251
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Comparing Ancient DNA Preservation in Petrous Bone and Tooth Cementum. PLoS One 2017; 12:e0170940. [PMID: 28129388 PMCID: PMC5271384 DOI: 10.1371/journal.pone.0170940] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 01/12/2017] [Indexed: 01/08/2023] Open
Abstract
Large-scale genomic analyses of ancient human populations have become feasible partly due to refined sampling methods. The inner part of petrous bones and the cementum layer in teeth roots are currently recognized as the best substrates for such research. We present a comparative analysis of DNA preservation in these two substrates obtained from the same human skulls, across a range of different ages and preservation environments. Both substrates display significantly higher endogenous DNA content (average of 16.4% and 40.0% for teeth and petrous bones, respectively) than parietal skull bone (average of 2.2%). Despite sample-to-sample variation, petrous bone overall performs better than tooth cementum (p = 0.001). This difference, however, is driven largely by a cluster of viking skeletons from one particular locality, showing relatively poor molecular tooth preservation (<10% endogenous DNA). In the remaining skeletons there is no systematic difference between the two substrates. A crude preservation (good/bad) applied to each sample prior to DNA-extraction predicted the above/below 10% endogenous DNA threshold in 80% of the cases. Interestingly, we observe signficantly higher levels of cytosine to thymine deamination damage and lower proportions of mitochondrial/nuclear DNA in petrous bone compared to tooth cementum. Lastly, we show that petrous bones from ancient cremated individuals contain no measurable levels of authentic human DNA. Based on these findings we discuss the pros and cons of sampling the different elements.
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252
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Szabó K, Erdei L, Bolla BS, Tax G, Bíró T, Kemény L. Factors shaping the composition of the cutaneous microbiota. Br J Dermatol 2017; 176:344-351. [PMID: 27518483 DOI: 10.1111/bjd.14967] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2016] [Indexed: 12/12/2022]
Abstract
From birth, we are constantly exposed to bacteria, fungi and viruses, some of which are capable of transiently or permanently inhabiting our different body parts as our microbiota. The majority of our microbial interactions occur during and after birth, and several different factors, including age, sex, genetic constitution, environmental conditions and lifestyle, have been suggested to shape the composition of this microbial community. Propionibacterium acnes is one of the most dominant lipophilic microbes of the postadolescent, sebum-rich human skin regions. Currently, the role of this bacterium in the pathogenesis of the most common inflammatory skin disease, acne vulgaris, is a topic of intense scientific debate. Recent results suggest that Westernization strongly increases the dominance of the Propionibacterium genus in human skin compared with natural populations living more traditional lifestyles. According to the disappearing microbiota hypothesis proposed by Martin Blaser, such alterations in the composition of our microbiota are the possible consequences of socioeconomic and lifestyle changes occurring after the industrial revolution. Evanescence of species that are important elements of the human ecosystem might lead to the overgrowth and subsequent dominance of others because of the lack of ecological competition. Such changes can disturb the fine-tuned balance of the human body and, accordingly, our microbes developed through a long co-evolutionary process. These processes might lead to the transformation of a seemingly harmless species into an opportunistic pathogen through bacterial dysbiosis. This might have happened in the case of P. acnes in acne pathogenesis.
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Affiliation(s)
- K Szabó
- MTA-SZTE Dermatological Research Group, Szeged, Hungary
| | - L Erdei
- Department of Dermatology and Allergology, University of Szeged, Szeged, Hungary
| | - B Sz Bolla
- Department of Dermatology and Allergology, University of Szeged, Szeged, Hungary
| | - G Tax
- Department of Dermatology and Allergology, University of Szeged, Szeged, Hungary
| | - T Bíró
- DE-MTA 'Lendület' Cellular Physiology Research Group, Departments of Physiology and Immunology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - L Kemény
- MTA-SZTE Dermatological Research Group, Szeged, Hungary.,Department of Dermatology and Allergology, University of Szeged, Szeged, Hungary
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253
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Crittenden AN, Schnorr SL. Current views on hunter‐gatherer nutrition and the evolution of the human diet. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 162 Suppl 63:84-109. [DOI: 10.1002/ajpa.23148] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Revised: 11/03/2016] [Accepted: 11/15/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Alyssa N. Crittenden
- Laboratory of Metabolism, Anthropometry, and Nutrition, Department of AnthropologyUniversity of NevadaLas Vegas, Las Vegas Nevada
| | - Stephanie L. Schnorr
- Laboratories of Molecular Anthropology and Microbiome Research, Department of AnthropologyUniversity of OklahomaNorman Oklahoma
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254
