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

Streptococcus abundance and oral site tropism in humans and non-human primates reflects host and lifestyle differences

The genus Streptococcus is highly diverse and a core member of the primate oral microbiome. Streptococcus species are grouped into at least eight phylogenetically-supported clades, five of which are found almost exclusively in the oral cavity. We explored the dominant Streptococcus phylogenetic clades in samples from multiple oral sites and from ancient and modern-day humans and non-human primates and found that clade dominance is conserved across human oral sites, with most Streptococcus reads assigned to species falling in the Sanguinis or Mitis clades. However, minor differences in the presence and abundance of individual species within each clade differentiated human lifestyles, with loss of S. sinensis appearing to correlate with toothbrushing. Of the non-human primates, only baboons show clade abundance patterns similar to humans, suggesting that a habitat and diet similar to that of early humans may favor the growth of Sanguinis and Mitis clade species.

Methanobrevibacter oralis: a comprehensive review

Methanobrevibacter oralis (M. oralis) has predominated human oral microbiota methanogenic archaea as far back as the Palaeolithic era in Neanderthal populations and gained dominance from the 18th century onwards. M. oralis was initially isolated from dental plaque samples collected from two apparently healthy individuals allowing its first characterization. The culture of M. oralis is fastidious and has been the subject of several studies to improve its laboratory growth. Various PCR methods are used to identify M. oralis, targeting either the 16S rRNA gene or the mcrA gene. However, only one RTQ-PCR system, based on a chaperonin gene, offers specificity, and allows for microbial load quantification. Next-generation sequencing contributed five draft genomes, each approximately 2.08 Mb (±0.052 Mb) with a 27.82 (±0.104) average GC%, and two ancient metagenomic assembled genomes. M. oralis was then detected in various oral cavity sites in healthy individuals and those diagnosed with oral pathologies, notably periodontal diseases, and endodontic infections. Transmission pathways, possibly involving maternal milk and breastfeeding, remain to be clarified. M. oralis was further detected in brain abscesses and respiratory tract samples, bringing its clinical significance into question. This review summarizes the current knowledge about M. oralis, emphasizing its prevalence, associations with dysbiosis and pathologies in oral and extra-oral situations, and symbiotic relationships, with the aim of paving the way for further investigations.

Oral microbial diversity in 18th century African individuals from South Carolina

As part of the Anson Street African Burial Ground Project, we characterized the oral microbiomes of twelve 18th century African-descended individuals (Ancestors) from Charleston, South Carolina, USA, to study their oral health and diet. We found that their oral microbiome composition resembled that of other historic (18th-19th century) dental calculus samples but differed from that of modern samples, and was not influenced by indicators of oral health and wear observed in the dentition. Phylogenetic analysis of the oral bacteria, Tannerella forsythia and Pseudoramibacter alactolyticus, revealed varied patterns of lineage diversity and replacement in the Americas, with the Ancestors carrying strains similar to historic period Europeans and Africans. Functional profiling of metabolic pathways suggested that the Ancestors consumed a diet low in animal protein. Overall, our study reveals important insights into the oral microbial histories of African-descended individuals, particularly oral health and diet in colonial North American enslavement contexts.

A Journey into the Evolution of Human Host-Oral Microbiome Relationship through Ancient Dental Calculus: A Scoping Review

One of the most promising areas of research in palaeomicrobiology is the study of the human microbiome. In particular, ancient dental calculus helps to reconstruct a substantial share of oral microbiome composition by mapping together human evolution with its state of health/oral disease. This review aims to trace microbial characteristics in ancient dental calculus to describe the evolution of the human host-oral microbiome relationship in oral health or disease in children and adults. Following the PRISMA-Extension for Scoping Reviews guidelines, the main scientific databases (PubMed, Scopus, Lilacs, Cochrane Library) have been drawn upon. Eligibility criteria were established, and all the data collected on a purpose-oriented collection form were analysed descriptively. From the initial 340 records, only 19 studies were deemed comprehensive enough for the purpose of this review. The knowledge of the composition of ancient oral microbiomes has broadened over the past few years thanks to increasingly well-performing decontamination protocols and additional analytical avenues. Above all, metagenomic sequencing, also implemented by state-of-the-art bioinformatics tools, allows for the determination of the qualitative-quantitative composition of microbial species associated with health status and caries/periodontal disease. Some microbial species, especially periodontal pathogens, do not appear to have changed in history, while others that support caries disease or oral health could be connected to human evolution through lifestyle and environmental contributing factors.

Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices

The human gut microbiota is influenced by various factors, including health status and environmental conditions, yet considerable inter-individual differences remain unexplained. Previous studies identified that the gut microbiota of men who have sex with men (MSM) is distinct from that of non-MSM. Here, we reveal through species-level microbiota analysis using shotgun metagenomics that the gut microbiota of many MSM with Western origin resembles gut microbial communities of non-Westernized populations. Specifically, MSM gut microbiomes are frequently dominated by members of the Prevotellaceae family, including co-colonization of species from the Segatella copri complex and unknown Prevotellaceae members. Questionnaire-based analysis exploring inter-individual differences in MSM links specific sexual practices to microbiota composition. Moreover, machine learning identifies microbial features associated with sexual activities in MSM. Together, this study shows associations of sexual activities with gut microbiome alterations in MSM, which may have a large impact on population-based microbiota studies.

Windows into the past: recent scientific techniques in dental analysis

Teeth are the hardest and most chemically stable tissues in the body, are well-preserved in archaeological remains and, being resistant to decomposition in the soil, survive long after their supporting structures have deteriorated. It has long been recognised that visual and radiographic examination of teeth can provide considerable information relating to the lifestyle of an individual. This paper examines the latest scientific approaches that have become available to investigate recent and ancient teeth. These techniques include DNA analysis, which can be used to determine the sex of an individual, indicate familial relationships, study population movements, provide phylogenetic information and identify the presence of disease pathogens. A stable isotopic approach can shed light on aspects of diet and mobility and even research climate change. Proteomic analysis of ancient dental calculus can reveal specific information about individual diets. Synchrotron microcomputed tomography is a non-invasive technique which can be used to visualise physiological impactful events, such as parturition, menopause and diseases in cementum microstructure - these being displayed as aberrant growth lines.

Methanobrevibacter massiliense and Pyramidobacter piscolens Co-Culture Illustrates Transkingdom Symbiosis

Among oral microbiota methanogens, Methanobrevibacter massiliense (M. massiliense) has remained less studied than the well-characterised and cultivated methanogens Methanobrevibacter oralis and Methanobrevibacter smithii. M. massiliense has been associated with different oral pathologies and was co-isolated with the Synergistetes bacterium Pyramidobacter piscolens (P. piscolens) in one case of severe periodontitis. Here, reporting on two additional necrotic pulp cases yielded the opportunity to characterise two co-cultivated M. massiliense isolates, both with P. piscolens, as non-motile, 1-2-µm-long and 0.6-0.8-µm-wide Gram-positive coccobacilli which were autofluorescent at 420 nm. The two whole genome sequences featured a 31.3% GC content, gapless 1,834,388-base-pair chromosome exhibiting an 85.9% coding ratio, encoding a formate dehydrogenase promoting M. massiliense growth without hydrogen in GG medium. These data pave the way to understanding a symbiotic, transkingdom association with P. piscolens and its role in oral pathologies.

Metagenomic analysis of Mesolithic chewed pitch reveals poor oral health among stone age individuals

Prehistoric chewed pitch has proven to be a useful source of ancient DNA, both from humans and their microbiomes. Here we present the metagenomic analysis of three pieces of chewed pitch from Huseby Klev, Sweden, that were dated to 9,890-9,540 before present. The metagenomic profile exposes a Mesolithic oral microbiome that includes opportunistic oral pathogens. We compared the data with healthy and dysbiotic microbiome datasets and we identified increased abundance of periodontitis-associated microbes. In addition, trained machine learning models predicted dysbiosis with 70-80% probability. Moreover, we identified DNA sequences from eukaryotic species such as red fox, hazelnut, red deer and apple. Our results indicate a case of poor oral health during the Scandinavian Mesolithic, and show that pitch pieces have the potential to provide information on material use, diet and oral health.

