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Acta Veterinaria Scandinavica Jun 2020Knowledge on dental disorders in commercial sows is limited although such conditions may have important animal welfare implications. In a pilot study, the dental and...
Knowledge on dental disorders in commercial sows is limited although such conditions may have important animal welfare implications. In a pilot study, the dental and periodontal health of 58 sows (Landrace*Yorkshire-crosses) from 8 Swedish commercial pig herds, slaughtered at one abattoir, were investigated. The oral cavity was inspected and abnormalities were recorded on a dental chart modified for pigs. Dental abnormalities, absence of teeth, supernumerary teeth, tooth fractures, signs of caries, and malalignment were recorded. The study revealed that 19% of the sows had supernumerary teeth and 59% of the sows missed at least one tooth. Periodontitis, calculus and malalignment were observed in 33%, 45% and 17%, respectively. Tooth wear was very common both in incisors (total 83%) and in premolars/molars (total 84%). One or more tooth fractures (between 1 and 6 per sow) was found in 41%. Signs of caries was found in 9%. In order to assess oral health, three indices were used: calculus index (CI), periodontal index (PDI) and tooth wear index (TWI). Severe periodontitis, tooth wear in incisors and tooth wear in premolars/molars were found in 7%, 34% and 35%, respectively. With respect to animal welfare, the etiology and the effects of the disorders on health, stress and pain need to be investigated.
Topics: Animals; Female; Periodontal Diseases; Pilot Projects; Sus scrofa; Sweden; Swine; Swine Diseases; Tooth Diseases
PubMed: 32498715
DOI: 10.1186/s13028-020-00521-7 -
Microbiome Sep 2021Dental calculus (mineralised dental plaque) preserves many types of microfossils and biomolecules, including microbial and host DNA, and ancient calculus are thus an...
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. Video abstract.
Topics: Archaea; Dental Calculus; Humans; Metagenome; Methanobrevibacter; Middle Aged; Phylogeny
PubMed: 34593021
DOI: 10.1186/s40168-021-01132-8 -
Scientific Reports Jun 2018Dental calculus (calcified dental plaque) is prevalent in archaeological skeletal collections and is a rich source of oral microbiome and host-derived ancient...
Dental calculus (calcified dental plaque) is prevalent in archaeological skeletal collections and is a rich source of oral microbiome and host-derived ancient biomolecules. Recently, it has been proposed that dental calculus may provide a more robust environment for DNA preservation than other skeletal remains, but this has not been systematically tested. In this study, shotgun-sequenced data from paired dental calculus and dentin samples from 48 globally distributed individuals are compared using a metagenomic approach. Overall, we find DNA from dental calculus is consistently more abundant and less contaminated than DNA from dentin. The majority of DNA in dental calculus is microbial and originates from the oral microbiome; however, a small but consistent proportion of DNA (mean 0.08 ± 0.08%, range 0.007-0.47%) derives from the host genome. Host DNA content within dentin is variable (mean 13.70 ± 18.62%, range 0.003-70.14%), and for a subset of dentin samples (15.21%), oral bacteria contribute > 20% of total DNA. Human DNA in dental calculus is highly fragmented, and is consistently shorter than both microbial DNA in dental calculus and human DNA in paired dentin samples. Finally, we find that microbial DNA fragmentation patterns are associated with guanine-cytosine (GC) content, but not aspects of cellular structure.
Topics: Bacteria; DNA, Bacterial; Dental Calculus; Dentin; Humans; Metagenomics; Microbiota; Preservation, Biological
PubMed: 29959351
DOI: 10.1038/s41598-018-28091-9 -
Nature Ecology & Evolution Jun 2022Archaeological and archaeogenetic evidence points to the Pontic-Caspian steppe zone between the Caucasus and the Black Sea as the crucible from which the earliest steppe...
Archaeological and archaeogenetic evidence points to the Pontic-Caspian steppe zone between the Caucasus and the Black Sea as the crucible from which the earliest steppe pastoralist societies arose and spread, ultimately influencing populations from Europe to Inner Asia. However, little is known about their economic foundations and the factors that may have contributed to their extensive mobility. Here, we investigate dietary proteins within the dental calculus proteomes of 45 individuals spanning the Neolithic to Greco-Roman periods in the Pontic-Caspian Steppe and neighbouring South Caucasus, Oka-Volga-Don and East Urals regions. We find that sheep dairying accompanies the earliest forms of Eneolithic pastoralism in the North Caucasus. During the fourth millennium BC, Maykop and early Yamnaya populations also focused dairying exclusively on sheep while reserving cattle for traction and other purposes. We observe a breakdown in livestock specialization and an economic diversification of dairy herds coinciding with aridification during the subsequent late Yamnaya and North Caucasus Culture phases, followed by severe climate deterioration during the Catacomb and Lola periods. The need for additional pastures to support these herds may have driven the heightened mobility of the Middle and Late Bronze Age periods. Following a hiatus of more than 500 years, the North Caucasian steppe was repopulated by Early Iron Age societies with a broad mobile dairy economy, including a new focus on horse milking.
