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Podar NA, Carrell AA, Cassidy KA, Klingeman DM, Yang Z, Stahler EA, Smith DW, Stahler DR, Podar M. From wolves to humans: oral microbiome resistance to transfer across mammalian hosts. mBio 2024; 15:e0334223. [PMID: 38299854 PMCID: PMC10936156 DOI: 10.1128/mbio.03342-23] [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: 12/18/2023] [Accepted: 12/21/2023] [Indexed: 02/02/2024] Open
Abstract
The mammalian mouth is colonized by complex microbial communities, adapted to specific niches, and in homeostasis with the host. Individual microbes interact metabolically and rely primarily on nutrients provided by the host, with which they have potentially co-evolved along the mammalian lineages. The oral environment is similar across mammals, but the diversity, specificity, and evolution of community structure in related or interacting mammals are little understood. Here, we compared the oral microbiomes of dogs with those of wild wolves and humans. In dogs, we found an increased microbial diversity relative to wolves, possibly related to the transition to omnivorous nutrition following domestication. This includes a larger diversity of Patescibacteria than previously reported in any other oral microbiota. The oral microbes are most distinct at bacterial species or strain levels, with few if any shared between humans and canids, while the close evolutionary relationship between wolves and dogs is reflected by numerous shared taxa. More taxa are shared at higher taxonomic levels including with humans, supporting their more ancestral common mammalian colonization followed by diversification. Phylogenies of selected oral bacterial lineages do not support stable human-dog microbial transfers but suggest diversification along mammalian lineages (apes and canids). Therefore, despite millennia of cohabitation and close interaction, the host and its native community controls and limits the assimilation of new microbes, even if closely related. Higher resolution metagenomic and microbial physiological studies, covering a larger mammalian diversity, should help understand how oral communities assemble, adapt, and interact with their hosts.IMPORTANCENumerous types of microbes colonize the mouth after birth and play important roles in maintaining oral health. When the microbiota-host homeostasis is perturbed, proliferation of some bacteria leads to diseases such as caries and periodontitis. Unlike the gut microbiome, the diversity of oral microbes across the mammalian evolutionary space is not understood. Our study compared the oral microbiomes of wild wolves, dogs, and apes (humans, chimpanzees, and bonobos), with the aim of identifying if microbes have been potentially exchanged between humans and dogs as a result of domestication and cohabitation. We found little if any evidence for such exchanges. The significance of our research is in finding that the oral microbiota and/or the host limit the acquisition of exogenous microbes, which is important in the context of natural exclusion of potential novel pathogens. We provide a framework for expanded higher-resolution studies across domestic and wild animals to understand resistance/resilience.
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Affiliation(s)
- Nicholas A. Podar
- School of Engineering, Vanderbilt University, Nashville, Tennessee, USA
| | - Alyssa A. Carrell
- Biosciences Department, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Kira A. Cassidy
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, Wyoming, USA
| | - Dawn M. Klingeman
- Biosciences Department, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Zamin Yang
- Biosciences Department, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Erin A. Stahler
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, Wyoming, USA
| | - Douglas W. Smith
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, Wyoming, USA
| | - Daniel R. Stahler
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, Wyoming, USA
| | - Mircea Podar
- Biosciences Department, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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2
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Michel A, Minocher R, Niehoff PP, Li Y, Nota K, Gadhvi MA, Su J, Iyer N, Porter A, Ngobobo-As-Ibungu U, Binyinyi E, Nishuli Pekeyake R, Parducci L, Caillaud D, Guschanski K. Isolated Grauer's gorilla populations differ in diet and gut microbiome. Mol Ecol 2023; 32:6523-6542. [PMID: 35976262 DOI: 10.1111/mec.16663] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 08/09/2022] [Accepted: 08/11/2022] [Indexed: 11/30/2022]
Abstract
The animal gut microbiome has been implicated in a number of key biological processes, ranging from digestion to behaviour, and has also been suggested to facilitate local adaptation. Yet studies in wild animals rarely compare multiple populations that differ ecologically, which is the level at which local adaptation may occur. Further, few studies simultaneously characterize diet and gut microbiome from the same sample, despite their probable interdependence. Here, we investigate the interplay between diet and gut microbiome in three geographically isolated populations of the critically endangered Grauer's gorilla (Gorilla beringei graueri), which we show to be genetically differentiated. We find population- and social group-specific dietary and gut microbial profiles and covariation between diet and gut microbiome, despite the presence of core microbial taxa. There was no detectable effect of age, and only marginal effects of sex and genetic relatedness on the microbiome. Diet differed considerably across populations, with the high-altitude population consuming a lower diversity of plants compared to low-altitude populations, consistent with plant availability constraining dietary choices. The observed pattern of covariation between diet and gut microbiome is probably a result of long-term social and environmental factors. Our study suggests that the gut microbiome is sufficiently plastic to support flexible food selection and hence contribute to local adaptation.
