. We additionally find evidence of shared genetic diversity in the oral bacteria of Neanderthal and Upper Palaeolithic modern humans that is not observed in later modern human populations. Differences in the oral microbiomes of African hominids provide insights into human evolution, the ancestral state of the human microbiome, and a temporal framework for understanding microbial health and disease.

2. Microorg.

   The adult phenylketonuria (PKU) gut microbiome

   Mancilla, V.J., Mann, A.E., Zhang, Y., and Allen, M.S.

   Microorganisms 2021

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   Phenylketonuria (PKU) is an inborn error of phenylalanine metabolism primarily treatedthrough a phenylalanine-restrictive diet that is frequently supplemented with an amino acid formulato maintain proper nutrition. Little is known of the effects of these dietary interventions on thegut microbiome of PKU patients, particularly in adults. In this study, we sequenced the V4 regionof the 16S rRNA gene from stool samples collected from adults with PKU (n= 11) and non-PKUcontrols (n= 21). Gut bacterial communities were characterized through measurements of diversityand taxa abundance. Additionally, metabolic imputation was performed based on detected bacteria.Gut community diversity was lower in PKU individuals, though this effect was only statisticallysuggestive. A total of 65 genera across 5 phyla were statistically differentially abundant betweenPKU and control samples (p< 0.001). Additionally, we identified six metabolic pathways that differedbetween groups (p< 0.05), with four enriched in PKU samples and two in controls. While the childPKU gut microbiome has been previously investigated, this is the first study to explore the gutmicrobiome of adult PKU patients. We find that microbial diversity in PKU children differs from PKUadults and highlights the need for further studies to understand the effects of dietary restrictions.

3. Quat. Int.

   Do I have something in my teeth? The trouble with genetic analyses of diet from archaeological dental calculus

   Mann, A.E., Fellows Yates, J.A., Fagernäs, Z., Austin, R.M., Nelson, E.A., and Hofman, C.A.

   Quaternary International 2020

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   Dental calculus and other preserved microbiome substrates are an attractive target for dietary reconstruction in past populations through a variety of physical, chemical, and molecular means. Recently, studies have attempted to reconstruct diet from archaeological dental calculus using archaeogenetic techniques. While dental calculus may provide a relatively stable environment for DNA preservation, the detection of plants and animals possibly consumed by an individual through DNA analysis is primarily hindered by microbial richness and incomplete reference databases. Moreover, high genomic similarity within eukaryotic groups - such as mammals - can obfuscate precise taxonomic identification. In the current study we demonstrate the challenges associated with accurate taxonomic identification and authentication of dietary taxa in ancient DNA data using both synthetic and ancient dental calculus datasets. We highlight common errors and sources of contamination across ancient DNA datasets, provide recommendations for dietary DNA validation, and call for caution in the interpretation of diet from dental calculus and other archaeological microbiome substrates.