Topics: Animals; Archaeology; Cattle; Dairying; Grassland; Horses; Humans; Livestock; Sheep; White People
PubMed: 35393601
DOI: 10.1038/s41559-022-01701-6 -
Scientific Reports Jun 2024Dental calculus is a microbial biofilm that contains biomolecules from oral commensals and pathogens, including those potentially related to cause of death (CoD). To...
Dental calculus is a microbial biofilm that contains biomolecules from oral commensals and pathogens, including those potentially related to cause of death (CoD). To assess the utility of calculus as a diagnostically informative substrate, in conjunction with paleopathological analysis, calculus samples from 39 individuals in the Smithsonian Institution's Robert J. Terry Collection with CoDs of either syphilis or tuberculosis were assessed via shotgun metagenomic sequencing for the presence of Treponema pallidum subsp. pallidum and Mycobacterium tuberculosis complex (MTBC) DNA. Paleopathological analysis revealed that frequencies of skeletal lesions associated with these diseases were partially inconsistent with diagnostic criteria. Although recovery of T. p. pallidum DNA from individuals with a syphilis CoD was elusive, MTBC DNA was identified in at least one individual with a tuberculosis CoD. The authenticity of MTBC DNA was confirmed using targeted quantitative PCR assays, MTBC genome enrichment, and in silico bioinformatic analyses; however, the lineage of the MTBC strain present could not be determined. Overall, our study highlights the utility of dental calculus for molecular detection of tuberculosis in the archaeological record and underscores the effect of museum preparation techniques and extensive handling on pathogen DNA preservation in skeletal collections.
Topics: Dental Calculus; Humans; Metagenomics; Paleopathology; Tuberculosis; Mycobacterium tuberculosis; DNA, Bacterial; Male; Treponema pallidum; Syphilis; Female; Adult; Metagenome; Middle Aged
PubMed: 38926415
DOI: 10.1038/s41598-024-64818-7 -
Frontiers in Plant Science 2022Reconstructing diet can offer an improved understanding toward the origin and evolution of modern humans. However, the diet of early modern humans in East Asia is poorly...
Reconstructing diet can offer an improved understanding toward the origin and evolution of modern humans. However, the diet of early modern humans in East Asia is poorly understood. Starch analysis of dental calculus is harmless to precious fossil hominins and provides the most direct evidence of plant food sources in early modern human dietary records. In this paper, we examined the starch grains in dental calculus from Fuyan Cave hominins in Daoxian (South China), which were the earliest modern humans in East Asia. Our results reveal the earliest direct evidence of a hominin diet made of acorns, roots, tubers, grass seeds, and other yet-unidentified plants in marine isotope stage 5 between 120 and 80 ka. Our study also provides the earliest evidence that acorns may have played an important role in subsistence strategies. There may have been a long-lasting tradition of using these plants during the Late Pleistocene in China. Plant foods would have been a plentiful source of carbohydrates that greatly increased energy availability to human tissues with high glucose demands. Our study provides the earliest direct consumption of carbohydrates-rich plant resources from modern humans in China for the first time. In addition, it also helps elucidate the evolutionary advantages of early modern humans in the late Middle and early Upper Pleistocene.
PubMed: 36119583
DOI: 10.3389/fpls.2022.989308 -
Scientific Reports Nov 2022Despite being one of the most important crops in the recent prehistory of Eurasia, the arrival and exploitation of millets in the westernmost part of Europe are still...
Despite being one of the most important crops in the recent prehistory of Eurasia, the arrival and exploitation of millets in the westernmost part of Europe are still largely underexplored. Here and for the first time, we report multipronged biomolecular evidence of millet consumption along the Atlantic façade of northern Iberia through a combination of radiocarbon dating, stable isotopes, and dental calculus analyses on the human individuals found in the burial site of El Espinoso cave (Asturias, Spain). The high-resolution chronological framework established for individuals placed the burials between 1235 and 1099 cal. BC. The discovery of high δC values on their bone collagen and the identification of polyhedral starch grains within their dental plaque underline the relevance of C plants in their diet and highlights the timing of the systematic consumption of millets in the Late Bronze Age. Our data support previous regional archaeobotanical evidence and establish a more precise chronology of the dispersal of millets into northern Iberia during the Bronze Age, becoming an essential crop until the arrival of maize from America after AD 1492. This study emphasizes the importance of multidisciplinary methods to ascertain the origin and development of agricultural practices during recent prehistory.
Topics: Humans; Millets; Archaeology; Radiometric Dating; Edible Grain; Crops, Agricultural
PubMed: 36329241
DOI: 10.1038/s41598-022-23227-4 -
Philosophical Transactions of the Royal... Nov 2020Human microbiome studies are increasingly incorporating macroecological approaches, such as community assembly, network analysis and functional redundancy to more fully...