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Radini A, Nikita E, Buckley S, Copeland L, Hardy K. Beyond food: The multiple pathways for inclusion of materials into ancient dental calculus. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 162 Suppl 63:71-83. [DOI: 10.1002/ajpa.23147] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 11/15/2016] [Accepted: 11/18/2016] [Indexed: 11/05/2022]
Affiliation(s)
| | - Efthymia Nikita
- Science and Technology in Archaeology Research Centre, The Cyprus InstituteNicosia Cyprus
| | | | - Les Copeland
- School of Life and Environmental SciencesUniversity of SydneyNSW 2006 Australia
| | - Karen Hardy
- ICREA, Pg. Lluís Companys 23. 08010 Barcelona
- Departament de Prehistòria, UAB, Campus UAB. 08193 Cerdanyola del Vallès
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255
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Sheridan SG. Bioarchaeology in the ancientNearEast: Challenges and future directions for the southern Levant. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 162 Suppl 63:110-152. [DOI: 10.1002/ajpa.23149] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 11/02/2016] [Accepted: 11/10/2016] [Indexed: 12/19/2022]
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256
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Lugli GA, Milani C, Mancabelli L, Turroni F, Ferrario C, Duranti S, van Sinderen D, Ventura M. Ancient bacteria of the Ötzi's microbiome: a genomic tale from the Copper Age. MICROBIOME 2017; 5:5. [PMID: 28095919 PMCID: PMC5240250 DOI: 10.1186/s40168-016-0221-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 12/13/2016] [Indexed: 05/19/2023]
Abstract
BACKGROUND Ancient microbiota information represents an important resource to evaluate bacterial evolution and to explore the biological spread of infectious diseases in history. The soft tissue of frozen mummified humans, such as the Tyrolean Iceman, has been shown to contain bacterial DNA that is suitable for population profiling of the prehistoric bacteria that colonized such ancient human hosts. RESULTS Here, we performed a microbial cataloging of the distal gut microbiota of the Tyrolean Iceman, which highlights a predominant abundance of Clostridium and Pseudomonas species. Furthermore, in silico analyses allowed the reconstruction of the genome sequences of five ancient bacterial genomes, including apparent pathogenic ancestor strains of Clostridium perfringens and Pseudomonas veronii species present in the gut of the Tyrolean Iceman. CONCLUSIONS Genomic analyses of the reconstructed C. perfringens chromosome clearly support the occurrence of a pathogenic profile consisting of virulence genes already existing in the ancient strain, thereby reinforcing the notion of a very early speciation of this taxon towards a pathogenic phenotype. In contrast, the evolutionary development of P. veronii appears to be characterized by the acquisition of antibiotic resistance genes in more recent times as well as an evolution towards an ecological niche outside of the (human) gastrointestinal tract.
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Affiliation(s)
- Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Chiara Ferrario
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy.
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257
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Velsko IM, Overmyer KA, Speller C, Klaus L, Collins MJ, Loe L, Frantz LAF, Sankaranarayanan K, Lewis CM, Martinez JBR, Chaves E, Coon JJ, Larson G, Warinner C. The dental calculus metabolome in modern and historic samples. Metabolomics 2017; 13:134. [PMID: 29046620 PMCID: PMC5626792 DOI: 10.1007/s11306-017-1270-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 09/21/2017] [Indexed: 12/23/2022]
Abstract
INTRODUCTION Dental calculus is a mineralized microbial dental plaque biofilm that forms throughout life by precipitation of salivary calcium salts. Successive cycles of dental plaque growth and calcification make it an unusually well-preserved, long-term record of host-microbial interaction in the archaeological record. Recent studies have confirmed the survival of authentic ancient DNA and proteins within historic and prehistoric dental calculus, making it a promising substrate for investigating oral microbiome evolution via direct measurement and comparison of modern and ancient specimens. OBJECTIVE We present the first comprehensive characterization of the human dental calculus metabolome using a multi-platform approach. METHODS Ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) quantified 285 metabolites in modern and historic (200 years old) dental calculus, including metabolites of drug and dietary origin. A subset of historic samples was additionally analyzed by high-resolution gas chromatography-MS (GC-MS) and UPLC-MS/MS for further characterization of metabolites and lipids. Metabolite profiles of modern and historic calculus were compared to identify patterns of persistence and loss. RESULTS Dipeptides, free amino acids, free nucleotides, and carbohydrates substantially decrease in abundance and ubiquity in archaeological samples, with some exceptions. Lipids generally persist, and saturated and mono-unsaturated medium and long chain fatty acids appear to be well-preserved, while metabolic derivatives related to oxidation and chemical degradation are found at higher levels in archaeological dental calculus than fresh samples. CONCLUSIONS The results of this study indicate that certain metabolite classes have higher potential for recovery over long time scales and may serve as appropriate targets for oral microbiome evolutionary studies.