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Affiliation(s)
- Alice Michel
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- Department of Anthropology, University of California, Davis, California, USA
| | - Riana Minocher
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- Department of Human Behavior, Ecology and Culture, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Peter-Philip Niehoff
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Yuhong Li
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- Conservation Ecology Group, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Kevin Nota
- Plant Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Maya A Gadhvi
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Jiancheng Su
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Neetha Iyer
- Department of Anthropology, University of California, Davis, California, USA
| | - Amy Porter
- Department of Anthropology, University of California, Davis, California, USA
| | | | - Escobar Binyinyi
- The Dian Fossey Gorilla Fund International, Kinshasa, Democratic Republic of the Congo
| | - Radar Nishuli Pekeyake
- Institut Congolais pour la Conservation de la Nature, Kinshasa, Democratic Republic of the Congo
| | - Laura Parducci
- Department of Human Behavior, Ecology and Culture, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - Damien Caillaud
- Department of Anthropology, University of California, Davis, California, USA
| | - Katerina Guschanski
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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3
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Klapper M, Hübner A, Ibrahim A, Wasmuth I, Borry M, Haensch VG, Zhang S, Al-Jammal WK, Suma H, Fellows Yates JA, Frangenberg J, Velsko IM, Chowdhury S, Herbst R, Bratovanov EV, Dahse HM, Horch T, Hertweck C, González Morales MR, Straus LG, Vilotijevic I, Warinner C, Stallforth P. Natural products from reconstructed bacterial genomes of the Middle and Upper Paleolithic. Science 2023; 380:619-624. [PMID: 37141315 DOI: 10.1126/science.adf5300] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
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.
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Affiliation(s)
- Martin Klapper
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Alexander Hübner
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Anan Ibrahim
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Ina Wasmuth
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Maxime Borry
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Veit G Haensch
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Shuaibing Zhang
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Walid K Al-Jammal
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Harikumar Suma
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - James A Fellows Yates
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Jasmin Frangenberg
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Irina M Velsko
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Somak Chowdhury
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Rosa Herbst
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Evgeni V Bratovanov
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Hans-Martin Dahse
- Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Therese Horch
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
- Faculty of Biological Sciences, Institute of Microbiology, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Manuel Ramon González Morales
- Instituto Internacional de Investigaciones Prehistóricas de Cantabria, Universidad de Cantabria, 39071 Santander, Spain
| | - Lawrence Guy Straus
- Department of Anthropology, University of New Mexico, Albuquerque, NM 87131, USA
- Grupo I+D+i EvoAdapta, Departmento de Ciencias Históricas, Universidad de Cantabria, 39005 Santander, Spain
| | - Ivan Vilotijevic
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
- Faculty of Biological Sciences, Institute of Microbiology, Friedrich Schiller University Jena, 07743 Jena, Germany
- Department of Anthropology, Harvard University, Cambridge, MA 02138, USA
| | - Pierre Stallforth
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany
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4
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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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5
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Ozga AT, Ottoni C. Dental calculus as a proxy for animal microbiomes. QUATERNARY INTERNATIONAL : THE JOURNAL OF THE INTERNATIONAL UNION FOR QUATERNARY RESEARCH 2023; 653-654:47-52. [PMID: 37559969 PMCID: PMC7614904 DOI: 10.1016/j.quaint.2021.06.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
The field of dental calculus research has exploded in recent years, predominantly due to the multitude of studies related to human genomes and oral pathogens. Despite having a subset of these studies devoted to non-human primates, little progress has been made in the distribution of oral pathogens across domestic and wild animal populations. This overlooked avenue of research is particularly important at present when many animal populations with the potentiality for zoonotic transmission continue to reside in close proximity to human groups due to reasons such as deforestation and climatic impacts on resource availability. Here, we analyze all previously available published oral microbiome data recovered from the skeletal remains of animals, all of which belong to the Mammalia class. Our genus level results emphasize the tremendous diversity of oral ecologies across mammals in spite of the clustering based primarily on host species. We also discuss the caveats and flaws in analyzing ancient animal oral microbiomes at the species level of classification. Lastly, we assess the benefits, challenges, and gaps in the current knowledge of dental calculus research within animals and postulate the future of the field as a whole.
