Oral metagenomes from Native American Ancestors reveal distinct microbial lineages in the pre-contact era.

OBJECTIVES: Limited studies have focused on how European contact and colonialism impacted Native American oral microbiomes, specifically, the diversity of commensal or opportunistically pathogenic oral microbes, which may be associated with oral diseases. Here, we studied the oral microbiomes of pre-contact Wichita Ancestors, in partnership with the Descendant community, The Wichita and Affiliated Tribes, Oklahoma, USA. MATERIALS AND METHODS: Skeletal remains of 28 Wichita Ancestors from 20 archeological sites (dating approximately to 1250-1450 CE) were paleopathologically assessed for presence of dental calculus and oral disease. DNA was extracted from calculus, and partial uracil deglycosylase-treated double-stranded DNA libraries were shotgun-sequenced using Illumina technology. DNA preservation was assessed, the microbial community was taxonomically profiled, and phylogenomic analyzes were conducted. RESULTS: Paleopathological analysis revealed signs of oral diseases such as caries and periodontitis. Calculus samples from 26 Ancestors yielded oral microbiomes with minimal extraneous contamination. Anaerolineaceae bacterium oral taxon 439 was found to be the most abundant bacterial species. Several Ancestors showed high abundance of bacteria typically associated with periodontitis such as Tannerella forsythia and Treponema denticola. Phylogenomic analyzes of Anaerolineaceae bacterium oral taxon 439 and T. forsythia revealed biogeographic structuring; strains present in the Wichita Ancestors clustered with strains from other pre-contact Native Americans and were distinct from European and/or post-contact American strains. DISCUSSION: We present the largest oral metagenome dataset from a pre-contact Native American population and demonstrate the presence of distinct lineages of oral microbes specific to the pre-contact Americas.

Shift in body fat distribution from lower body to upper body among urban Colombian women, 1988-1989 to 2007-2008.

OBJECTIVE: Body fat distribution may be a stronger predictor of metabolic risk than BMI. Yet, few studies have investigated secular changes in body fat distribution in middle-income countries or how those changes vary by socioeconomic status (SES). This study evaluated changes in body fat distribution by SES in Colombia, a middle-income country where BMI is increasing rapidly. DESIGN: We applied factor analysis to previously published data to assess secular changes in adiposity and body fat distribution in cross-sectional samples of urban Colombian women. Anthropometry was used to assess weight, height and skinfolds (biceps, triceps, subscapular, suprailiac, thigh, calf). SETTING: Cali, Colombia. PARTICIPANTS: Women (18-44 years) in 1988-1989 (n 1533) and 2007-2009 (n 577) from three SES groups. RESULTS: We identified an overall adiposity factor, which increased between 1988-1989 and 2007-2008 in all SES groups, particularly in the middle SES group. We also identified arm, leg and trunk adiposity factors. In all SES groups, leg adiposity decreased, while trunk and arm adiposity increased. CONCLUSIONS: Factor analysis highlighted three trends that were not readily visible in BMI data and variable-by-variable analysis of skinfolds: (i) overall adiposity increased between time periods in all SES groups; (ii) the adiposity increase was driven by a shift from lower body to upper body; (iii) the adiposity increase was greatest in the middle SES group. Factor analysis provided novel insights into secular changes and socioeconomic variation in body fat distribution during a period of rapid economic development in a middle-income country.

The stable isotope ecology of Pan in Uganda and beyond.

Stable isotope analysis has long been used to study the dietary ecology of living and fossil primates, and there has been increasing interest in using stable isotopes to study primate habitat use and anthropogenic impacts on non-human primates. Here, we examine the stable carbon and nitrogen isotope compositions of chimpanzees (Pan troglodytes) from seven communities in Uganda across a continuum of habitat structure (closed to more open) and access to anthropogenic resources (no reliance to heavy reliance). In general, the hair δ(13) C, but not δ(15) N, values of these communities vary depending on forest structure and degree of anthropogenic influence. When integrated with previously published hair δ(13) C and δ(15) N values for Pan, it is apparent that modern "savanna" and "forest" Pan form discrete clusters in carbon and nitrogen isotope space, although there are exceptions probably relating to microhabitat specialization. The combined dataset also reveals that Pan δ(13) C values (but not δ(15) N values) are inversely related to rainfall (r(2) = 0.62). We converted Pan hair δ(13) C values to enamel equivalents and made comparisons to the fossil hominoids Sivapithecus sp., Gigantopithecus blacki, Ardipithecus ramidus, and Australopithecus anamensis. The δ(13) C values of the fossil hominins Ar. ramidus and Au. anamensis do not cluster with the δ(13) C values of modern Pan in "forest" habitats, or with fossil hominoids that are believed to have inhabited forests. Am. J. Primatol. 78:1070-1085, 2016. © 2016 Wiley Periodicals, Inc.