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Affiliation(s)
- Irina M. Velsko
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, OX1 3QY UK
- Present Address: Department of Biological Sciences, Clemson University, Clemson, SC 29634 USA
| | | | - Camilla Speller
- BioArCh, Department of Archaeology, University of York, York, YO10 5DD UK
| | - Lauren Klaus
- Department of Periodontics, University of Oklahoma Health Sciences Center, Oklahoma, OK USA
| | - Matthew J. Collins
- BioArCh, Department of Archaeology, University of York, York, YO10 5DD UK
- Museum of Natural History, University of Copenhagen, Copenhagen, Denmark
| | - Louise Loe
- Heritage Burial Services, Oxford Archaeology, Oxford, UK
| | - Laurent A. F. Frantz
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, OX1 3QY UK
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS UK
| | | | - Cecil M. Lewis
- Department of Anthropology, University of Oklahoma, Norman, OK 73019 USA
| | | | - Eros Chaves
- Department of Periodontics, University of Oklahoma Health Sciences Center, Oklahoma, OK USA
- Present Address: Pinellas Dental Specialties, Largo, FL 33776 USA
| | - Joshua J. Coon
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706 USA
- Departments of Chemistry and Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
- Morgridge Institute for Research, Madison, WI 53706 USA
| | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, OX1 3QY UK
| | - Christina Warinner
- Department of Periodontics, University of Oklahoma Health Sciences Center, Oklahoma, OK USA
- Department of Anthropology, University of Oklahoma, Norman, OK 73019 USA
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07743 Jena, Germany
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258
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Hardy K, Radini A, Buckley S, Blasco R, Copeland L, Burjachs F, Girbal J, Yll R, Carbonell E, Bermúdez de Castro JM. Diet and environment 1.2 million years ago revealed through analysis of dental calculus from Europe’s oldest hominin at Sima del Elefante, Spain. Naturwissenschaften 2016; 104:2. [DOI: 10.1007/s00114-016-1420-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 10/02/2016] [Accepted: 11/03/2016] [Indexed: 11/30/2022]
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259
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Rascovan N, Huynh H, Chouin G, Adekola K, Georges-Zimmermann P, Signoli M, Desfosses Y, Aboudharam G, Drancourt M, Desnues C. Tracing back ancient oral microbiomes and oral pathogens using dental pulps from ancient teeth. NPJ Biofilms Microbiomes 2016. [PMID: 28649400 PMCID: PMC5460193 DOI: 10.1038/s41522-016-0008-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Ancient dental pulps are highly precious samples because they conserve DNA from humans and blood-borne pathogens for ages. However, little is known about the microbial communities present in dental pulps. Here, we analyzed ancient and modern dental pulp samples from different time periods and geographic regions and found that they are colonized by distinct microbial communities, which can be differentiated from other oral cavity samples. We found that despite the presence of environmental bacteria, ancient dental pulps conserve a clear and well-conserved record of oral microbes. We were able to detect several different oral pathogens in ancient and modern dental pulps, which are commonly associated with periodontal diseases. We thus showed that ancient dental pulps are not only valuable sources of DNA from humans and systemic infections, but also an open window for the study of ancient oral microbiomes.
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Affiliation(s)
- Nicolás Rascovan
- Aix Marseille University, URMITE, UM63, CNRS 7278, IRD 198, INSERM, Marseille, France
| | - Hong Huynh
- Aix Marseille University, URMITE, UM63, CNRS 7278, IRD 198, INSERM, Marseille, France
| | - Gérard Chouin
- Lyon G. Tyler Department of History, William & Mary, Virginia, USA
| | - Kolawole Adekola
- Department of Archaeology and Anthropology, University of Ibadan, Ibadan, Nigeria
| | | | - Michel Signoli
- Department of Medicine, Aix Marseille University, UMR 7268 ADES, EFS CNRS, Secteur Nord, Marseille, France
| | - Yves Desfosses
- Department of Medicine, Aix Marseille University, UMR 7268 ADES, EFS CNRS, Secteur Nord, Marseille, France
| | - Gérard Aboudharam
- Aix Marseille University, URMITE, UM63, CNRS 7278, IRD 198, INSERM, Marseille, France
| | - Michel Drancourt
- Aix Marseille University, URMITE, UM63, CNRS 7278, IRD 198, INSERM, Marseille, France
| | - Christelle Desnues
- Aix Marseille University, URMITE, UM63, CNRS 7278, IRD 198, INSERM, Marseille, France
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260
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Drancourt M. Palaeomicrobiology teaches modern infectious diseases. Clin Microbiol Infect 2016; 22:910. [PMID: 27789377 DOI: 10.1016/j.cmi.2016.10.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 10/12/2016] [Accepted: 10/15/2016] [Indexed: 11/17/2022]
Affiliation(s)
- M Drancourt
- Aix Marseille Université - URMITE, 27 bd Jean Moulin Marseille, 13385, France.