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Affiliation(s)
- Andrew T. Ozga
- Nova Southeastern University, Halmos College of Arts and Sciences, Fort Lauderdale, FL, 33314, USA
| | - Claudio Ottoni
- DANTE - Diet and ANcient TEchnology Laboratory, Department of Oral and Maxillo-Facial Sciences, “Sapienza” University of Rome, 00161, Rome, Italy
- Centre of Molecular Anthropology for Ancient DNA Studies; Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
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6
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Warinner C. An Archaeology of Microbes. JOURNAL OF ANTHROPOLOGICAL RESEARCH 2022. [DOI: 10.1086/721976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Christina Warinner
- Department of Anthropology, Harvard University, Cambridge MA, USA 02138, and Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany 04103
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7
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Moraitou M, Forsythe A, Fellows Yates JA, Brealey JC, Warinner C, Guschanski K. Ecology, Not Host Phylogeny, Shapes the Oral Microbiome in Closely Related Species. Mol Biol Evol 2022; 39:6874787. [PMID: 36472532 PMCID: PMC9778846 DOI: 10.1093/molbev/msac263] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/25/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Host-associated microbiomes are essential for a multitude of biological processes. Placed at the contact zone between external and internal environments, the little-studied oral microbiome has important roles in host physiology and health. Here, we investigate the roles of host evolutionary relationships and ecology in shaping the oral microbiome in three closely related gorilla subspecies (mountain, Grauer's, and western lowland gorillas) using shotgun metagenomics of 46 museum-preserved dental calculus samples. We find that the oral microbiomes of mountain gorillas are functionally and taxonomically distinct from the other two subspecies, despite close evolutionary relationships and geographic proximity with Grauer's gorillas. Grauer's gorillas show intermediate bacterial taxonomic and functional, and dietary profiles. Altitudinal differences in gorilla subspecies ranges appear to explain these patterns, suggesting a close connection between dental calculus microbiomes and the environment, likely mediated through diet. This is further supported by the presence of gorilla subspecies-specific phyllosphere/rhizosphere taxa in the oral microbiome. Mountain gorillas show a high abundance of nitrate-reducing oral taxa, which may promote adaptation to a high-altitude lifestyle by modulating blood pressure. Our results suggest that ecology, rather than evolutionary relationships and geographic distribution, shape the oral microbiome in these closely related species.
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Affiliation(s)
| | | | - James A Fellows Yates
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany,Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, 07745 Jena, Germany
| | - Jaelle C Brealey
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany,Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, 07745 Jena, Germany,Faculty of Biological Sciences, Friedrich Schiller University, 07743 Jena, Germany,Department of Anthropology, Harvard University, Cambridge, MA 02138, USA
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8
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Adi Wicaksono W, Braun M, Bernhardt J, Riedel K, Cernava T, Berg G. Trade-off for survival: Microbiome response to chemical exposure combines activation of intrinsic resistances and adapted metabolic activity. ENVIRONMENT INTERNATIONAL 2022; 168:107474. [PMID: 35988321 DOI: 10.1016/j.envint.2022.107474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
The environmental microbiota is increasingly exposed to chemical pollution. While the emergence of multi-resistant pathogens is recognized as a global challenge, our understanding of antimicrobial resistance (AMR) development from native microbiomes and the risks associated with chemical exposure is limited. By implementing a lichen asa bioindicatororganism and model for a native microbiome, we systematically examined responses towards antimicrobials (colistin, tetracycline, glyphosate, and alkylpyrazine). Despite an unexpectedly high resilience, we identified potential evolutionary consequences of chemical exposure in terms of composition and functioning of native bacterial communities. Major shifts in bacterial composition were observed due to replacement of naturally abundant taxa; e.g. Chthoniobacterales by Pseudomonadales. A general response, which comprised activation of intrinsic resistance and parallel reduction of metabolic activity at RNA and protein levels was deciphered by a multi-omics approach. Targeted analyses of key taxa based on metagenome-assembled genomes reflected these responses but also revealed diversified strategies of their players. Chemical-specific responses were also observed, e.g., glyphosate enriched bacterial r-strategists and activated distinct ARGs. Our work demonstrates that the high resilience of the native microbiota toward antimicrobial exposure is not only explained by the presence of antibiotic resistance genes but also adapted metabolic activity as a trade-off for survival. Moreover, our results highlight the importance of native microbiomes as important but so far neglected AMR reservoirs. We expect that this phenomenon is representative for a wide range of environmental microbiota exposed to chemicals that potentially contribute to the emergence of antibiotic-resistant bacteria from natural environments.
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Affiliation(s)
- Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.
| | - Maria Braun
- Institute of Microbiology, University of Greifswald, Greifswald, Germany.
| | - Jörg Bernhardt
- Institute of Microbiology, University of Greifswald, Greifswald, Germany.
| | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Greifswald, Germany.
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria; Leibniz-Institute for Agricultural Engineering and Bioeconomy Potsdam (ATB), Potsdam, Germany; Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
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9
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Wang R, Jia C, Zheng N, Liu S, Qi Z, Wang R, Zhang L, Niu Y, Pan S. Effects of Photodynamic Therapy on Streptococcus mutans and Enamel Remineralization of Multifunctional TiO2-HAP Composite Nanomaterials. Photodiagnosis Photodyn Ther 2022; 42:103141. [PMID: 36202321 DOI: 10.1016/j.pdpdt.2022.103141] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/05/2022] [Accepted: 09/29/2022] [Indexed: 01/19/2023]
Abstract
BACKGROUND As photosensitizer and photocatalyst, titanium dioxide (TiO2) can produce a photodynamic reaction for antibacterial treatment. This study aims to explore a Titanium dioxide/nano-hydroxyapatite (TiO2-HAP) composite combined with the dental curing lamp (385-515 nm) in clinical which could inhibit the dental plaque biofilm formed by Streptococcus mutans (S. mutans) and promote the enamel surface remineralization simultaneously. METHODS X-ray Diffraction (XRD) and high resolution transmission electron microscope (HRTEM) were used to detect the characterization of TiO2-HAP composite nanomaterials. Photodynamic properties of TiO2-HAP were detected by Diffuse reflectance spectrum (DRS) and fluorescence spectroscopy. Bacterial growth was measured by reading the absorbance of bacterial cultures and confocal microscope was used to observe the biofilm removal ability of nanomaterials. The ability of TiO2-HAP to promote enamel remineralization was measured by Scanning electron microscope (SEM). RESULTS The OD 600 of S. mutans was 0.76 in the control group and 0.13 in group of TiO2-HAP with exposure to light-emitting diode (LED) (150 mW/cm2) for 5 min, suggesting its sustained antibacterial potency and inhibition of the metabolic activity of dental plaque microcosm biofilm. Also, the release of calcium and phosphorus ions in TiO2-HAP can promote enamel mineralization simultaneously. After 15 days of remineralization, the Ca/P ratio of demineralized enamel surface increased from 1.28 to 1.67, which was similar to that of normal enamel. CONCLUSIONS The TiO2-HAP exhibit a promising anti-bacterial activity and remineralization capacity which can prevent the occurrence of caries to the greatest extent and promote the biomimetic mineralization of dental tissues.
