scholarly journals Metagenomic analysis of ancient dental calculus reveals unexplored diversity of oral archaeal Methanobrevibacter

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Lena Granehäll ◽  
Kun D. Huang ◽  
Adrian Tett ◽  
Paolo Manghi ◽  
Alice Paladin ◽  
...  
Keyword(s):  
Middle Ages ◽  
De Novo ◽  
Oral Microbiome ◽  
Dental Calculus ◽  
Human Skeletal Remains ◽  
Metagenome Assembly ◽  
Metagenomic Assembly ◽  
Source Of Information ◽  
Archaeal Genus ◽  
Geographical Locations

Abstract Background Dental calculus (mineralised dental plaque) preserves many types of microfossils and biomolecules, including microbial and host DNA, and ancient calculus are thus an important source of information regarding our ancestral human oral microbiome. In this study, we taxonomically characterised the dental calculus microbiome from 20 ancient human skeletal remains originating from Trentino-South Tyrol, Italy, dating from the Neolithic (6000–3500 BCE) to the Early Middle Ages (400–1000 CE). Results We found a high abundance of the archaeal genus Methanobrevibacter in the calculus. However, only a fraction of the sequences showed high similarity to Methanobrevibacter oralis, the only described Methanobrevibacter species in the human oral microbiome so far. To further investigate the diversity of this genus, we used de novo metagenome assembly to reconstruct 11 Methanobrevibacter genomes from the ancient calculus samples. Besides the presence of M. oralis in one of the samples, our phylogenetic analysis revealed two hitherto uncharacterised and unnamed oral Methanobrevibacter species that are prevalent in ancient calculus samples sampled from a broad range of geographical locations and time periods. Conclusions We have shown the potential of using de novo metagenomic assembly on ancient samples to explore microbial diversity and evolution. Our study suggests that there has been a possible shift in the human oral microbiome member Methanobrevibacter over the last millennia.

scholarly journals METAMVGL: a multi-view graph-based metagenomic contig binning algorithm by integrating assembly and paired-end graphs

2021 ◽  
Vol 22 (S10) ◽  
Author(s):  
Zhenmiao Zhang ◽  
Lu Zhang
Keyword(s):  
De Novo ◽  
Label Propagation ◽  
Next Generation Sequencing Data ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Fecal Samples ◽  
Microbial Genomes ◽  
Metagenome Assembly ◽  
High Chance ◽  
Mock Communities

Abstract Background Due to the complexity of microbial communities, de novo assembly on next generation sequencing data is commonly unable to produce complete microbial genomes. Metagenome assembly binning becomes an essential step that could group the fragmented contigs into clusters to represent microbial genomes based on contigs’ nucleotide compositions and read depths. These features work well on the long contigs, but are not stable for the short ones. Contigs can be linked by sequence overlap (assembly graph) or by the paired-end reads aligned to them (PE graph), where the linked contigs have high chance to be derived from the same clusters. Results We developed METAMVGL, a multi-view graph-based metagenomic contig binning algorithm by integrating both assembly and PE graphs. It could strikingly rescue the short contigs and correct the binning errors from dead ends. METAMVGL learns the two graphs’ weights automatically and predicts the contig labels in a uniform multi-view label propagation framework. In experiments, we observed METAMVGL made use of significantly more high-confidence edges from the combined graph and linked dead ends to the main graph. It also outperformed many state-of-the-art contig binning algorithms, including MaxBin2, MetaBAT2, MyCC, CONCOCT, SolidBin and GraphBin on the metagenomic sequencing data from simulation, two mock communities and Sharon infant fecal samples. Conclusions Our findings demonstrate METAMVGL outstandingly improves the short contig binning and outperforms the other existing contig binning tools on the metagenomic sequencing data from simulation, mock communities and infant fecal samples.

scholarly journals How Does Diet Influence Our Lives? Evaluating the Relationship between Isotopic Signatures and Mortality Patterns in Italian Roman Imperial and Medieval Periods

Molecules ◽  
2021 ◽  
Vol 26 (13) ◽  
pp. 3895
Author(s):  
Marica Baldoni ◽  
Alessandra Nardi ◽  
Flavio De Angelis ◽  
Olga Rickards ◽  
Cristina Martínez-Labarga
Keyword(s):  
Middle Ages ◽  
Dietary Habits ◽  
Roman Period ◽  
Survivorship Analysis ◽  
Linear Effect ◽  
Isotopic Signatures ◽  
Carbon Isotopic ◽  
Religious Aspects ◽  
The Relationship ◽  
Source Of Information

