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Ķimsis J, Pokšāne A, Kazarina A, Vilcāne A, Petersone‐Gordina E, Zayakin P, Gerhards G, Ranka R. Tracing microbial communities associated with archaeological human samples in Latvia, 7-11th centuries AD. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:383-391. [PMID: 37057308 PMCID: PMC10472514 DOI: 10.1111/1758-2229.13157] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/23/2023] [Indexed: 06/19/2023]
Abstract
In the grave environment, microorganisms are major ecological participants in the successional decomposition of vertebrates and could infiltrate the skeleton/skeletal material during taphonomic processes. The diversity of archaeological skeleton-associated microbial assemblages and the impact of various factors are poorly understood. This study aimed to evaluate the taxonomic microbial composition of archaeological human bone and teeth samples from the 7th to 11th centuries AD from two burial sites in Latvia. Samples were analysed by a shotgun metagenomics-based approach. The results showed a strong presence of the environmental DNA in the samples, and variability in microbial community structure between individual samples. Differences in microbial composition were observed between bone and tooth samples, as well as between different burial sites. Furthermore, the presence of endogenous ancient DNA (aDNA) in tooth samples was detected. Overall, compositions of microbial communities associated with archaeological human remains in Latvia dated 7-11th century AD were influenced by the sample type and burial location. These findings indicate that, while the content of historical DNA in archaeological samples is low, the comparison of archaeological skeleton-associated microbial assemblages across time and space, along with aDNA damage profile analysis, is important and could help to reveal putative ancient microorganisms.
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Affiliation(s)
- Jānis Ķimsis
- Latvian Biomedical Research and Study CentreLaboratory of molecular microbiologyRigaLatvia
| | - Alise Pokšāne
- Latvian Biomedical Research and Study CentreLaboratory of molecular microbiologyRigaLatvia
| | - Alisa Kazarina
- Latvian Biomedical Research and Study CentreLaboratory of molecular microbiologyRigaLatvia
| | | | | | - Pawel Zayakin
- Latvian Biomedical Research and Study CentreLaboratory of molecular microbiologyRigaLatvia
| | | | - Renate Ranka
- Latvian Biomedical Research and Study CentreLaboratory of molecular microbiologyRigaLatvia
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2
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Kaur Boparai A, Jain A, Arora S, Abullais Saquib S, Abdullah Alqahtani N, Fadul A Elagib M, Grover V. Dental calculus - An emerging bio resource for past SARS CoV2 detection, studying its evolution and relationship with oral microflora. JOURNAL OF KING SAUD UNIVERSITY. SCIENCE 2023; 35:102646. [PMID: 36987442 PMCID: PMC10023199 DOI: 10.1016/j.jksus.2023.102646] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 02/20/2023] [Accepted: 03/13/2023] [Indexed: 05/28/2023]
Abstract
The most grievous threat to human health has been witnessed worldwide with the recent outbreak of Corona virus disease 2019 (COVID-19). There is mounting evidence available regarding theconnect of COVID -19 and oral cavity, particularly periodontal disease. The current review provides an update on the diagnostic potential of dental calculus and how this bio resource may help in providing us huge amount of diagnostic regarding the causative virus. Contemporary standard method of diagnosis via nasopharyngeal swabs (NPS) is tedious, may enhance the risk of aerosol contamination by inducing sneezing and detects the presence of active infection only.However,dental calculus being a mineralized deposit serves as a reservoir for biomoleculesand provides detection of past SARS CoV2 infection. Further, the abundance of information that can be obtained from this remarkable mineralized deposit on teeth regarding the viral genome, its evolution and interactions with the oral microflora shall enhance the understanding of the viral disease process and its connection with the periodontal disease. Additional diagnostic information, which may be obtained from this simple bio reservoir can complement the contemporary diagnostic strategies adopted in the management of COVID-19pandemic and enhance our existing knowledge for developing improvised novel approaches to mitigate the effects of mutated variants of the infectious agent.