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Affiliation(s)
- Ranxu Wang
- The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, China
| | - Conghui Jia
- The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, China
| | - Nannan Zheng
- School of Life Science and Technology, Key Laboratory of Micro-systems and Micro-structures Manufacturing Ministry of Education, Micro/Nano Technology Research Center, Harbin Institute of Technology, Harbin 150080, China
| | - Shujuan Liu
- School of Materials Science and Engineering, Harbin Institute of Technology, Harbin 150001, PR China
| | - Zhilin Qi
- School of Life Science and Technology, Key Laboratory of Micro-systems and Micro-structures Manufacturing Ministry of Education, Micro/Nano Technology Research Center, Harbin Institute of Technology, Harbin 150080, China
| | - Ruiwen Wang
- Material Science and Engineering college, Northeast Forestry University, Harbin, Heilongjiang 150080, China
| | - Lu Zhang
- School of Life Science and Technology, Key Laboratory of Micro-systems and Micro-structures Manufacturing Ministry of Education, Micro/Nano Technology Research Center, Harbin Institute of Technology, Harbin 150080, China
| | - Yumei Niu
- The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, China.
| | - Shuang Pan
- The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, China.
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10
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Velsko IM, Semerau L, Inskip SA, García-Collado MI, Ziesemer K, Ruber MS, Benítez de Lugo Enrich L, Molero García JM, Valle DG, Peña Ruiz AC, Salazar-García DC, Hoogland MLP, Warinner C. Ancient dental calculus preserves signatures of biofilm succession and interindividual variation independent of dental pathology. PNAS NEXUS 2022; 1:pgac148. [PMID: 36714834 PMCID: PMC9802386 DOI: 10.1093/pnasnexus/pgac148] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/29/2022] [Indexed: 02/01/2023]
Abstract
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.
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Affiliation(s)
- Irina M Velsko
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Lena Semerau
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany.,Faculty of Biological Sciences, Friedrich Schiller University, Jena 07743, Germany
| | - Sarah A Inskip
- School of Archaeology and Ancient History, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Maite I García-Collado
- GIPYPAC, Department of Geography, Prehistory and Archaeology, University of the Basque Country, Leioa 48940, Spain.,BioArCh, Department of Archaeology, University of York, York YO10 5NG, UK
| | - Kirsten Ziesemer
- University Library, Vrije Universiteit, Einsteinweg 2, Amsterdam 1081 HV, The Netherlands
| | - Maria Serrano Ruber
- School of Archaeology and Ancient History, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Luis Benítez de Lugo Enrich
- Departmento de Prehistoria, Historia Antigua y Arqueología, Universidad Complutense de Madrid, Madrid 28040, Spain
| | | | - David Gallego Valle
- Facultad de Letras, Universidad de Castilla-La Mancha, Ciudad Real 13004, Spain
| | | | - Domingo C Salazar-García
- Departament de Prehistòria, Historia i Arqueología, Universitat de València, València 46010, Spain.,Department of Geological Sciences, University of Cape Town, Rondebosch 7701, South Africa
| | - Menno L P Hoogland
- Faculty of Archaeology, Leiden University, Einsteinweg, Leiden 2333 CC, The Netherlands
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany.,Faculty of Biological Sciences, Friedrich Schiller University, Jena 07743, Germany.,Department of Anthropology, Harvard University, Cambridge, MA 02138, USA
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11
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Gao Y, Kang K, Luo B, Sun X, Lan F, He J, Wu Y. Graphene oxide and mineralized collagen-functionalized dental implant abutment with effective soft tissue seal and romotely repeatable photodisinfection. Regen Biomater 2022; 9:rbac024. [PMID: 35529047 PMCID: PMC9071057 DOI: 10.1093/rb/rbac024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 03/21/2022] [Accepted: 04/10/2022] [Indexed: 11/13/2022] Open
Abstract
Grasping the boundary of antibacterial function may be better for the sealing of soft tissue around dental implant abutment. Inspired by ‘overdone is worse than undone’, we prepared a sandwich-structured dental implant coating on the percutaneous part using graphene oxide (GO) wrapped under mineralized collagen. Our unique coating structure ensured the high photothermal conversion capability and good photothermal stability of GO. The prepared coating not only achieved suitable inhibition on colonizing bacteria growth of Streptococcus sanguinis, Fusobacterium nucleatum and Porphyromonas gingivalis but also disrupted the wall/membrane permeability of free bacteria. Further enhancements on the antibacterial property were generally observed through the additional incorporation of dimethylaminododecyl methacrylate. Additionally, the coating with sandwich structure significantly enhanced the adhesion, cytoskeleton organization and proliferation of human gingival fibroblasts, which was effective to improve soft tissue sealing. Furthermore, cell viability was preserved when cells and bacteria were cultivated in the same environment by a coculture assay. This was attributed to the sandwich structure and mineralized collagen as the outmost layer, which would protect tissue cells from photothermal therapy and GO, as well as accelerate the recovery of cell activity. Overall, the coating design would provide a useful alternative method for dental implant abutment surface modification and functionalization.