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261
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MacHugh DE, Larson G, Orlando L. Taming the Past: Ancient DNA and the Study of Animal Domestication. Annu Rev Anim Biosci 2016; 5:329-351. [PMID: 27813680 DOI: 10.1146/annurev-animal-022516-022747] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
During the last decade, ancient DNA research has been revolutionized by the availability of increasingly powerful DNA sequencing and ancillary genomics technologies, giving rise to the new field of paleogenomics. In this review, we show how our understanding of the genetic basis of animal domestication and the origins and dispersal of livestock and companion animals during the Upper Paleolithic and Neolithic periods is being rapidly transformed through new scientific knowledge generated with paleogenomic methods. These techniques have been particularly informative in revealing high-resolution patterns of artificial and natural selection and evidence for significant admixture between early domestic animal populations and their wild congeners.
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Affiliation(s)
- David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin 4, Ireland; .,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Greger Larson
- Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, United Kingdom;
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark; .,Université de Toulouse, University Paul Sabatier, Laboratoire AMIS, CNRS UMR 5288, 31000 Toulouse, France
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262
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Abstract
The recent Ebola epidemic provides a dramatic example of the devastation and fear generated by epidemics, particularly those caused by new emerging or reemerging diseases. A focus on the control and prevention of diseases in living populations dominates most epidemic disease research. However, research on epidemics in the past provides a temporal depth to our understanding of the context and consequences of diseases and is crucial for predicting how diseases might shape human biology and demography in the future. This article reviews recent research on historic epidemics of plague and tuberculosis, both of which have affected human populations for millennia. Research on these diseases demonstrates the range (and differential availability) of various lines of evidence (e.g., burial context, diagnostic skeletal lesions, molecular data) that inform about past disease in general. I highlight how research on past epidemics may be informative in ways that benefit living populations.
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Affiliation(s)
- Sharon N. DeWitte
- Department of Anthropology and Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208
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263
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Abdul-Aziz MA, Cooper A, Weyrich LS. Exploring Relationships between Host Genome and Microbiome: New Insights from Genome-Wide Association Studies. Front Microbiol 2016; 7:1611. [PMID: 27785127 PMCID: PMC5061000 DOI: 10.3389/fmicb.2016.01611] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 09/26/2016] [Indexed: 12/20/2022] Open
Abstract
As our understanding of the human microbiome expands, impacts on health and disease continue to be revealed. Alterations in the microbiome can result in dysbiosis, which has now been linked to subsequent autoimmune and metabolic diseases, highlighting the need to identify factors that shape the microbiome. Research has identified that the composition and functions of the human microbiome can be influenced by diet, age, sex, and environment. More recently, studies have explored how human genetic variation may also influence the microbiome. Here, we review several recent analytical advances in this new research area, including those that use genome-wide association studies to examine host genome-microbiome interactions, while controlling for the influence of other factors. We find that current research is limited by small sample sizes, lack of cohort replication, and insufficient confirmatory mechanistic studies. In addition, we discuss the importance of understanding long-term interactions between the host genome and microbiome, as well as the potential impacts of disrupting this relationship, and explore new research avenues that may provide information about the co-evolutionary history of humans and their microorganisms.
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Affiliation(s)
| | | | - Laura S. Weyrich
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, The University of Adelaide, AdelaideSA, Australia
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264
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Rascovan N, Telke A, Raoult D, Rolain JM, Desnues C. Exploring divergent antibiotic resistance genes in ancient metagenomes and discovery of a novel beta-lactamase family. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:886-895. [PMID: 27518706 DOI: 10.1111/1758-2229.12453] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 08/04/2016] [Indexed: 05/28/2023]
Abstract
Antibiotic resistance in pathogenic bacteria is a major problem for human health. We analyzed metagenomic datasets from ancient and remote samples from diverse environmental sources and observed the presence of all the eleven antibiotic resistance genes (ARG) groups evaluated. Since ancient samples are not subjected to modern effects of antibiotic misuse, they represent a clean model to explore the natural diversity of ARG in the environment. Most sequences showed high divergence compared with known ARG, representing a much larger universe than the currently known and characterized ARGs. We explored whether proteins within the "divergent resistome" may correspond to functional ARG by characterizing a beta-lactamase hit with very low similarity to any known sequence (<45% to best BLAST hit in NCBI). By starting from purely in-silico data, we revived a new family of class B beta-lactamases from ancient medieval samples, which exhibited a very high penicillinase activity. In this work, we explored ancient resistomes and added novel support to previous works showing that the universe of ARG is naturally vast and diverse in microbial communities. Our results bring a new perspective to the exploration of environmental ARG and indicate that this gigantic reservoir represents a natural endless source of emerging resistances.
