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.
The Tyrolean Iceman, a 5,300-year-old Copper age individual, was discovered in 1991 on the Tisenjoch Pass in the Italian part of the Ötztal Alps. Here we report the complete genome sequence of the Iceman and show 100% concordance between the previously reported mitochondrial genome sequence and the consensus sequence generated from our genomic data. We present indications for recent common ancestry between the Iceman and presentday inhabitants of the Tyrrhenian sea, that the Iceman probably had brown eyes, belonged to blood group o and was lactose intolerant. His genetic predisposition shows an increased risk for coronary heart disease and may have contributed to the development of previously reported vascular calcifications. sequences corresponding to ~60% of the genome of Borrelia burgdorferi are indicative of the earliest human case of infection with the pathogen for Lyme borreliosis.
Within the last few years a considerable number of molecular studies have provided evidence for the presence of Mycobacterium tuberculosis complex DNA in ancient skeletal and mummified material (1,7,9,18,27,28,34,38,41,47). Besides the mere evidence of M. tuberculosis complex DNA, initial information suggested a high frequency of tuberculosis in ancient populations (13), and we have recently provided evidence that this also holds true for pharaonic Egypt (47 (20), which is based on the variation of the direct-repeat (DR) region in M. tuberculosis complex members. Using this technique, differentiation up to a subspecies level is possible. Spoligotyping is widely used and accepted in medical microbiology for the initial genotyping of the M. tuberculosis complex at the population level. In addition, spoligotyping seems to be the most suitable method for analyzing ancient material, since usually only minute amounts of a significantly fragmented mycobacterial ancient DNA (aDNA) remains in the samples under investigation. Likewise, other recent methods, such as IS6110 restriction fragment length polymorphism (43), ligation-mediated PCR (31), and variable number of tandem repeat typing (24), require cell culture conditions or at least high-molecular-weight bacterial DNA and are therefore not applicable to ancient tissue material.In addition, spoligotyping seems to be suitable for investigating evolutionary aspects of human tuberculosis (36) and may clarify the origin and transmission of the disease in humans of various historical periods and populations (35). When its results are combined with other data, they can be used to construct phylogenetic trees reaching back to the beginning of the pathogenesis and spread of the disease in humans and animals (37).In this regard, there is still an open debate about the origins of tuberculosis in human and animal species. One previous hypothesis (5) suggests that M. bovis is the probable ancestor which was transmitted from cattle to humans during domestication. Other theories assume that an M. tuberculosis complex precursor evolved from M. africanum and that the present-day M. tuberculosis and M. bovis developed in parallel (39). This theory is supported by nucleotide sequence analyses of current M. tuberculosis isolates, revealing an absence of allelic variation. The evolutionary origin of M. tuberculosis was therefore suggested to be 15,000 to 20,000 years ago (39).In a recent paper, a new evolutionary scenario was presented based on the occurrence of several deletions in the genomes of the tubercle bacilli (4). These findings allow a differentiation of M. tuberculosis strains into modern and ancestral strains depending on the presence or absence of an M. tuberculosis-* Corresponding author. Mailing address:
The stomach bacterium Helicobacter pylori is one of the most prevalent human pathogens. It has dispersed globally with its human host resulting in a distinct phylogeographic pattern that can be used to reconstruct both recent and ancient human migrations. The extant European population of H. pylori is known to be a hybrid between Asian and African bacteria, but there exist different hypotheses about when and where the hybridization took place, reflecting the complex demographic history of Europeans. Here, we present a 5,300-year-old H. pylori genome from a European Copper Age glacier mummy. The “Iceman” H. pylori is a nearly-pure representative of the bacterial population of Asian origin that existed in Europe prior to hybridization, suggesting the African population arrived in Europe within the last few thousand years.
HE 18TH DYNASTY (CIRCA 1550-1295 of the New Kingdom (circa 1550-1070 BC) was one of the most powerful royal houses of ancient Egypt. The pharaoh Akhenaten, who ruled from circa 1351 to 1334 BC, is considered one of the most controversial of the Egyptian pharaohs, because his attempt to radically transform traditional religion affected all facets of society and caused great turmoil.Akhenaten's eventual successor, Tutankhamun, is probably the most famous of all pharaohs, although his tenure was brief. He died in the ninth year of his reign, circa 1324 BC, at age 19 years. Little was known of Tutankhamun and his ancestry prior to Howard Carter's discovery of his intact tomb (KV62) in For editorial comment see p 667.
Modern next generation sequencing technologies produce vast amounts of data in the context of large--scale metagenomic studies, in which complex microbial communities can be reconstructed to an unprecedented level of detail. Most prominent examples are human microbiome studies that correlate the bacterial taxonomic profile with specific physiological conditions or diseases. In order to perform these analyses high--throughput computational tools are needed that are able to process these data within a short time while preserving a high level of sensitivity and specificity. Here we present MALT (MEGAN ALignment Tool) a program for the ultrafast alignment and analysis of metagenomic DNA sequencing data. MALT processes hundreds of millions of sequencing reads within only a few hours. In addition to the alignment procedure MALT implements a taxonomic binning algorithm that is able to specifically assign reads to bacterial species. Its tight integration with the interactive metagenomic analysis software MEGAN allows for visualization and further analyses of results. We demonstrate MALT by its application to the metagenomic analysis of two ancient microbiomes from oral cavity and lung samples of the 5,300--year--old Tyrolean Iceman. Despite the strong environmental background, MALT is able to pick up the weak signal of the original microbiomes and identifies multiple species that are typical representatives of the respective host environment.
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