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Affiliation(s)
- Yichun Gao
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, P. R. China
| | - Ke Kang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, P. R. China
| | - Bin Luo
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, P. R. China
| | - Xiaoqing Sun
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, P. R. China
| | - Fang Lan
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, P. R. China
| | - Jing He
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, P. R. China
| | - Yao Wu
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, P. R. China
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12
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Abstract
Like modern metagenomics, ancient metagenomics is a highly data-rich discipline, with the added challenge that the DNA of interest is degraded and, depending on the sample type, in low abundance. This requires the application of specialized measures during molecular experiments and computational analyses. Furthermore, researchers often work with finite sample sizes, which impedes optimal experimental design and control of confounding factors, and with ethically sensitive samples necessitating the consideration of additional guidelines. In September 2020, early career researchers in the field of ancient metagenomics met (Standards, Precautions & Advances in Ancient Metagenomics 2 [SPAAM2] community meeting) to discuss the state of the field and how to address current challenges. Here, in an effort to bridge the gap between ancient and modern metagenomics, we highlight and reflect upon some common misconceptions, provide a brief overview of the challenges in our field, and point toward useful resources for potential reviewers and newcomers to the field.
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13
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Abstract
Natural history collections are invaluable repositories of biological information that provide an unrivaled record of Earth's biodiversity. Museum genomics-genomics research using traditional museum and cryogenic collections and the infrastructure supporting these investigations-has particularly enhanced research in ecology and evolutionary biology, the study of extinct organisms, and the impact of anthropogenic activity on biodiversity. However, leveraging genomics in biological collections has exposed challenges, such as digitizing, integrating, and sharing collections data; updating practices to ensure broadly optimal data extraction from existing and new collections; and modernizing collections practices, infrastructure, and policies to ensure fair, sustainable, and genomically manifold uses of museum collections by increasingly diverse stakeholders. Museum genomics collections are poised to address these challenges and, with increasingly sensitive genomics approaches, will catalyze a future era of reproducibility, innovation, and insight made possible through integrating museum and genome sciences.
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Affiliation(s)
- Daren C Card
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California 95064, USA.,Howard Hughes Medical Institute, University of California, Santa Cruz, California 95064, USA
| | - Gonzalo Giribet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Craig Moritz
- Centre for Biodiversity Analysis and Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA
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14
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Brealey JC, Leitão HG, Hofstede T, Kalthoff DC, Guschanski K. The oral microbiota of wild bears in Sweden reflects the history of antibiotic use by humans. Curr Biol 2021; 31:4650-4658.e6. [PMID: 34437844 DOI: 10.1016/j.cub.2021.08.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/23/2021] [Accepted: 08/02/2021] [Indexed: 12/23/2022]
Abstract
Following the advent of industrial-scale antibiotic production in the 1940s,1 antimicrobial resistance (AMR) has been on the rise and now poses a major global health threat in terms of mortality, morbidity, and economic burden.2,3 Because AMR can be exchanged between humans, livestock, and wildlife, wild animals can be used as indicators of human-associated AMR contamination of the environment.4 However, AMR is a normal function of natural environments and is present in host-associated microbiomes, which makes it challenging to distinguish between anthropogenic and natural sources.4,5 One way to overcome this difficulty is to use historical samples that span the period from before the mass production of antibiotics to today. We used shotgun metagenomic sequencing of dental calculus, the calcified form of the oral microbial biofilm, to determine the abundance and repertoire of AMR genes in the oral microbiome of Swedish brown bears collected over the last 180 years. Our temporal metagenomics approach allowed us to establish a baseline of natural AMR in the pre-antibiotics era and to quantify a significant increase in total AMR load and diversity of AMR genes that is consistent with patterns of national human antibiotic use. We also demonstrated a significant decrease in total AMR load in bears in the last two decades, which coincides with Swedish strategies to mitigate AMR. Our study suggests that public health policies can be effective in limiting human-associated AMR contamination of the environment and wildlife.