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Affiliation(s)
- Nicolás Rascovan
- Aix Marseille University, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Amar Telke
- Aix Marseille University, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Didier Raoult
- Aix Marseille University, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
- Fédération de Microbiologie Clinique, Hôpital de la Timone, Marseille, France
| | - Jean Marc Rolain
- Aix Marseille University, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
- Fédération de Microbiologie Clinique, Hôpital de la Timone, Marseille, France
| | - Christelle Desnues
- Aix Marseille University, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
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265
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Palaeoproteomic evidence identifies archaic hominins associated with the Châtelperronian at the Grotte du Renne. Proc Natl Acad Sci U S A 2016; 113:11162-11167. [PMID: 27638212 DOI: 10.1073/pnas.1605834113] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
In Western Europe, the Middle to Upper Paleolithic transition is associated with the disappearance of Neandertals and the spread of anatomically modern humans (AMHs). Current chronological, behavioral, and biological models of this transitional period hinge on the Châtelperronian technocomplex. At the site of the Grotte du Renne, Arcy-sur-Cure, morphological Neandertal specimens are not directly dated but are contextually associated with the Châtelperronian, which contains bone points and beads. The association between Neandertals and this "transitional" assemblage has been controversial because of the lack either of a direct hominin radiocarbon date or of molecular confirmation of the Neandertal affiliation. Here we provide further evidence for a Neandertal-Châtelperronian association at the Grotte du Renne through biomolecular and chronological analysis. We identified 28 additional hominin specimens through zooarchaeology by mass spectrometry (ZooMS) screening of morphologically uninformative bone specimens from Châtelperronian layers at the Grotte du Renne. Next, we obtain an ancient hominin bone proteome through liquid chromatography-MS/MS analysis and error-tolerant amino acid sequence analysis. Analysis of this palaeoproteome allows us to provide phylogenetic and physiological information on these ancient hominin specimens. We distinguish Late Pleistocene clades within the genus Homo based on ancient protein evidence through the identification of an archaic-derived amino acid sequence for the collagen type X, alpha-1 (COL10α1) protein. We support this by obtaining ancient mtDNA sequences, which indicate a Neandertal ancestry for these specimens. Direct accelerator mass spectometry radiocarbon dating and Bayesian modeling confirm that the hominin specimens date to the Châtelperronian at the Grotte du Renne.
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266
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Cui H, Li Y, Zhang X. An overview of major metagenomic studies on human microbiomes in health and disease. QUANTITATIVE BIOLOGY 2016. [DOI: 10.1007/s40484-016-0078-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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267
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Andam CP, Worby CJ, Chang Q, Campana MG. Microbial Genomics of Ancient Plagues and Outbreaks. Trends Microbiol 2016; 24:978-990. [PMID: 27618404 DOI: 10.1016/j.tim.2016.08.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Revised: 07/29/2016] [Accepted: 08/16/2016] [Indexed: 01/22/2023]
Abstract
The recent use of next-generation sequencing methods to investigate historical disease outbreaks has provided us with an unprecedented ability to address important and long-standing questions in epidemiology, pathogen evolution, and human history. In this review, we present major findings that illustrate how microbial genomics has provided new insights into the nature and etiology of infectious diseases of historical importance, such as plague, tuberculosis, and leprosy. Sequenced isolates collected from archaeological remains also provide evidence for the timing of historical evolutionary events as well as geographic spread of these pathogens. Elucidating the genomic basis of virulence in historical diseases can provide relevant information on how we can effectively understand the emergence and re-emergence of infectious diseases today and in the future.
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Affiliation(s)
- Cheryl P Andam
- Harvard T. H. Chan School of Public Health, Department of Epidemiology, Boston, MA 02115, USA; University of New Hampshire, Department of Molecular, Cellular and Biomedical Sciences, Durham, NH 03824, USA.
| | - Colin J Worby
- Harvard T. H. Chan School of Public Health, Department of Epidemiology, Boston, MA 02115, USA
| | - Qiuzhi Chang
- Harvard T. H. Chan School of Public Health, Department of Epidemiology, Boston, MA 02115, USA
| | - Michael G Campana
- Smithsonian Conservation Biology Institute, Center for Conservation Genomics, 3001 Connecticut Avenue NW, Washington, DC 20008, USA.