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Affiliation(s)
| | - Ashish Jain
- Department of Periodontology & Oral Implantology, Dr. H. S. J. lnstitute Dental Sciences & Hospital, Punjab University, Chandigarh, India
| | - Suraj Arora
- Department of Restorative Dental Sciences, College of Dentistry, King Khalid University, Abha 61321, Saudi Arabia
| | - Shahabe Abullais Saquib
- Periodontics and Community Dental Sciences, College of Dentistry, King Khalid University, Abha 61321, Saudi Arabia
| | - Nabeeh Abdullah Alqahtani
- Department of Periodontics and Community Dental Sciences, College of Dentistry, King Khalid University, Abha 61321, Saudi Arabia
| | | | - Vishakha Grover
- Department of Periodontology & Oral Implantology, Dr. H. S. J. lnstitute Dental Sciences & Hospital, Punjab University, Chandigarh, India
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3
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Kumar D, Mandal S, Bailey JV, Flood BE, Jones RS. Fluoride and gallein inhibit polyphosphate accumulation by oral pathogen Rothia dentocariosa. Lett Appl Microbiol 2023; 76:ovad017. [PMID: 36715153 PMCID: PMC9990172 DOI: 10.1093/lambio/ovad017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 01/27/2023] [Indexed: 01/31/2023]
Abstract
The uptake and storage of extracellular orthophosphate (Pi) by polyphosphate (polyP) accumulating bacteria may contribute to mineral dissolution in the oral cavity. To test the effect of potential inhibitors of polyP kinases on Rothia dentocariosa, gallein (0, 25, 50, and 100 μM) and fluoride (0, 50, and 100 ppm) were added to R. dentocariosa cultures grown in brain-heart infusion broth. At a late log growth phase (8 h), extracellular Pi was measured using an ascorbic acid assay, and polyP was isolated from bacterial cells treated with RNA/DNAases using a neutral phenol/chloroform extraction. Extracts were hydrolyzed and quantified as above. Gallein and fluoride had minor effects on bacterial growth with NaF having a direct effect on media pH. Gallein (≥25 μM) and fluoride (≥50 ppm) attenuated the bacterial drawdown of extracellular Pi by 56.7% (P < 0.05) and 37.3% (P < 0.01). There was a corresponding polyP synthesis decrease of 73.2% (P < 0.0001) from gallein and 83.1% (P < 0.0001) from fluoride. Attenuated total reflectance-Fourier-transform infrared spectroscopy validated the presence of polyP and its reduced concentration in R. dentocariosa bacterial cells following gallein and fluoride treatment. Rothia dentocariosa can directly change extracellular Pi and accumulate intracellular polyP, but the mechanism is attenuated by gallein and NaF.
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Affiliation(s)
- Dhiraj Kumar
- Department of Developmental and Surgical Sciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - Subhrangshu Mandal
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jake V Bailey
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - Beverly E Flood
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - Robert S Jones
- Department of Developmental and Surgical Sciences, University of Minnesota, Minneapolis, MN 55455, USA
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4
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Shiba T, Komatsu K, Sudo T, Sawafuji R, Saso A, Ueda S, Watanabe T, Nemoto T, Kano C, Nagai T, Ohsugi Y, Katagiri S, Takeuchi Y, Kobayashi H, Iwata T. Comparison of Periodontal Bacteria of Edo and Modern Periods Using Novel Diagnostic Approach for Periodontitis With Micro-CT. Front Cell Infect Microbiol 2021; 11:723821. [PMID: 34616690 PMCID: PMC8488429 DOI: 10.3389/fcimb.2021.723821] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/17/2021] [Indexed: 11/07/2022] Open
Abstract
Ancient dental calculus, formed from dental plaque, is a rich source of ancient DNA and can provide information regarding the food and oral microbiology at that time. Genomic analysis of dental calculus from Neanderthals has revealed the difference in bacterial composition of oral microbiome between Neanderthals and modern humans. There are few reports investigating whether the pathogenic bacteria of periodontitis, a polymicrobial disease induced in response to the accumulation of dental plaque, were different between ancient and modern humans. This study aimed to compare the bacterial composition of the oral microbiome in ancient and modern human samples and to investigate whether lifestyle differences depending on the era have altered the bacterial composition of the oral microbiome and the causative bacteria of periodontitis. Additionally, we introduce a novel diagnostic approach for periodontitis in ancient skeletons using micro-computed tomography. Ancient 16S rDNA sequences were obtained from 12 samples at the Unko-in site (18th-19th century) of the Edo era (1603–1867), a characteristic period in Japan when immigrants were not accepted. Furthermore, modern 16S rDNA data from 53 samples were obtained from a database to compare the modern and ancient microbiome. The microbial co-occurrence network was analyzed based on 16S rDNA read abundance. Eubacterium species, Mollicutes species, and Treponema socranskii were the core species in the Edo co-occurrence network. The co-occurrence relationship between Actinomyces oricola and Eggerthella lenta appeared to have played a key role in causing periodontitis in the Edo era. However, Porphyromonas gingivalis, Fusobacterium nucleatum subsp. vincentii, and Prevotella pleuritidis were the core and highly abundant species in the co-occurrence network of modern samples. These results suggest the possibility of differences in the pathogens causing periodontitis during different eras in history.