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Affiliation(s)
- Jaelle C Brealey
- Department of Ecology and Genetics/Animal Ecology, Uppsala University, Norbyvägen 18D, Uppsala 75236, Sweden.
| | - Henrique G Leitão
- Department of Ecology and Genetics/Animal Ecology, Uppsala University, Norbyvägen 18D, Uppsala 75236, Sweden
| | - Thijs Hofstede
- Department of Ecology and Genetics/Animal Ecology, Uppsala University, Norbyvägen 18D, Uppsala 75236, Sweden
| | - Daniela C Kalthoff
- Department of Zoology, Swedish Museum of Natural History, PO Box 50007, Stockholm 10405, Sweden
| | - Katerina Guschanski
- Department of Ecology and Genetics/Animal Ecology, Uppsala University, Norbyvägen 18D, Uppsala 75236, Sweden; Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Ashworth Laboratories, The Kings Buildings, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK.
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15
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Granehäll L, Huang KD, Tett A, Manghi P, Paladin A, O’Sullivan N, Rota-Stabelli O, Segata N, Zink A, Maixner F. Metagenomic analysis of ancient dental calculus reveals unexplored diversity of oral archaeal Methanobrevibacter. MICROBIOME 2021; 9:197. [PMID: 34593021 PMCID: PMC8485483 DOI: 10.1186/s40168-021-01132-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 07/01/2021] [Indexed: 05/22/2023]
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. Video abstract.
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Affiliation(s)
- Lena Granehäll
- Institute for Mummy Studies, Eurac Research, 39100 Bolzano, Italy
- Faculty of Biology, Department of Biology II, Anthropology and Human Genomics, Ludwig-Maximilians-University of Munich, 82152 Planegg-Martinsried, Germany
| | - Kun D. Huang
- CIBIO Department, University of Trento, 38123 Trento, Italy
- Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy
| | - Adrian Tett
- CIBIO Department, University of Trento, 38123 Trento, Italy
- CUBE - Division of Computational Systems Biology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Paolo Manghi
- CIBIO Department, University of Trento, 38123 Trento, Italy
| | - Alice Paladin
- Institute for Mummy Studies, Eurac Research, 39100 Bolzano, Italy
| | - Niall O’Sullivan
- Institute for Mummy Studies, Eurac Research, 39100 Bolzano, Italy
| | - Omar Rota-Stabelli
- Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy
- Center Agriculture Food Environment, University of Trento, 38123 Trento, Italy
| | - Nicola Segata
- CIBIO Department, University of Trento, 38123 Trento, Italy
| | - Albert Zink
- Institute for Mummy Studies, Eurac Research, 39100 Bolzano, Italy
| | - Frank Maixner
- Institute for Mummy Studies, Eurac Research, 39100 Bolzano, Italy
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16
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Ottoni C, Borić D, Cheronet O, Sparacello V, Dori I, Coppa A, Antonović D, Vujević D, Price TD, Pinhasi R, Cristiani E. Tracking the transition to agriculture in Southern Europe through ancient DNA analysis of dental calculus. Proc Natl Acad Sci U S A 2021; 118:e2102116118. [PMID: 34312252 PMCID: PMC8364157 DOI: 10.1073/pnas.2102116118] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Archaeological dental calculus, or mineralized plaque, is a key tool to track the evolution of oral microbiota across time in response to processes that impacted our culture and biology, such as the rise of farming during the Neolithic. However, the extent to which the human oral flora changed from prehistory until present has remained elusive due to the scarcity of data on the microbiomes of prehistoric humans. Here, we present our reconstruction of oral microbiomes via shotgun metagenomics of dental calculus in 44 ancient foragers and farmers from two regions playing a pivotal role in the spread of farming across Europe-the Balkans and the Italian Peninsula. We show that the introduction of farming in Southern Europe did not alter significantly the oral microbiomes of local forager groups, and it was in particular associated with a higher abundance of the species Olsenella sp. oral taxon 807. The human oral environment in prehistory was dominated by a microbial species, Anaerolineaceae bacterium oral taxon 439, that diversified geographically. A Near Eastern lineage of this bacterial commensal dispersed with Neolithic farmers and replaced the variant present in the local foragers. Our findings also illustrate that major taxonomic shifts in human oral microbiome composition occurred after the Neolithic and that the functional profile of modern humans evolved in recent times to develop peculiar mechanisms of antibiotic resistance that were previously absent.