Ancient dental calculus reveals oral microbiome shifts associated with lifestyle and disease in Great Britain

The prevalence of chronic, non-communicable diseases has risen sharply in recent decades, especially in industrialized countries. While several studies implicate the microbiome in this trend, few have examined the evolutionary history of industrialized microbiomes. Here we sampled 235 ancient dental calculus samples from individuals living in Great Britain (∼2200 BCE to 1853 CE), including 127 well-contextualized London adults. We reconstructed their microbial history spanning the transition to industrialization. After controlling for oral geography and technical biases, we identified multiple oral microbial communities that coexisted in Britain for millennia, including a community associated with Methanobrevibacter, an anaerobic Archaea not commonly prevalent in the oral microbiome of modern industrialized societies. Calculus analysis suggests that oral hygiene contributed to oral microbiome composition, while microbial functions reflected past differences in diet, specifically in dairy and carbohydrate consumption. In London samples, Methanobrevibacter-associated microbial communities are linked with skeletal markers of systemic diseases (for example, periostitis and joint pathologies), and their disappearance is consistent with temporal shifts, including the arrival of the Second Plague Pandemic. This suggests pre-industrialized microbiomes were more diverse than previously recognized, enhancing our understanding of chronic, non-communicable disease origins in industrialized populations.

Metagenomics-based inference of microbial metabolism towards neuroactive amino acids and the response to antibiotics in piglet colon

Gut-derived neuroactive metabolites from amino acids perform a broad range of physiological roles in the body. However, the interaction between microbiota and epithelium in the metabolism of amino acids with neuroactive properties remains unclear in the colon of piglets. To investigate the microbial and epithelial metabolism, metagenomics and mucosal metabolomics were performed using colonic samples from 12 ileum-canulated piglets subjected to a 25-day infusion with saline or antibiotics. We categorized 23 metabolites derived from the metabolism of tryptophan, glutamate, and tyrosine, known as precursors of neuroactive metabolites. Microbial enzymes involved in the kynurenine synthesis via arylformamidase, 4-aminobutyric acid (GABA) synthesis via putrescine aminotransferase, and tyramine synthesis via tyrosine decarboxylase were identified in Clostridiales bacterium, uncultured Blautia sp., and Methanobrevibacter wolinii, respectively. Antibiotics significantly affected the microbiota involved in tryptophan-kynurenine and glutamate-GABA metabolism. An increase in the relative abundance of putrescine aminotransferase and Blautia sp. correlated positively with an increase in luminal GABA concentration. Overall, our findings provide new insights into the microbial ability to metabolize key amino acids that are precursors of neuroactive metabolites.

Natural products from reconstructed bacterial genomes of the Middle and Upper Paleolithic

Major advances over the past decade in the field of ancient DNA are providing access to past paleogenomic diversity, but the diverse functions and biosynthetic capabilities of this growing paleome remain largely elusive. Here, we investigated the dental calculus of 12 Neanderthals and 52 anatomically modern humans spanning 100 kya to the present and reconstructed 459 bacterial metagenome-assembled genomes (MAGs). We identified a biosynthetic gene cluster (BGC) shared by seven Middle and Upper Paleolithic individuals that allows for the heterologous production of a class of previously unknown metabolites we name paleofurans. This paleobiotechnological approach demonstrates that viable biosynthetic machinery can be produced from the preserved genetic material of ancient organisms, allowing access to natural products from the Pleistocene and providing a promising area for natural product exploration.

Ancient DNA suggests anaemia and low bone mineral density as the cause for porotic hyperostosis in ancient individuals

Porotic hyperostosis (PH) is a disease that had high prevalence during the Neolithic. Several hypotheses have been suggested to explain the origin of the disease, such as an iron deficiency diet, low B12 intake, malaria caused by Plasmodium spp., low haemoglobin levels or low vitamin D levels. None of these hypotheses have been tested genetically. Here, I calculated different genetic scores to test each hypothesis. Additionally, I calculated a genetic score of bone mineral density as it is a phenotype that seems to be selected in ancient Europeans. I apply these genetic scores on 80 ancient samples, 33 with diagnosed PH. The results seem to suggest anaemia and low bone mineral density as the main cause for this disease. Additionally, Neolithic individuals show the lowest genetic risk score for bone mineral density of all other periods tested here, which may explain the highest prevalence of the porotic hyperostosis during this age.

