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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. Corrigendum: Comparison of Periodontal Bacteria of Edo and Modern Periods Using Novel Diagnostic Approach for Periodontitis With Micro-CT. Front Cell Infect Microbiol 2022; 12:871340. [PMID: 35493745 PMCID: PMC9044965 DOI: 10.3389/fcimb.2022.871340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 03/07/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Takahiko Shiba
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
- *Correspondence: Takahiko Shiba, ; Rikai Sawafuji, ; Hiroaki Kobayashi,
| | - 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
- The Graduate University for Advanced Studies, School of Advanced Sciences, Kanagawa, Japan
- *Correspondence: Takahiko Shiba, ; Rikai Sawafuji, ; Hiroaki Kobayashi,
| | - Aiko Saso
- Department of Physical Therapy, Faculty of Rehabilitation, Niigata University of Health and Welfare, Kita-ku, 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
- *Correspondence: Takahiko Shiba, ; Rikai Sawafuji, ; Hiroaki Kobayashi,
| | - Takanori Iwata
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Kanzawa-Kiriyama H, Kryukov K, Jinam TA, Hosomichi K, Saso A, Suwa G, Ueda S, Yoneda M, Tajima A, Shinoda KI, Inoue I, Saitou N. A partial nuclear genome of the Jomons who lived 3000 years ago in Fukushima, Japan. J Hum Genet 2016; 62:213-221. [PMID: 27581845 PMCID: PMC5285490 DOI: 10.1038/jhg.2016.110] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 07/22/2016] [Accepted: 07/26/2016] [Indexed: 12/11/2022]
Abstract
The Jomon period of the Japanese Archipelago, characterized by cord-marked ‘jomon' potteries, has yielded abundant human skeletal remains. However, the genetic origins of the Jomon people and their relationships with modern populations have not been clarified. We determined a total of 115 million base pair nuclear genome sequences from two Jomon individuals (male and female each) from the Sanganji Shell Mound (dated 3000 years before present) with the Jomon-characteristic mitochondrial DNA haplogroup N9b, and compared these nuclear genome sequences with those of worldwide populations. We found that the Jomon population lineage is best considered to have diverged before diversification of present-day East Eurasian populations, with no evidence of gene flow events between the Jomon and other continental populations. This suggests that the Sanganji Jomon people descended from an early phase of population dispersals in East Asia. We also estimated that the modern mainland Japanese inherited <20% of Jomon peoples' genomes. Our findings, based on the first analysis of Jomon nuclear genome sequence data, firmly demonstrate that the modern mainland Japanese resulted from genetic admixture of the indigenous Jomon people and later migrants.
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Affiliation(s)
- Hideaki Kanzawa-Kiriyama
- Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Mishima, Japan.,Division of Population Genetics, National Institute of Genetics, Mishima, Japan
| | - Kirill Kryukov
- Department of Molecular Life Science, School of Medicine, Tokai University, Isehara, Japan
| | - Timothy A Jinam
- Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Mishima, Japan.,Division of Population Genetics, National Institute of Genetics, Mishima, Japan
| | - Kazuyoshi Hosomichi
- Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Mishima, Japan.,Division of Human Genetics, National Institute of Genetics, Mishima, Japan
| | - Aiko Saso
- The University Museum, The University of Tokyo, Tokyo, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Gen Suwa
- The University Museum, The University of Tokyo, Tokyo, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Shintaroh Ueda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Minoru Yoneda
- The University Museum, The University of Tokyo, Tokyo, Japan
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Ken-Ichi Shinoda
- Department of Anthropology, National Museum of Nature and Science, Tsukuba, Japan
| | - Ituro Inoue
- Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Mishima, Japan.,Division of Human Genetics, National Institute of Genetics, Mishima, Japan
| | - Naruya Saitou
- Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Mishima, Japan.,Division of Population Genetics, National Institute of Genetics, Mishima, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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Suzuki K, Saso A, Hoshino K, Sakurai J, Tanigawa K, Luo Y, Ishido Y, Mori S, Hirata K, Ishii N. Paleopathological evidence and detection of Mycobacterium leprae DNA from archaeological skeletal remains of Nabe-kaburi (head-covered with iron pots) burials in Japan. PLoS One 2014; 9:e88356. [PMID: 24516638 PMCID: PMC3917912 DOI: 10.1371/journal.pone.0088356] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 01/11/2014] [Indexed: 11/18/2022] Open
Abstract
The Nabe-kaburi is a unique burial method, the purpose of which is shrouded in mystery. The burials were performed during the 15th to 18th centuries in eastern Japan, and involved covering the heads of the deceased with iron pots or mortars. The identification of leprosy-specific osteological lesions among some of the excavated remains has led to the suggestion that Nabe-kaburi burials were a reflection of the social stigma against certain infectious diseases, such as leprosy, tuberculosis or syphilis. However, molecular evidence for the presence of disease has been lacking. The goal of this study was to detect Mycobacterium leprae (M. leprae) DNA in archaeological human skeletal remains from Nabe-kaburi burials. The paleopathological data from three Nabe-kaburi burials were re-evaluated before small samples were taken from affected and control areas. DNA was extracted and used as a template to target the M. leprae-specific DNA using a combination of whole genome amplification, PCR analysis and DNA sequencing. M. leprae DNA fragments were detected in the two sets of skeletal remains that had also shown paleopathological evidence of leprosy. These findings provide definitive evidence that some of the Nabe-kaburi burials were performed for people affected by leprosy. Demonstration of the presence of M. leprae DNA, combined with archeological and anthropological examinations, will aid in solving the mystery of why Nabe-kaburi burials were performed in medieval Japan.
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Affiliation(s)
- Koichi Suzuki
- Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- * E-mail:
| | - Aiko Saso
- The University Museum, The University of Tokyo, Tokyo, Japan
- Department of Biological Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Keigo Hoshino
- Department of Anatomy, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Junya Sakurai
- Faculty of Policy Management, Shobi University, Kawagoe, Japan
| | - Kazunari Tanigawa
- Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yuqian Luo
- Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yuko Ishido
- Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shuichi Mori
- Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kazuaki Hirata
- Department of Anatomy, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Norihisa Ishii
- Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
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