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Affiliation(s)
- Takahiko Shiba
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Keiji Komatsu
- Department of Lifetime Oral Health Care Sciences, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takeaki Sudo
- Institute of Education, Tokyo Medical and Dental University, Tokyo, Japan
| | - Rikai Sawafuji
- Department of Evolutionary Studies of Biosystems, The Graduate University for Advanced Studies (SOKENDAI), Kanagawa, Japan
| | - Aiko Saso
- Department of Physical Therapy, Faculty of Rehabilitation, Niigata University of Health and Welfare, Niigata, Japan
| | - Shintaroh Ueda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan
| | - Takayasu Watanabe
- Department of Chemistry, Nihon University School of Dentistry, Tokyo, Japan
| | - Takashi Nemoto
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Chihiro Kano
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takahiko Nagai
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yujin Ohsugi
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Sayaka Katagiri
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yasuo Takeuchi
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroaki Kobayashi
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takanori Iwata
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
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5
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Nodari R, Drancourt M, Barbieri R. Paleomicrobiology of the human digestive tract: A review. Microb Pathog 2021; 157:104972. [PMID: 34029658 DOI: 10.1016/j.micpath.2021.104972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 04/23/2021] [Accepted: 05/14/2021] [Indexed: 10/21/2022]
Abstract
The microbiota is a hot topic of research in medical microbiology, boosted by culturomics and metagenomics, with unanticipated knowledge outputs in physiology and pathology. Knowledge of the microbiota in ancient populations may therefore be of prime interest in understanding factors shaping the coevolution of the microbiota and populations. Studies on ancient human microbiomes can help us understand how the community of microorganisms presents in the oral cavity and the gut was shaped during the evolution of our species and what environmental, social or cultural changes may have changed it. This review cumulates and summarizes the discoveries in the field of the ancient human microbiota, focusing on the remains used as samples and techniques used to handle and analyze them.
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Affiliation(s)
- Riccardo Nodari
- Department of Biosciences and Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", University of Milan, Milan, 20133, Italy
| | - Michel Drancourt
- Aix-Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Rémi Barbieri
- Aix-Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France; UMR 7268, Anthropologie Bioculturelle, Droit, Ethique et Santé, Aix Marseille Univ., 11 CNRS, EFS, ADES, Marseille, France.
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6
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Ozga AT, Gilby I, Nockerts RS, Wilson ML, Pusey A, Stone AC. Oral microbiome diversity in chimpanzees from Gombe National Park. Sci Rep 2019; 9:17354. [PMID: 31758037 PMCID: PMC6874655 DOI: 10.1038/s41598-019-53802-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 10/28/2019] [Indexed: 12/27/2022] Open
Abstract
Historic calcified dental plaque (dental calculus) can provide a unique perspective into the health status of past human populations but currently no studies have focused on the oral microbial ecosystem of other primates, including our closest relatives, within the hominids. Here we use ancient DNA extraction methods, shotgun library preparation, and next generation Illumina sequencing to examine oral microbiota from 19 dental calculus samples recovered from wild chimpanzees (Pan troglodytes schweinfurthii) who died in Gombe National Park, Tanzania. The resulting sequences were trimmed for quality, analyzed using MALT, MEGAN, and alignment scripts, and integrated with previously published dental calculus microbiome data. We report significant differences in oral microbiome phyla between chimpanzees and anatomically modern humans (AMH), with chimpanzees possessing a greater abundance of Bacteroidetes and Fusobacteria, and AMH showing higher Firmicutes and Proteobacteria. Our results suggest that by using an enterotype clustering method, results cluster largely based on host species. These clusters are driven by Porphyromonas and Fusobacterium genera in chimpanzees and Haemophilus and Streptococcus in AMH. Additionally, we compare a nearly complete Porphyromonas gingivalis genome to previously published genomes recovered from human gingiva to gain perspective on evolutionary relationships across host species. Finally, using shotgun sequence data we assessed indicators of diet from DNA in calculus and suggest exercising caution when making assertions related to host lifestyle. These results showcase core differences between host species and stress the importance of continued sequencing of nonhuman primate microbiomes in order to fully understand the complexity of their oral ecologies.