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268
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Dental calculus reveals Mesolithic foragers in the Balkans consumed domesticated plant foods. Proc Natl Acad Sci U S A 2016; 113:10298-303. [PMID: 27573829 DOI: 10.1073/pnas.1603477113] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Researchers agree that domesticated plants were introduced into southeast Europe from southwest Asia as a part of a Neolithic "package," which included domesticated animals and artifacts typical of farming communities. It is commonly believed that this package reached inland areas of the Balkans by ∼6200 calibrated (cal.) BC or later. Our analysis of the starch record entrapped in dental calculus of Mesolithic human teeth at the site of Vlasac in the Danube Gorges of the central Balkans provides direct evidence that already by ∼6600 cal. BC, if not earlier, Late Mesolithic foragers of this region consumed domestic cereals, such as Triticum monococcum, Triticum dicoccum, and Hordeum distichon, which were also the main crops found among Early Neolithic communities of southeast Europe. We infer that "exotic" Neolithic domesticated plants were introduced to southern Europe independently almost half a millennium earlier than previously thought, through networks that enabled exchanges between inland Mesolithic foragers and early farming groups found along the Aegean coast of Turkey.
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269
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Santiago-Rodriguez TM, Fornaciari G, Luciani S, Dowd SE, Toranzos GA, Marota I, Cano RJ. Taxonomic and predicted metabolic profiles of the human gut microbiome in pre-Columbian mummies. FEMS Microbiol Ecol 2016; 92:fiw182. [PMID: 27559027 DOI: 10.1093/femsec/fiw182] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2016] [Indexed: 11/15/2022] Open
Abstract
Characterization of naturally mummified human gut remains could potentially provide insights into the preservation and evolution of commensal and pathogenic microorganisms, and metabolic profiles. We characterized the gut microbiome of two pre-Columbian Andean mummies dating to the 10-15th centuries using 16S rRNA gene high-throughput sequencing and metagenomics, and compared them to a previously characterized gut microbiome of an 11th century AD pre-Columbian Andean mummy. Our previous study showed that the Clostridiales represented the majority of the bacterial communities in the mummified gut remains, but that other microbial communities were also preserved during the process of natural mummification, as shown with the metagenomics analyses. The gut microbiome of the other two mummies were mainly comprised by Clostridiales or Bacillales, as demonstrated with 16S rRNA gene amplicon sequencing, many of which are facultative anaerobes, possibly consistent with the process of natural mummification requiring low oxygen levels. Metagenome analyses showed the presence of other microbial groups that were positively or negatively correlated with specific metabolic profiles. The presence of sequences similar to both Trypanosoma cruzi and Leishmania donovani could suggest that these pathogens were prevalent in pre-Columbian individuals. Taxonomic and functional profiling of mummified human gut remains will aid in the understanding of the microbial ecology of the process of natural mummification.
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Affiliation(s)
- Tasha M Santiago-Rodriguez
- Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA 93407, USA Department of Biology, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Gino Fornaciari
- Department of Translational Research on New Technologies in Medicine and Surgery, Division of Paleopathology, University of Pisa, Pisa 56126, Italy Center for Anthropological, Paleopathological and Historical Studies of the Sardinian and Mediterranean Populations, Department of Biomedical Sciences, University of Sassari, Sassari 07100, Italy
| | - Stefania Luciani
- Laboratory of Molecular Archaeo-Anthropology/ancient DNA, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino 62032, Italy
| | - Scot E Dowd
- Molecular Research LP (MR DNA), Shallowater, Texas 79363, USA
| | - Gary A Toranzos
- Department of Biology, University of Puerto Rico, Julio Garcia Diaz Building, San Juan 00931, Puerto Rico
| | - Isolina Marota
- Laboratory of Molecular Archaeo-Anthropology/ancient DNA, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino 62032, Italy
| | - Raul J Cano
- Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA 93407, USA Department of Biology, California Polytechnic State University, San Luis Obispo, CA 93407, USA
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270
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Schnorr SL, Sankaranarayanan K, Lewis CM, Warinner C. Insights into human evolution from ancient and contemporary microbiome studies. Curr Opin Genet Dev 2016; 41:14-26. [PMID: 27507098 DOI: 10.1016/j.gde.2016.07.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/01/2016] [Accepted: 07/04/2016] [Indexed: 12/11/2022]
Abstract
Over the past decade, human microbiome research has energized the study of human evolution through a complete shift in our understanding of what it means to be human. The microbiome plays a pivotal role in human biology, performing key functions in digestion, mood and behavior, development and immunity, and a range of acute and chronic diseases. It is therefore critical to understand its evolution and changing ecology through time. Here we review recent findings on the microbiota of diverse human populations, non-human primates, and past human populations and discuss the implications of this research in formulating a deeper evolutionary understanding of the human holobiont.
