Biology subjects

Warinner, C.

Publications and source records attributed to Warinner, C..

5 recordsLinked to original sources

bioRxiv2018

Biogeographic study of human gut associated crAssphage suggests impacts from industrialization and recent expansion.

CrAssphage (cross-assembly phage) is a bacteriophage that was first discovered in human gut metagenomic data. CrAssphage belongs to a diverse family of crAss-like bacteriophages thought to infect gut commensal bacteria belonging to Bacteroides species. However, not much is known about the biogeography of crAssphage and whether certain strains are associated with specific human populations. In this study, we screened publicly available human gut metagenomic data from 3,341 samples for the presence of crAssphage sensu stricto (NC_024711.1). We found that crAssphage prevalence is low in traditional, hunter-gatherer populations, such as the Hadza from Tanzania and Matses from Peru, as compared to industrialized, urban populations. Statistical comparisons showed no association of crAssphage prevalence with variables such as age, sex, body mass index, and health status of individuals. Phylogenetic analyses show that crAssphage strains reconstructed from the same individual over multiple time-points, cluster together. CrAssphage strains from individuals from the same study population do not always cluster together. Some evidence of clustering is seen at the level of broadly defined geographic regions, however, the relative positions of these clusters within the crAssphage phylogeny are not well-supported. We hypothesize that this lack of strong biogeographic structuring is suggestive of a recent expansion event within crAssphage. Using a Bayesian dating approach, we estimate this expansion has occurred within the past 200 years. Overall, we determine that crAssphage presence is associated with an industrialized lifestyle. The absence of strong biogeographic structuring within global crAssphage strains is likely due to a recent population expansion within this bacteriophage.

evolutionary biology↗

bioRxiv2018

The genetic prehistory of the Andean highlands 7,000 Years BP though European contact

The peopling of the Andean highlands above 2500m in elevation was a complex process that included cultural, biological and genetic adaptations. Here we present a time series of ancient whole genomes from the Andes of Peru, dating back to 7,000 calendar years before present (BP), and compare them to 64 new genome-wide genetic variation datasets from both high and lowland populations. We infer three significant features: a split between low and high elevation populations that occurred between 9200-8200 BP; a population collapse after European contact that is significantly more severe in South American lowlanders than in highland populations; and evidence for positive selection at genetic loci related to starch digestion and plausibly pathogen resistance after European contact. Importantly, we do not find selective sweep signals related to known components of the human hypoxia response, which may suggest more complex modes of genetic adaptation to high altitude.\n\nOne Sentence SummaryAncient DNA from the Andes reveals a complex picture of human adaptation from early settlement to the colonial period.

genomics↗

bioRxiv2018

Selection of appropriate metagenome taxonomic classifiers for ancient microbiome research