Paleoproteomic evidence reveals dairying supported prehistoric occupation of the highland Tibetan Plateau

The extreme environments of the Tibetan Plateau offer considerable challenges to human survival, demanding novel adaptations. While the role of biological and agricultural adaptations in enabling early human colonization of the plateau has been widely discussed, the contribution of pastoralism is less well understood, especially the dairy pastoralism that has historically been central to Tibetan diets. Here, we analyze ancient proteins from the dental calculus (n = 40) of all human individuals with sufficient calculus preservation from the interior plateau. Our paleoproteomic results demonstrate that dairy pastoralism began on the highland plateau by ~3500 years ago. Patterns of milk protein recovery point to the importance of dairy for individuals who lived in agriculturally poor regions above 3700 m above sea level. Our study suggests that dairy was a critical cultural adaptation that supported expansion of early pastoralists into the region's vast, non-arable highlands, opening the Tibetan Plateau up to widespread, permanent human occupation.

Gut Microbiota in Nutrition and Health with a Special Focus on Specific Bacterial Clusters

Health is influenced by how the gut microbiome develops as a result of external and internal factors, such as nutrition, the environment, medication use, age, sex, and genetics. Alpha and beta diversity metrics and (enterotype) clustering methods are commonly employed to perform population studies and to analyse the effects of various treatments, yet, with the continuous development of (new) sequencing technologies, and as various omics fields as a result become more accessible for investigation, increasingly sophisticated methodologies are needed and indeed being developed in order to disentangle the complex ways in which the gut microbiome and health are intertwined. Diseases of affluence, such as type 2 diabetes (T2D) and cardiovascular diseases (CVD), are commonly linked to species associated with the Bacteroides enterotype(s) and a decline of various (beneficial) complex microbial trophic networks, which are in turn linked to the aforementioned factors. In this review, we (1) explore the effects that some of the most common internal and external factors have on the gut microbiome composition and how these in turn relate to T2D and CVD, and (2) discuss research opportunities enabled by and the limitations of some of the latest technical developments in the microbiome sector, including the use of artificial intelligence (AI), strain tracking, and peak to trough ratios.

Ancient dental calculus preserves signatures of biofilm succession and interindividual variation independent of dental pathology

Dental calculus preserves oral microbes, enabling comparative studies of the oral microbiome and health through time. However, small sample sizes and limited dental health metadata have hindered health-focused investigations to date. Here, we investigate the relationship between tobacco pipe smoking and dental calculus microbiomes. Dental calculus from 75 individuals from the 19th century Middenbeemster skeletal collection (Netherlands) were analyzed by metagenomics. Demographic and dental health parameters were systematically recorded, including the presence/number of pipe notches. Comparative data sets from European populations before and after the introduction of tobacco were also analyzed. Calculus species profiles were compared with oral pathology to examine associations between microbiome community, smoking behavior, and oral health status. The Middenbeemster individuals exhibited relatively poor oral health, with a high prevalence of periodontal disease, caries, heavy calculus deposits, and antemortem tooth loss. No associations between pipe notches and dental pathologies, or microbial species composition, were found. Calculus samples before and after the introduction of tobacco showed highly similar species profiles. Observed interindividual microbiome differences were consistent with previously described variation in human populations from the Upper Paleolithic to the present. Dental calculus may not preserve microbial indicators of health and disease status as distinctly as dental plaque.

Detection of Ancient Viruses and Long-Term Viral Evolution

The COVID-19 outbreak has reminded us of the importance of viral evolutionary studies as regards comprehending complex viral evolution and preventing future pandemics. A unique approach to understanding viral evolution is the use of ancient viral genomes. Ancient viruses are detectable in various archaeological remains, including ancient people's skeletons and mummified tissues. Those specimens have preserved ancient viral DNA and RNA, which have been vigorously analyzed in the last few decades thanks to the development of sequencing technologies. Reconstructed ancient pathogenic viral genomes have been utilized to estimate the past pandemics of pathogenic viruses within the ancient human population and long-term evolutionary events. Recent studies revealed the existence of non-pathogenic viral genomes in ancient people's bodies. These ancient non-pathogenic viruses might be informative for inferring their relationships with ancient people's diets and lifestyles. Here, we reviewed the past and ongoing studies on ancient pathogenic and non-pathogenic viruses and the usage of ancient viral genomes to understand their long-term viral evolution.