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Affiliation(s)
- Stephanie L Schnorr
- Department of Anthropology, University of Oklahoma, 455 W. Lindsey St., Norman, OK 73019, USA
| | | | - Cecil M Lewis
- Department of Anthropology, University of Oklahoma, 455 W. Lindsey St., Norman, OK 73019, USA
| | - Christina Warinner
- Department of Anthropology, University of Oklahoma, 455 W. Lindsey St., Norman, OK 73019, USA.
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271
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Gogarten JF, Düx A, Schuenemann VJ, Nowak K, Boesch C, Wittig RM, Krause J, Calvignac-Spencer S, Leendertz FH. Tools for opening new chapters in the book of Treponema pallidum evolutionary history. Clin Microbiol Infect 2016; 22:916-921. [PMID: 27498082 DOI: 10.1016/j.cmi.2016.07.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 07/04/2016] [Accepted: 07/25/2016] [Indexed: 10/21/2022]
Abstract
Treponema pallidum infections causing yaws disease and venereal syphilis are globally widespread in human populations, infecting hundreds of thousands and millions annually respectively; endemic syphilis is much less common, and pinta has not been observed in decades. We discuss controversy surrounding the origin, evolution and history of these pathogens in light of available molecular and anthropological evidence. These bacteria (or close relatives) seem to affect many wild African nonhuman primate (NHP) species, though to date only a single NHP Treponema pallidum genome has been published, hindering detection of spillover events and our understanding of potential wildlife reservoirs. Similarly, only ten genomes of Treponema pallidum infecting humans have been published, impeding a full understanding of their diversity and evolutionary history. Research efforts have been hampered by the difficulty of culturing and propagating Treponema pallidum. Here we highlight avenues of research recently opened by the coupling of hybridization capture and next-generation sequencing. We present data generated with such an approach suggesting that asymptomatic bones from NHP occasionally contain enough treponemal DNA to recover large fractions of their genomes. We expect that these methods, which naturally can be applied to modern biopsy samples and ancient human bones, will soon considerably improve our understanding of these enigmatic pathogens and lay rest to old yet unresolved controversies.
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Affiliation(s)
- J F Gogarten
- Epidemiology of Highly Pathogenic Microorganisms, Germany; Primatology Department, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany; Department of Biology, McGill University, Montreal, Quebec, Canada
| | - A Düx
- Epidemiology of Highly Pathogenic Microorganisms, Germany; Viral Evolution, Robert Koch Institute, Berlin, Germany
| | - V J Schuenemann
- Institute for Archeological Sciences, University of Tübingen, Tübingen, Germany
| | - K Nowak
- Epidemiology of Highly Pathogenic Microorganisms, Germany
| | - C Boesch
- Primatology Department, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - R M Wittig
- Primatology Department, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany; Taï Chimpanzee Project, CSRS, Abidjan, Cote d'Ivoire
| | - J Krause
- Institute for Archeological Sciences, University of Tübingen, Tübingen, Germany; Max Planck Institute for the Science of Human History, Jena, Germany
| | - S Calvignac-Spencer
- Epidemiology of Highly Pathogenic Microorganisms, Germany; Viral Evolution, Robert Koch Institute, Berlin, Germany.
| | - F H Leendertz
- Epidemiology of Highly Pathogenic Microorganisms, Germany.
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272
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Louvel G, Der Sarkissian C, Hanghøj K, Orlando L. metaBIT, an integrative and automated metagenomic pipeline for analysing microbial profiles from high-throughput sequencing shotgun data. Mol Ecol Resour 2016; 16:1415-1427. [PMID: 27238636 DOI: 10.1111/1755-0998.12546] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 05/03/2016] [Accepted: 05/13/2016] [Indexed: 12/18/2022]
Abstract
Micro-organisms account for most of the Earth's biodiversity and yet remain largely unknown. The complexity and diversity of microbial communities present in clinical and environmental samples can now be robustly investigated in record times and prices thanks to recent advances in high-throughput DNA sequencing (HTS). Here, we develop metaBIT, an open-source computational pipeline automatizing routine microbial profiling of shotgun HTS data. Customizable by the user at different stringency levels, it performs robust taxonomy-based assignment and relative abundance calculation of microbial taxa, as well as cross-sample statistical analyses of microbial diversity distributions. We demonstrate the versatility of metaBIT within a range of published HTS data sets sampled from the environment (soil and seawater) and the human body (skin and gut), but also from archaeological specimens. We present the diversity of outputs provided by the pipeline for the visualization of microbial profiles (barplots, heatmaps) and for their characterization and comparison (diversity indices, hierarchical clustering and principal coordinates analyses). We show that metaBIT allows an automatic, fast and user-friendly profiling of the microbial DNA present in HTS shotgun data sets. The applications of metaBIT are vast, from monitoring of laboratory errors and contaminations, to the reconstruction of past and present microbiota, and the detection of candidate species, including pathogens.
