Phylotyping and Functional Analysis of Two Ancient Human Microbiomes

Tito, Raúl Y.; Macmil, Simone; Wiley, Graham B.; Najar, Fares Z.; Cleeland, Lauren M.; Qu, Chunmei; Wang, Ping; Romagné, Frédéric; Léonard, Sylvain; Ruiz, Agustı́n; Reinhard, Karl J.; Roe, Bruce A.; Lewis, Cecil M.

doi:10.1371/journal.pone.0003703

Cited by 92 publications

(96 citation statements)

References 37 publications

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“…Unlike paleontological coprolites, archaeological coprolites were not initially recognized as an important biological data source and were only irregularly curated throughout the nineteenth and early twentieth centuries. Even now that their potential is recognized, coprolites and preserved intestinal contents remain rare finds, and they tend to preserve intact only under extremely dry or frozen conditions (e.g., Cano et al, 2000; Tito et al, 2008). Additionally, because human coprolites are not fully fossilized and may be fragmentary or amorphous, they are often difficult to identify or recover in situ, and may not be found until downstream screening contexts (Reinhard and Bryant, 2008).…”

Section: Ancient Microbiome Researchmentioning

confidence: 99%

Ancient human microbiomes

Warinner

Speller

Collins

et al. 2015

Journal of Human Evolution

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137

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Very recently, we discovered a vast new microbial self: the human microbiome. Our native microbiota interface with our biology and culture to influence our health, behavior, and quality of life, and yet we know very little about their origin, evolution, or ecology. With the advent of industrialization, globalization, and modern sanitation, it is intuitive that we have changed our relationship with microbes, but we have little information about the ancestral state of our microbiome, and therefore, we lack a foundation for characterizing this change. High-throughput sequencing has opened up new opportunities in the field of paleomicrobiology, allowing us to investigate the evolution of the complex microbial ecologies that inhabit our bodies. By focusing on recent coprolite and dental calculus research, we explore how emerging research on ancient human microbiomes is changing the way we think about ancient disease and how archaeological studies can contribute to a medical understanding of health and nutrition today.

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Section: Ancient Microbiome Researchmentioning

confidence: 99%

Ancient human microbiomes

Warinner

Speller

Collins

et al. 2015

Journal of Human Evolution

Self Cite

137

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“…There have only been a handful of studies of extant (De Filippo et al, 2010;Yatsunenko et al, 2012) and extinct (Tito et al, 2008Adler et al, 2013) native peoples. Inclusion of more data from a broader sample of human diversity may facilitate better understanding of vaginal microbial dynamics and aid in improving health .…”

Section: Summary Implications and Future Directionsmentioning

confidence: 99%

The primate vaginal microbiome: Comparative context and implications for human health and disease

Stumpf

Wilson

Rivera

et al. 2013

American J Phys Anthropol

119

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The primate body hosts trillions of microbes. Interactions between primate hosts and these microbes profoundly affect primate physiology, reproduction, health, survival, and ultimately, evolution. It is increasingly clear that primate health cannot be understood fully without knowledge of host-microbial interactions. Our goals here are to review what is known about microbiomes of the female reproductive tract and to explore several factors that influence variation within individuals, as well as within and between primate species. Much of our knowledge of microbial variation derives from studies of humans, and from microbes located in nonreproductive regions (e.g., the gut). We review work suggesting that the vaginal microbiota affects female health, fecundity, and pregnancy outcomes, demonstrating the selective potential for these agents. We explore the factors that correlate with microbial variation within species. Initial colonization by microbes depends on the manner of birth; most microbial variation is structured by estrogen levels that change with age (i.e., at puberty and menopause) and through the menstrual cycle. Microbial communities vary by location within the vagina and can depend on the sampling methods used (e.g., swab, lavage, or pap smear). Interindividual differences also exist, and while this variation is not completely understood, evidence points more to differences in estrogen levels, rather than differences in external physical environment. When comparing across species, reproductive-age humans show distinct microbial communities, generally dominated by Lactobacillus, unlike other primates. We develop evolutionary hypotheses to explain the marked differences in microbial communities. While much remains to be done to test these hypotheses, we argue that the ample variation in primate mating and reproductive behavior offers excellent opportunities to evaluate host-microbe coevolution and adaptation. Am J Phys Anthropol 57:119-134,

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“…Preliminary work focusing on gut bacteria has been published. (Tito et al 2008) and analysis of helminth DNA is ongoing.…”

Section: Current Centers For Archaeoparasitologymentioning

confidence: 99%