The present research investigates the relationship between dietary habits and mortality patterns in the Roman Imperial and Medieval periods. The reconstructions of population dynamics and subsistence strategies provide a fascinating source of information for understanding our history. This is particularly true given that the changes in social, economic, political, and religious aspects related to the transition from the Roman period to the Middle Ages have been widely discussed. We analyzed the isotopic and mortality patterns of 616 individuals from 18 archeological sites (the Medieval Latium sites of Colonna, Santa Severa, Allumiere, Cencelle, and 14 Medieval and Imperial funerary contexts from Rome) to compile a survivorship analysis. A semi-parametric approach was applied, suggesting variations in mortality patterns between sexes in the Roman period. Nitrogen isotopic signatures influenced mortality in both periods, showing a quadratic and a linear effect for Roman Imperial and Medieval populations, respectively. No influence of carbon isotopic signatures has been detected for Roman Imperial populations. Conversely, increased mortality risk for rising carbon isotopic values was observed in Medieval samples.

scholarly journals Preliminary Reviews Of The Late Medieval Historical Geography Of Jizzakh (On The Basis Of Written Sources And Archaeological Data)

2020 ◽  
Vol 02 (10) ◽  
pp. 1-10
Author(s):  
Pardaev Ahrorqul Hasanovich ◽  
Keyword(s):  
Middle Ages ◽  
Historical Geography ◽  
Late Medieval ◽  
Modern City ◽  
Archaeological Data ◽  
Late Middle Ages ◽  
Scientific Analysis ◽  
Geographical Locations ◽  
Written Sources

The article examines the historical medieval towns, fortresses and other geographical areas of the Jizzakh oasis based on written sources and data obtained from archeological excavations. As a result of scientific analysis, the geographical locations of the Jizzakh Horde and its environs, which are the location of the modern city of Jizzakh in the late Middle Ages, have been clarified.

scholarly journals MetaCompass: Reference-guided Assembly of Metagenomes

2017 ◽  
Author(s):  
Victoria Cepeda ◽  
Bo Liu ◽  
Mathieu Almeida ◽  
Christopher M. Hill ◽  
Sergey Koren ◽  
...  
Keyword(s):  
De Novo ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Bacterial Genomes ◽  
Guided Assembly ◽  
Metagenomic Assembly

ABSTRACTMetagenomic studies have primarily relied on de novo approaches for reconstructing genes and genomes from microbial mixtures. While database driven approaches have been employed in certain analyses, they have not been used in the assembly of metagenomes. Here we describe the first effective approach for reference-guided metagenomic assembly of low-abundance bacterial genomes that can complement and improve upon de novo metagenomic assembly methods. When combined with de novo assembly approaches, we show that MetaCompass can generate more complete assemblies than can be obtained by de novo assembly alone, and improve on assemblies from the Human Microbiome Project (over 2,000 samples).

scholarly journals Choice of assembly software has a critical impact on virome characterisation

2018 ◽  
Author(s):  
Thomas D.S. Sutton ◽  
Adam G. Clooney ◽  
Feargal J. Ryan ◽  
R. Paul Ross ◽  
Colin Hill
Keyword(s):  
De Novo ◽  
Vital Role ◽  
Well Performance ◽  
Community Members ◽  
Reference Databases ◽  
Downstream Analysis ◽  
Metagenomic Assembly ◽  
Assembly Performance ◽  
Genomic Repeats

AbstractBackgroundThe viral component of microbial communities play a vital role in driving bacterial diversity, facilitating nutrient turnover and shaping community composition. Despite their importance, the vast majority of viral sequences are poorly annotated and share little or no homology to reference databases. As a result, investigation of the viral metagenome (virome) relies heavily on de novo assembly of short sequencing reads to recover compositional and functional information. Metagenomic assembly is particularly challenging for virome data, often resulting in fragmented assemblies and poor recovery of viral community members. Despite the essential role of assembly in virome analysis and difficulties posed by these data, current assembly comparisons have been limited to subsections of virome studies or bacterial datasets.DesignThis study presents the most comprehensive virome assembly comparison to date, featuring 16 metagenomic assembly approaches which have featured in human virome studies. Assemblers were assessed using four independent virome datasets, namely; simulated reads, two mock communities, viromes spiked with a known phage and human gut viromes.ResultsAssembly performance varied significantly across all test datasets, with SPAdes (meta) performing consistently well. Performance of MIRA and VICUNA varied, highlighting the importance of using a range of datasets when comparing assembly programs. It was also found that while some assemblers addressed the challenges of virome data better than others, all assemblers had limitations. Low read coverage and genomic repeats resulted in assemblies with poor genome recovery, high degrees of fragmentation and low accuracy contigs across all assemblers. These limitations must be considered when setting thresholds for downstream analysis and when drawing conclusions from virome data.