Human microbiome studies are increasingly incorporating macroecological approaches, such as community assembly, network analysis and functional redundancy to more fully characterize the microbiome. Such analyses have not been applied to ancient human microbiomes, preventing insights into human microbiome evolution. We address this issue by analysing published ancient microbiome datasets: coprolites from Rio Zape ( = 7; 700 CE Mexico) and historic dental calculus ( = 44; 1770-1855 CE, UK), as well as two novel dental calculus datasets: Maya ( = 7; 170 BCE-885 CE, Belize) and Nuragic Sardinians ( = 11; 1400-850 BCE, Italy). Periodontitis-associated bacteria (, and ) were identified as keystone taxa in the dental calculus datasets. Coprolite keystone taxa included known short-chain fatty acid producers () and potentially disease-associated bacteria (, . Overlap in ecological profiles between ancient and modern microbiomes was indicated by similarity in functional response diversity profiles between contemporary hunter-gatherers and ancient coprolites, as well as parallels between ancient Maya, historic UK, and modern Spanish dental calculus; however, the ancient Nuragic dental calculus shows a distinct ecological structure. We detected key ecological signatures from ancient microbiome data, paving the way to expand understanding of human microbiome evolution. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.
Topics: Archaeology; Bacteria; Belize; DNA, Ancient; DNA, Bacterial; Dental Calculus; Feces; High-Throughput Nucleotide Sequencing; History, Ancient; History, Medieval; Humans; Italy; Mexico; Microbiota
PubMed: 33012230
DOI: 10.1098/rstb.2019.0586 -
Acta Clinica Croatica Aug 2022Numerous oral changes develop as a result of dysfunctional eating behavior in patients with eating disorders (ED). The aim of this study was to evaluate the correlation...
Numerous oral changes develop as a result of dysfunctional eating behavior in patients with eating disorders (ED). The aim of this study was to evaluate the correlation among oral manifestations, age, disease duration and nutritional status in pediatric patients with ED. The study included 50 female ED patients, median age 14 (range 10-18) years and median disease duration 9 (range 1-42) months. Nutritional status was expressed as z-score for body mass index (BMI). Mean BMI z-score was -2.10±1.64. The most commonly observed oral findings were dental plaque, marginal gingivitis, morsicatio, dental calculus, caries, pharyngeal erythema, exfoliative cheilitis and angular cheilitis. Dental plaque and pharyngeal erythema were correlated with shorter disease duration (p=0.048; p=0.040), while frictional keratosis of tongue was correlated with longer disease duration (0.011). Linea alba and pain in the temporomandibular joint were associated with younger age (p=0.012; p=0.024), and tooth impression on tongue with lower degree of nutrition (p=0.030). This study showed that there was a link among oral manifestations, age, disease duration and degree of nutritional disorder, although further investigations comparing the groups of ED patients with different age, disease duration and nutritional status would give better, concrete and precise conclusions.
Topics: Humans; Child; Female; Infant; Cheilitis; Dental Plaque; Gingivitis; Feeding and Eating Disorders; Erythema; Dental Caries
PubMed: 36818917
DOI: 10.20471/acc.2022.61.02.03 -
Journal of Clinical Medicine Apr 2023Supervised deep learning requires labelled data. On medical images, data is often labelled inconsistently (e.g., too large) with varying accuracies. We aimed to assess...
Supervised deep learning requires labelled data. On medical images, data is often labelled inconsistently (e.g., too large) with varying accuracies. We aimed to assess the impact of such label noise on dental calculus detection on bitewing radiographs. On 2584 bitewings calculus was accurately labeled using bounding boxes (BBs) and artificially increased and decreased stepwise, resulting in 30 consistently and 9 inconsistently noisy datasets. An object detection network (YOLOv5) was trained on each dataset and evaluated on noisy and accurate test data. Training on accurately labeled data yielded an mAP50: 0.77 (SD: 0.01). When trained on consistently too small BBs model performance significantly decreased on accurate and noisy test data. Model performance trained on consistently too large BBs decreased immediately on accurate test data (e.g., 200% BBs: mAP50: 0.24; SD: 0.05; < 0.05), but only after drastically increasing BBs on noisy test data (e.g., 70,000%: mAP50: 0.75; SD: 0.01; < 0.05). Models trained on inconsistent BB sizes showed a significant decrease of performance when deviating 20% or more from the original when tested on noisy data (mAP50: 0.74; SD: 0.02; < 0.05), or 30% or more when tested on accurate data (mAP50: 0.76; SD: 0.01; < 0.05). In conclusion, accurate predictions need accurate labeled data in the training process. Testing on noisy data may disguise the effects of noisy training data. Researchers should be aware of the relevance of accurately annotated data, especially when testing model performances.
PubMed: 37176499
DOI: 10.3390/jcm12093058