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Affiliation(s)
- Andrew T Ozga
- Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA. .,Institute of Human Origins, Arizona State University, Tempe, Arizona, USA. .,Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, Florida, USA.
| | - Ian Gilby
- Institute of Human Origins, Arizona State University, Tempe, Arizona, USA.,School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
| | - Rebecca S Nockerts
- Department of Anthropology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Michael L Wilson
- Department of Anthropology, University of Minnesota, Minneapolis, Minnesota, USA.,Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, Minnesota, USA
| | - Anne Pusey
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, USA
| | - Anne C Stone
- Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA.,Institute of Human Origins, Arizona State University, Tempe, Arizona, USA.,School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
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7
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Commensal and Pathogenic Members of the Dental Calculus Microbiome of Badia Pozzeveri Individuals from the 11th to 19th Centuries. Genes (Basel) 2019; 10:genes10040299. [PMID: 31013797 PMCID: PMC6523138 DOI: 10.3390/genes10040299] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/03/2019] [Accepted: 04/05/2019] [Indexed: 12/13/2022] Open
Abstract
The concept of the human oral microbiome was applied to understand health and disease, lifestyles, and dietary habits throughout part of human history. In the present study, we augment the understanding of ancient oral microbiomes by characterizing human dental calculus samples recovered from the ancient Abbey of Badia Pozzeveri (central Italy), with differences in socioeconomic status, time period, burial type, and sex. Samples dating from the Middle Ages (11th century) to the Industrial Revolution era (19th century) were characterized using high-throughput sequencing of the 16S ribosomal RNA (rRNA) gene V4 region. Consistent with previous studies, individuals from Badia Pozzeveri possessed commensal oral bacteria that resembled modern oral microbiomes. These results suggest that members of the oral microbiome are ubiquitous despite differences in geographical regions, time period, sex, and socioeconomic status. The presence of fecal bacteria could be in agreement with poor hygiene practices, consistent with the time period. Respiratory tract, nosocomial, and other rare pathogens detected in the dental calculus samples are intriguing and could suggest subject-specific comorbidities that could be reflected in the oral microbiome.
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8
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Siles JA, Öhlinger B, Cajthaml T, Kistler E, Margesin R. Characterization of soil bacterial, archaeal and fungal communities inhabiting archaeological human-impacted layers at Monte Iato settlement (Sicily, Italy). Sci Rep 2018; 8:1903. [PMID: 29382933 PMCID: PMC5789874 DOI: 10.1038/s41598-018-20347-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 01/17/2018] [Indexed: 12/05/2022] Open
Abstract
Microbial communities in human-impacted soils of ancient settlements have been proposed to be used as ecofacts (bioindicators) of different ancient anthropogenic activities. In this study, bacterial, archaeal and fungal communities inhabiting soil of three archaic layers, excavated at the archaeological site on Monte Iato (Sicily, Italy) and believed to have been created in a chronological order in archaic times in the context of periodic cultic feasts, were investigated in terms of (i) abundance (phospholipid fatty acid (PLFA) analysis and quantitative PCR)), (ii) carbon(C)-source consumption patterns (Biolog-Ecoplates) and (iii) diversity and community composition (Illumina amplicon sequencing). PLFA analyses demonstrated the existence of living bacteria and fungi in the soil samples of all three layers. The upper layer showed increased levels of organic C, which were not concomitant with an increment in the microbial abundance. In taxonomic terms, the results indicated that bacterial, archaeal and fungal communities were highly diverse, although differences in richness or diversity among the three layers were not detected for any of the communities. However, significantly different microbial C-source utilization patterns and structures of bacterial, archaeal and fungal communities in the three layers confirmed that changing features of soil microbial communities reflect different past human activities.
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Affiliation(s)
- José A Siles
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, A-6020, Innsbruck, Austria
| | - Birgit Öhlinger
- Institute of Archaeologies, University of Innsbruck, Langer Weg 11, A-6020, Innsbruck, Austria
| | - Tomas Cajthaml
- Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, CZ-142 20, Prague 4, Czech Republic
- Institute for Environmental Studies, Faculty of Science, Charles University in Prague, Benatska 2, CZ-128 01, Prague 2, Czech Republic
| | - Erich Kistler
- Institute of Archaeologies, University of Innsbruck, Langer Weg 11, A-6020, Innsbruck, Austria
| | - Rosa Margesin
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, A-6020, Innsbruck, Austria.
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