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Affiliation(s)
- Claudio Ottoni
- DANTE - Diet and Ancient Technology Laboratory, Department of Oral and Maxillo-Facial Sciences, Sapienza University of Rome, 00161 Rome, Italy;
| | - Dušan Borić
- The Italian Academy for Advanced Studies in America, Columbia University, New York, NY 10027
- Department of Environmental Biology, Sapienza University of Rome, 00185 Rome, Italy
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
| | - Vitale Sparacello
- Department of Environmental and Life Sciences, University of Cagliari, 09042 Monserrato, Italy
| | - Irene Dori
- Soprintendenza Archeologia, Belle Arti e Paesaggio per le province di Verona, Rovigo e Vicenza, 37121 Verona, Italy
| | - Alfredo Coppa
- Department of Environmental Biology, Sapienza University of Rome, 00185 Rome, Italy
- Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
- Department of Genetics, Harvard Medical School, Harvard University, Cambridge, MA 02138
| | | | - Dario Vujević
- Department of Archaeology, University of Zadar, 23000 Zadar, Croatia
| | - T Douglas Price
- Laboratory for Archaeological Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
| | - Emanuela Cristiani
- DANTE - Diet and Ancient Technology Laboratory, Department of Oral and Maxillo-Facial Sciences, Sapienza University of Rome, 00161 Rome, Italy;
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17
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Borry M, Hübner A, Rohrlach AB, Warinner C. PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly. PeerJ 2021; 9:e11845. [PMID: 34395085 PMCID: PMC8323603 DOI: 10.7717/peerj.11845] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 07/01/2021] [Indexed: 01/19/2023] Open
Abstract
DNA de novo assembly can be used to reconstruct longer stretches of DNA (contigs), including genes and even genomes, from short DNA sequencing reads. Applying this technique to metagenomic data derived from archaeological remains, such as paleofeces and dental calculus, we can investigate past microbiome functional diversity that may be absent or underrepresented in the modern microbiome gene catalogue. However, compared to modern samples, ancient samples are often burdened with environmental contamination, resulting in metagenomic datasets that represent mixtures of ancient and modern DNA. The ability to rapidly and reliably establish the authenticity and integrity of ancient samples is essential for ancient DNA studies, and the ability to distinguish between ancient and modern sequences is particularly important for ancient microbiome studies. Characteristic patterns of ancient DNA damage, namely DNA fragmentation and cytosine deamination (observed as C-to-T transitions) are typically used to authenticate ancient samples and sequences, but existing tools for inspecting and filtering aDNA damage either compute it at the read level, which leads to high data loss and lower quality when used in combination with de novo assembly, or require manual inspection, which is impractical for ancient assemblies that typically contain tens to hundreds of thousands of contigs. To address these challenges, we designed PyDamage, a robust, automated approach for aDNA damage estimation and authentication of de novo assembled aDNA. PyDamage uses a likelihood ratio based approach to discriminate between truly ancient contigs and contigs originating from modern contamination. We test PyDamage on both on simulated aDNA data and archaeological paleofeces, and we demonstrate its ability to reliably and automatically identify contigs bearing DNA damage characteristic of aDNA. Coupled with aDNA de novo assembly, Pydamage opens up new doors to explore functional diversity in ancient metagenomic datasets.
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Affiliation(s)
- Maxime Borry
- Microbiome Sciences Group, Max Planck Institute for the Science of Human History, Department of Archaeogenetics, Jena, Germany
| | - Alexander Hübner
- Microbiome Sciences Group, Max Planck Institute for the Science of Human History, Department of Archaeogenetics, Jena, Germany.,Faculty of Biological Sciences, Friedrich-Schiller Universität Jena, Jena, Germany
| | - Adam B Rohrlach
- Population Genetics Group, Max Planck Institute for the Science of Human History, Department of Archaeogenetics, Jena, Germany.,ARC Centre of Excellence for Mathematical and Statistical Frontiers, The University of Adelaide, Adelaide, Australia
| | - Christina Warinner
- Microbiome Sciences Group, Max Planck Institute for the Science of Human History, Department of Archaeogenetics, Jena, Germany.,Faculty of Biological Sciences, Friedrich-Schiller Universität Jena, Jena, Germany.,Department of Anthropology, Harvard University, Cambridge, MA, United States of America
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18
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Wibowo MC, Yang Z, Borry M, Hübner A, Huang KD, Tierney BT, Zimmerman S, Barajas-Olmos F, Contreras-Cubas C, García-Ortiz H, Martínez-Hernández A, Luber JM, Kirstahler P, Blohm T, Smiley FE, Arnold R, Ballal SA, Pamp SJ, Russ J, Maixner F, Rota-Stabelli O, Segata N, Reinhard K, Orozco L, Warinner C, Snow M, LeBlanc S, Kostic AD. Reconstruction of ancient microbial genomes from the human gut. Nature 2021; 594:234-239. [PMID: 33981035 PMCID: PMC8189908 DOI: 10.1038/s41586-021-03532-0] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 04/12/2021] [Indexed: 12/26/2022]
Abstract
Loss of gut microbial diversity1–6 in industrial populations is associated with chronic diseases7, underscoring the importance of studying our ancestral gut microbiome. However, relatively little is known about the composition of pre-industrial gut microbiomes. Here we performed a large-scale de novo assembly of microbial genomes from palaeofaeces. From eight authenticated human palaeofaeces samples (1,000–2,000 years old) with well-preserved DNA from southwestern USA and Mexico, we reconstructed 498 medium- and high-quality microbial genomes. Among the 181 genomes with the strongest evidence of being ancient and of human gut origin, 39% represent previously undescribed species-level genome bins. Tip dating suggests an approximate diversification timeline for the key human symbiont Methanobrevibacter smithii. In comparison to 789 present-day human gut microbiome samples from eight countries, the palaeofaeces samples are more similar to non-industrialized than industrialized human gut microbiomes. Functional profiling of the palaeofaeces samples reveals a markedly lower abundance of antibiotic-resistance and mucin-degrading genes, as well as enrichment of mobile genetic elements relative to industrial gut microbiomes. This study facilitates the discovery and characterization of previously undescribed gut microorganisms from ancient microbiomes and the investigation of the evolutionary history of the human gut microbiota through genome reconstruction from palaeofaeces. Ancient microbiomes from palaeofaeces are more similar to non-industrialized than industrialized human gut microbiomes regardless of geography, but 39% of their de novo reconstructed genomes represent previously undescribed microbial species.
