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.

In an effort to better understand the ancestral state of the human distal gut microbiome, we examine feces retrieved from archaeological contexts (coprolites). To accomplish this, we pyrosequenced the 16S rDNA V3 region from duplicate coprolite samples recovered from three archaeological sites, each representing a different depositional environment: Hinds Cave (∼8000 years B.P.) in the southern United States, Caserones (1600 years B.P.) in northern Chile, and Rio Zape in northern Mexico (1400 years B.P.). Clustering algorithms grouped samples from the same site. Phyletic representation was more similar within sites than between them. A Bayesian approach to source-tracking was used to compare the coprolite data to published data from known sources that include, soil, compost, human gut from rural African children, human gut, oral and skin from US cosmopolitan adults and non-human primate gut. The data from the Hinds Cave samples largely represented unknown sources. The Caserones samples, retrieved directly from natural mummies, matched compost in high proportion. A substantial and robust proportion of Rio Zape data was predicted to match the gut microbiome found in traditional rural communities, with more minor matches to other sources. One of the Rio Zape samples had taxonomic representation consistent with a child. To provide an idealized scenario for sample preservation, we also applied source tracking to previously published data for Ötzi the Iceman and a soldier frozen for 93 years on a glacier. Overall these studies reveal that human microbiome data has been preserved in some coprolites, and these preserved human microbiomes match more closely to those from the rural communities than to those from cosmopolitan communities. These results suggest that the modern cosmopolitan lifestyle resulted in a dramatic change to the human gut microbiome.

Since the original description and naming of Ascaris lumbricoides from humans by Linnaeus in 1758 and later of Ascaris suum from pigs by Goeze 1782, these species have been considered to be valid. Four hypotheses relative to the conspecificity or lack thereof (and thus origin of these species) are possible: 1) Ascaris lumbricoides (usually infecting humans) and Ascaris suum (recorded mostly from pigs) are both valid species, with the two species originating via a speciation event from a common ancestor sometime before the domestication of pigs by humans, or 2) Ascaris lumbricoides in humans is derived directly from the species A. suum found in pigs with A. suum then existing as a persistent ancestor after formation of A. lumbricoides, or 3) Ascaris suum is derived directly from A. lumbricoides with the persistent ancestor being A. lumbricoides and A. suum being the newly derived species, and finally, 4) Ascaris lumbricoides and A. suum are the same species, this hypothesis being supported by studies showing both low morphological and low genetic divergence at several genes. We present and discuss paleoparasitological and genetic evidence that complement new data to evaluate the origin and evolution of Ascaris spp. in humans and pigs, and the uniqueness of the species in both hosts. Finally, we conclude that Ascaris lumbricoides and A. suum are a single species and that the name A. lumbricoides Linnaeus 1758 has taxonomic priority; therefore A. suum Goeze 1782 should be considered a synonym of A. lumbricoides.

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Loss of gut microbial diversity1–6 in industrial populations is associated with chronic diseases7, underscoring the importance of studying our ancestral gut microbiome. However, relatively little is known about the composition of pre-industrial gut microbiomes. Here we performed a large-scale de novo assembly of microbial genomes from palaeofaeces. From eight authenticated human palaeofaeces samples (1,000–2,000 years old) with well-preserved DNA from southwestern USA and Mexico, we reconstructed 498 medium- and high-quality microbial genomes. Among the 181 genomes with the strongest evidence of being ancient and of human gut origin, 39% represent previously undescribed species-level genome bins. Tip dating suggests an approximate diversification timeline for the key human symbiont Methanobrevibacter smithii. In comparison to 789 present-day human gut microbiome samples from eight countries, the palaeofaeces samples are more similar to non-industrialized than industrialized human gut microbiomes. Functional profiling of the palaeofaeces samples reveals a markedly lower abundance of antibiotic-resistance and mucin-degrading genes, as well as enrichment of mobile genetic elements relative to industrial gut microbiomes. This study facilitates the discovery and characterization of previously undescribed gut microorganisms from ancient microbiomes and the investigation of the evolutionary history of the human gut microbiota through genome reconstruction from palaeofaeces.