Intra-tooth stable isotope analysis of dentine: a step toward addressing selective mortality in the reconstruction of life history in the archaeological record.

Intra-tooth stable isotope analysis of dentine provides a more sensitive means to examine infant and childhood life history in the past than conventional cross-sectional analyses that rely on age-at-death. In addition, reconstructions of early diet and life history using an intra-tooth approach circumvent potential problems associated with mortality bias, which may operate strongly during infancy and childhood. We present new intra-tooth stable carbon and nitrogen isotope profiles in dentine collagen of early forming permanent teeth in a sample of adults from the Medieval Nubian site of Kulubnarti. We interpret the profiles in terms of weaning behavior and dietary history, and we compare profiles generated from first molars and canines to explore the degree to which these tooth types correspond. We then compare the profiles to the occurrence of linear enamel hypoplasia to assess the relationship between the timing of the weaning process and stress events. Finally, we compare the longitudinal profiles to cross-sectional stable isotope data obtained from rib collagen to investigate how life histories might differ between those that survived into adulthood and those that did not. Results suggest that canine and first molar profiles are in broad agreement, that hypoplastic stress events occurred during rather than before or after the weaning process in our sample, and that survivors appear to have weaned earlier than the average non-survivor. We suggest that this approach may be useful for addressing the effects of selective mortality on reconstructions of early life history and the relationship between early life history and morbidity.

Stable isotope analysis in primatology: a critical review.

Stable isotope analysis has become an important tool in ecology over the last 25 years. A wealth of ecological information is stored in animal tissues in the relative abundances of the stable isotopes of several elements, particularly carbon and nitrogen, because these isotopes navigate through ecological processes in predictable ways. Stable carbon and nitrogen isotopes have been measured in most primate taxonomic groups and have yielded information about dietary content, dietary variability, and habitat use. Stable isotopes have recently proven useful for addressing more fine-grained questions about niche dynamics and anthropogenic effects on feeding ecology. Here, we discuss stable carbon and nitrogen isotope systematics and critically review the published stable carbon and nitrogen isotope data for modern primates with a focus on the problems and prospects for future stable isotope applications in primatology.

The diet of Australopithecus sediba.

Specimens of Australopithecus sediba from the site of Malapa, South Africa (dating from approximately 2 million years (Myr) ago) present a mix of primitive and derived traits that align the taxon with other Australopithecus species and with early Homo. Although much of the available cranial and postcranial material of Au. sediba has been described, its feeding ecology has not been investigated. Here we present results from the first extraction of plant phytoliths from dental calculus of an early hominin. We also consider stable carbon isotope and dental microwear texture data for Au. sediba in light of new palaeoenvironmental evidence. The two individuals examined consumed an almost exclusive C(3) diet that probably included harder foods, and both dicotyledons (for example, tree leaves, fruits, wood and bark) and monocotyledons (for example, grasses and sedges). Like Ardipithecus ramidus (approximately 4.4 Myr ago) and modern savanna chimpanzees, Au. sediba consumed C(3) foods in preference to widely available C(4) resources. The inferred consumption of C(3) monocotyledons, and wood or bark, increases the known variety of early hominin foods. The overall dietary pattern of these two individuals contrasts with available data for other hominins in the region and elsewhere.

Neurobehavioral assessment of transplanted porcine Sertoli cells into the intact rat striatum.

Sertoli cells, a testes-derived cell with immunosuppressive and trophic properties, may serve as an alternative cell source for transplantation in a number of neurodegenerative diseases. However, before Sertoli cells can be considered for clinical use, safety studies must be conducted to ensure that the cells themselves produce no adverse effects when transplanted into the central nervous system. The present study assessed the behavioral effects of transplanting porcine Sertoli cells into the striatum of normal rats and provided a histological examination of the graft site and host striatum. Activity monitors revealed significant increases in nocturnal locomotor activity over time following both sham and Sertoli transplants. Ambulation and rearing, but not stereotypic measures, were increased compared to pre-transplant levels. Sertoli animals exhibited less behavioral alteration than sham controls. Histological examination of the striatum demonstrated surviving Sertoli cell transplants in an intact striatum. These results indicated that Sertoli cell xenografts might be a safe alternative cell source for neurotransplantation procedures requiring immune or trophic support.