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Affiliation(s)
- Marsha C Wibowo
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Zhen Yang
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA.,Department of Combinatorics and Optimization, University of Waterloo, Waterloo, Ontario, Canada
| | - Maxime Borry
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Alexander Hübner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Kun D Huang
- CIBIO Department, University of Trento, Trento, Italy.,Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Braden T Tierney
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Samuel Zimmerman
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Francisco Barajas-Olmos
- Immunogenomics and Metabolic Diseases Laboratory, Secretaría de Salud, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Cecilia Contreras-Cubas
- Immunogenomics and Metabolic Diseases Laboratory, Secretaría de Salud, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Humberto García-Ortiz
- Immunogenomics and Metabolic Diseases Laboratory, Secretaría de Salud, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Angélica Martínez-Hernández
- Immunogenomics and Metabolic Diseases Laboratory, Secretaría de Salud, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Jacob M Luber
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA.,Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Philipp Kirstahler
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Tre Blohm
- Department of Anthropology, University of Montana, Missoula, MT, USA
| | - Francis E Smiley
- Department of Anthropology, Northern Arizona University, Flagstaff, AZ, USA
| | - Richard Arnold
- Pahrump Paiute Tribe and Consolidated Group of Tribes and Organizations, Pahrump, NV, USA
| | - Sonia A Ballal
- Department of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
| | - Sünje Johanna Pamp
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Julia Russ
- Morrison Microscopy Core Research Facility, Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Frank Maixner
- Institute for Mummy Studies, EURAC Research, Bolzano, Italy
| | - Omar Rota-Stabelli
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.,Center Agriculture Food Environment (C3A), University of Trento, Trento, Italy
| | - Nicola Segata
- CIBIO Department, University of Trento, Trento, Italy
| | - Karl Reinhard
- School of Natural Resources, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Lorena Orozco
- Immunogenomics and Metabolic Diseases Laboratory, Secretaría de Salud, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.,Department of Anthropology, Harvard University, Cambridge, MA, USA.,Faculty of Biological Sciences, Friedrich-Schiller University, Jena, Germany
| | - Meradeth Snow
- Department of Anthropology, University of Montana, Missoula, MT, USA
| | - Steven LeBlanc
- Peabody Museum of Archaeology and Ethnology, Harvard University, Cambridge, MA, USA
| | - Aleksandar D Kostic
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA. .,Department of Microbiology, Harvard Medical School, Boston, MA, USA.
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19
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Jacobson DK, Honap TP, Monroe C, Lund J, Houk BA, Novotny AC, Robin C, Marini E, Lewis CM. Functional diversity of microbial ecologies estimated from ancient human coprolites and dental calculus. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190586. [PMID: 33012230 PMCID: PMC7702801 DOI: 10.1098/rstb.2019.0586] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
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 (n = 7; 700 CE Mexico) and historic dental calculus (n = 44; 1770–1855 CE, UK), as well as two novel dental calculus datasets: Maya (n = 7; 170 BCE-885 CE, Belize) and Nuragic Sardinians (n = 11; 1400–850 BCE, Italy). Periodontitis-associated bacteria (Treponema denticola, Fusobacterium nucleatum and Eubacterium saphenum) were identified as keystone taxa in the dental calculus datasets. Coprolite keystone taxa included known short-chain fatty acid producers (Eubacterium biforme, Phascolarctobacterium succinatutens) and potentially disease-associated bacteria (Escherichia, Brachyspira). 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’.
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Affiliation(s)
- David K Jacobson
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, Norman, OK, USA.,Department of Anthropology, University of Oklahoma, Norman, OK, USA
| | - Tanvi P Honap
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, Norman, OK, USA.,Department of Anthropology, University of Oklahoma, Norman, OK, USA
| | - Cara Monroe
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, Norman, OK, USA
| | - Justin Lund
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, Norman, OK, USA.,Department of Anthropology, University of Oklahoma, Norman, OK, USA
| | - Brett A Houk
- Department of Sociology, Anthropology, and Social Work, Texas Tech University, Lubbock, TX, USA
| | - Anna C Novotny
- Department of Sociology, Anthropology, and Social Work, Texas Tech University, Lubbock, TX, USA
| | - Cynthia Robin
- Department of Anthropology, Northwestern University, Evanston, IL, USA
| | - Elisabetta Marini
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Sardinia, Italy
| | - Cecil M Lewis
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, Norman, OK, USA.,Department of Anthropology, University of Oklahoma, Norman, OK, USA
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