BackgroundThe Human Microbiome Project (HMP) is one of the U.S. National Institutes of Health Roadmap for Medical Research. Primary interests of the HMP include the distinctiveness of different gut microbiomes, the factors influencing microbiome diversity, and the functional redundancies of the members of human microbiotas. In this present work, we contribute to these interests by characterizing two extinct human microbiotas.Methodology/Principal FindingsWe examine two paleofecal samples originating from cave deposits in Durango Mexico and dating to approximately 1300 years ago. Contamination control is a serious issue in ancient DNA research; we use a novel approach to control contamination. After we determined that each sample originated from a different human, we generated 45 thousand shotgun DNA sequencing reads. The phylotyping and functional analysis of these reads reveals a signature consistent with the modern gut ecology. Interestingly, inter-individual variability for phenotypes but not functional pathways was observed. The two ancient samples have more similar functional profiles to each other than to a recently published profile for modern humans. This similarity could not be explained by a chance sampling of the databases.Conclusions/SignificanceWe conduct a phylotyping and functional analysis of ancient human microbiomes, while providing novel methods to control for DNA contamination and novel hypotheses about past microbiome biogeography. We postulate that natural selection has more of an influence on microbiome functional profiles than it does on the species represented in the microbial ecology. We propose that human microbiomes were more geographically structured during pre-Columbian times than today.

Examination of coprolites excavated from archaeological sites in the Americas demonstrates excellent preservation of helminth eggs and, in some cases, larvae. To gain an understanding of helminth parasitism in prehistory on the Colorado Plateau of Arizona, New Mexico, and Utah, 319 coprolites from 5 archaeological sites were analyzed. Helminth eggs and larvae were recovered after the coprolites were rehydrated, screened, and sedimented. At a sixth site, soils excavated from 5 rooms used as latrine areas were processed with palynological techniques. The results indicate that all but 1 of the prehistoric populations examined were infected with intestinal worms. The helminths implicated are Enterobius vermicularis, Trichuris trichiura, cf. Ascaris lumbricoides, cf. Trichostrongylus sp., cf. Strongyloides sp., taeniid cestodes, and hymenolepidid cestodes. The study suggests that prehistoric hunter-gatherer peoples carried fewer helminth parasites than agriculturalists. At 1 site, it appears that increased helminth parasitism preceded abandonment of the village. In North America, some of the first analyses were done in the Great Basin of Nevada and northwestern Utah (Fig. 1) The report presented below, of analyses of coprolites from the Colorado Plateau, doubles the total number of coprolites that have been analyzed for helminth remains from the western states. The coprolite samples represent both prehistoric hunter-gatherers and agriculturalists. The analyses constitute a significant contribution to our knowledge of parasitism in the prehistory of the American Southwest. MATERIALS AND METHODSThree hundred nineteen coprolites, as well as soil samples, were examined from 6 sites ( For the purposes ofhelminthological study, only 0.5-g samples were rehydrated from each coprolite. Before the samples were taken, the coprolites were examined for evidence of bore holes through which nematodes from the surrounding environment may have entered the feces. All coprolites were rehydrated in a 0.5% trisodium phosphate solution. To ensure rehydration, the coprolites were completely immersed in the solution for a minimum of 48 hr and a maximum of 72 hr. After 24 hr, acetic formalin alcohol was added to each rehydrating coprolite to retard fungal and bacterial decomposition. Disaggregation of the rehydrated coprolites was usually accomplished by washing the material with a jet of distilled water. In many cases, high fiber content of the feces impaired disaggregation. In these cases, the feces were disaggregated with a magnetic stirrer. After disaggregation, the feces were screened with distilled water through 0.95-mm and 0.5-mm screens. The fluid that passed through the screens was centrifuged to concentrate microscopic remains containing helminth eggs. The microscopic remains were transferred to vials in acetic formalin alcohol and allowed to settle. After sedimentation, the upper levels of the remains were pipetted onto microscopic slides, mounted in glycerol, and scanned for the presence of eggs or larvae. Three prepara...

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