Metagenomics enables the study of complex microbial communities from myriad sources, including the remains of oral and gut microbiota preserved in archaeological dental calculus and paleofeces, respectively. While accurate taxonomic assignment is essential to this process, DNA damage, characteristic to ancient samples (e.g. reduction in fragment size), may reduce the accuracy of read taxonomic assignment. Using a set of in silico-generated metagenomic datasets we investigated how the addition of ancient DNA (aDNA) damage patterns influences microbial taxonomic assignment by five widely-used profilers: QIIME/UCLUST, MetaPhlAn2, MIDAS, CLARK-S, and MALT (BLAST-X-mode). In silico-generated datasets were designed to mimic dental plaque, consisting of 40, 100, and 200 microbial species/strains, both with and without simulated aDNA damage patterns. Following taxonomic assignment, the profiles were evaluated for species presence/absence, relative abundance, alpha-diversity, beta-diversity, and specific taxonomic assignment biases. Unifrac metrics indicated that both MIDAS and MetaPhlAn2 provided the most accurate community structure reconstruction. QIIME/UCLUST, CLARK-S, and MALT had the highest number of inaccurate taxonomic assignments; however, filtering out species present at <0.1% abundance greatly increased the accuracy of CLARK-S and MALT. All programs except CLARK-S failed to detect some species from the input file that were in their databases. Ancient DNA damage resulted in minimal differences in species detection and relative abundance between simulated ancient and modern datasets for most programs. In conclusion, taxonomic profiling biases are program-specific rather than damage-dependent, and the choice of taxonomic classification program to use should be tailored to the research question.\n\nImportanceAncient biomolecules from oral and gut microbiome samples have been shown to preserve in the archaeological record. Studying ancient microbiome communities using metagenomic techniques offer a unique opportunity to reconstruct the evolutionary trajectories of microbial communities through time. DNA accumulates specific damage over time, which could potentially affect taxonomic classification and our ability to reconstruct community assemblages accurately. It is therefore necessary to assess whether ancient DNA (aDNA) damage patterns affect metagenomic taxonomic profiling. Here, we assessed biases in community structure, diversity, species detection, and relative abundance estimates by five popular metagenomic taxonomic classification programs using in silico-generated datasets with aDNA damage. Age-related damage patterns had minimal impact on the taxonomic profiles produced by each program, and biases were intrinsic to each program. Therefore, an appropriate classification program should be chosen that minimizes the biases related to the questions being addressed.

microbiology↗

bioRxiv2017

The dental calculus metabolome in modern and historic samples

IntroductionDental calculus is a mineralized microbial dental plaque biofilm that forms throughout life by precipitation of salivary calcium salts. Successive cycles of dental plaque growth and calcification make it an unusually well-preserved, long-term record of host-microbial interaction in the archaeological record. Recent studies have confirmed the survival of authentic ancient DNA and proteins within historic and prehistoric dental calculus, making it a promising substrate for investigating oral microbiome evolution via direct measurement and comparison of modern and ancient specimens.\n\nObjectiveWe present the first comprehensive characterization of the human dental calculus metabolome using a multi-platform approach.\n\nMethodsUltra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) quantified 285 metabolites in modern and historic (200 years old) dental calculus, including metabolites of drug and dietary origin. A subset of historic samples was additionally analyzed by high-resolution gas chromatography-MS (GC-MS) and UPLC- MS/MS for further characterization of polar metabolites and lipids, respectively. Metabolite profiles of modern and historic calculus were compared to identify patterns of persistence and loss.\n\nResultsDipeptides, free amino acids, free nucleotides, and carbohydrates substantially decrease in abundance and ubiquity in archaeological samples, with some exceptions. Lipids generally persist, and saturated and mono-unsaturated medium and long chain fatty acids appear to be well-preserved, while metabolic derivatives related to oxidation and chemical degradation are found at higher levels in archaeological dental calculus than fresh samples.\n\nConclusionsThe results of this study indicate that certain metabolite classes have higher potential for recovery over long time scales and may serve as appropriate targets for oral microbiome evolutionary studies.

microbiology↗

bioRxiv2017

Salmonella enterica genomes recovered from victims of a major 16th century epidemic in Mexico

Indigenous populations of the Americas experienced high mortality rates during the early contact period as a result of infectious diseases, many of which were introduced by Europeans. Most of the pathogenic agents that caused these outbreaks remain unknown. Using a metagenomic tool called MALT to search for traces of ancient pathogen DNA, we were able to identify Salmonella enterica in individuals buried in an early contact era epidemic cemetery at Teposcolula-Yucundaa, Oaxaca in southern Mexico. This cemetery is linked to the 1545-1550 CE epidemic locally known as \"cocoliztli\", the cause of which has been debated for over a century. Here we present two reconstructed ancient genomes for Salmonella enterica subsp. enterica serovar Paratyphi C, a bacterial cause of enteric fever. We propose that S. Paratyphi C contributed to the population decline during the 1545 cocoliztli outbreak in Mexico.\n\nOne Sentence SummaryGenomic evidence of enteric fever identified in an indigenous population from early contact period Mexico.

genomics↗