scholarly journals The dental calculus metabolome in modern and historic samples

2017 ◽  
Author(s):  
Irina M. Velsko ◽  
Katherine A. Overmyer ◽  
Camilla Speller ◽  
Matthew Collins ◽  
Louise Loe ◽  
...  
Keyword(s):  
Dental Plaque ◽  
Ultra Performance Liquid Chromatography ◽  
Oral Microbiome ◽  
Chemical Degradation ◽  
Dental Calculus ◽  
Metabolite Profiles ◽  
Free Nucleotides ◽  
Liquid Chromatography Tandem Mass ◽  
Long Time

AbstractIntroductionDental 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.ObjectiveWe present the first comprehensive characterization of the human dental calculus metabolome using a multi-platform approach.MethodsUltra 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.ResultsDipeptides, 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.ConclusionsThe 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.

scholarly journals Advantages and limits of metagenomic assembly and binning of a giant virus

2020 ◽  
Author(s):  
Frederik Schulz ◽  
Julien Andreani ◽  
Rania Francis ◽  
Jacques Yaacoub Bou Khalil ◽  
Janey Lee ◽  
...  
Keyword(s):  
Size Range ◽  
Sequence Data ◽  
Giant Virus ◽  
Sample Matrix ◽  
Environmental Sequence ◽  
Successful Recovery ◽  
Metagenome Assembly ◽  
Giant Viruses ◽  
Metagenomic Assembly ◽  
Virus Genomes

AbstractGiant viruses have large genomes, often within the size range of cellular organisms. This distinguishes them from most other viruses and demands additional effort for the successful recovery of their genomes from environmental sequence data. Here we tested the performance of genome-resolved metagenomics on a recently isolated giant virus, Fadolivirus, by spiking it into an environmental sample from which two other giant viruses were isolated. At high spike-in levels, metagenome assembly and binning led to the successful genomic recovery of Fadolivirus from the sample. A complementary survey of viral hallmark genes indicated the presence of other giant viruses in the sample matrix, but did not detect the two isolated from this sample. Our results indicate that genome-resolved metagenomics is a valid approach for the recovery of near-complete giant virus genomes given that sufficient clonal particles are present. Our data also underline that a vast majority of giant viruses remain currently undetected, even in an era of terabase-scale metagenomics.

Practical evaluation of 11 de novo assemblers in metagenome assembly

2018 ◽  
Vol 151 ◽  
pp. 99-105 ◽  
Author(s):  
Esmaeil Forouzan ◽  
Parvin Shariati ◽  
Masoumeh Sadat Mousavi Maleki ◽  
Ali Asghar Karkhane ◽  
Bagher Yakhchali
Keyword(s):  
De Novo ◽  
Practical Evaluation ◽  
Metagenome Assembly

Human Skeletal Remains from the Southern Cape Province and Their Bearing on the Stone Age Prehistory of South Africa

1978 ◽  
Vol 9 (2) ◽  
pp. 219-230 ◽  
Author(s):  
G. P. Rightmire
Keyword(s):  
South Africa ◽  
River Mouth ◽  
Middle Stone Age ◽  
Stone Age ◽  
Later Stone Age ◽  
Human Skeletal Remains ◽  
Upper Pleistocene ◽  
Skeletal Samples ◽  
Source Of Information ◽  
Cave Sediment

Substantial numbers of human skeletons have been recovered from caves and shelters of the southern Cape Province, South Africa, and these constitute a valuable source of information about evolutionary change and population movement during Upper Pleistocene and Holocene times. A few fragments from Klasies River Mouth and Die Kelders are firmly associated with Middle Stone Age cultural assemblages, but most of the material is probably linked with the Later Stone Age Albany and Wilton industries. Unfortunately the largest collections of relatively well-preserved remains have come from earlier excavations (Matjes River Shelter, Oakhurst), and the stratigraphic provenance of these burials is frequently in doubt. Other skeletal samples are small, and paleodemographic approaches are diffcult to apply. However, Bushman- or Hottentot-like individuals can certainly be identified, and this is important to the questions of Bushman antiquity or origins. Other problems concerning early Cape populations can also be examined, and this work on the human skeletons should complement ongoing cave sediment and other geological studies, faunal and plant analyses, and archaeological investigations of associated cultural remains.

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