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Affiliation(s)
- Guillaume Louvel
- Centre for Geogenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark
| | - Clio Der Sarkissian
- Centre for Geogenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark
| | - Kristian Hanghøj
- Centre for Geogenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark
| | - Ludovic Orlando
- Centre for Geogenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark. .,Université de Toulouse, University Paul Sabatier (UPS), Laboratoire AMIS, CNRS UMR 5288, 37 allées Jules Guesde, 31000, Toulouse, France.
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273
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Zhang Y, Ji P, Wang J, Zhao F. RiboFR-Seq: a novel approach to linking 16S rRNA amplicon profiles to metagenomes. Nucleic Acids Res 2016; 44:e99. [PMID: 26984526 PMCID: PMC4889936 DOI: 10.1093/nar/gkw165] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 02/16/2016] [Accepted: 03/02/2016] [Indexed: 12/30/2022] Open
Abstract
16S rRNA amplicon analysis and shotgun metagenome sequencing are two main culture-independent strategies to explore the genetic landscape of various microbial communities. Recently, numerous studies have employed these two approaches together, but downstream data analyses were performed separately, which always generated incongruent or conflict signals on both taxonomic and functional classifications. Here we propose a novel approach, RiboFR-Seq (Ribosomal RNA gene flanking region sequencing), for capturing both ribosomal RNA variable regions and their flanking protein-coding genes simultaneously. Through extensive testing on clonal bacterial strain, salivary microbiome and bacterial epibionts of marine kelp, we demonstrated that RiboFR-Seq could detect the vast majority of bacteria not only in well-studied microbiomes but also in novel communities with limited reference genomes. Combined with classical amplicon sequencing and shotgun metagenome sequencing, RiboFR-Seq can link the annotations of 16S rRNA and metagenomic contigs to make a consensus classification. By recognizing almost all 16S rRNA copies, the RiboFR-seq approach can effectively reduce the taxonomic abundance bias resulted from 16S rRNA copy number variation. We believe that RiboFR-Seq, which provides an integrated view of 16S rRNA profiles and metagenomes, will help us better understand diverse microbial communities.
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Affiliation(s)
- Yanming Zhang
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Peifeng Ji
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinfeng Wang
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Fangqing Zhao
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
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274
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Ozga AT, Nieves‐Colón MA, Honap TP, Sankaranarayanan K, Hofman CA, Milner GR, Lewis CM, Stone AC, Warinner C. Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2016; 160:220-8. [PMID: 26989998 PMCID: PMC4866892 DOI: 10.1002/ajpa.22960] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 01/05/2016] [Accepted: 01/25/2016] [Indexed: 11/06/2022]
Abstract
OBJECTIVES Archaeological dental calculus is a rich source of host-associated biomolecules. Importantly, however, dental calculus is more accurately described as a calcified microbial biofilm than a host tissue. As such, concerns regarding destructive analysis of human remains may not apply as strongly to dental calculus, opening the possibility of obtaining human health and ancestry information from dental calculus in cases where destructive analysis of conventional skeletal remains is not permitted. Here we investigate the preservation of human mitochondrial DNA (mtDNA) in archaeological dental calculus and its potential for full mitochondrial genome (mitogenome) reconstruction in maternal lineage ancestry analysis. MATERIALS AND METHODS Extracted DNA from six individuals at the 700-year-old Norris Farms #36 cemetery in Illinois was enriched for mtDNA using in-solution capture techniques, followed by Illumina high-throughput sequencing. RESULTS Full mitogenomes (7-34×) were successfully reconstructed from dental calculus for all six individuals, including three individuals who had previously tested negative for DNA preservation in bone using conventional PCR techniques. Mitochondrial haplogroup assignments were consistent with previously published findings, and additional comparative analysis of paired dental calculus and dentine from two individuals yielded equivalent haplotype results. All dental calculus samples exhibited damage patterns consistent with ancient DNA, and mitochondrial sequences were estimated to be 92-100% endogenous. DNA polymerase choice was found to impact error rates in downstream sequence analysis, but these effects can be mitigated by greater sequencing depth. DISCUSSION Dental calculus is a viable alternative source of human DNA that can be used to reconstruct full mitogenomes from archaeological remains. Am J Phys Anthropol 160:220-228, 2016. © 2016 The Authors American Journal of Physical Anthropology Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Andrew T. Ozga
- Department of AnthropologyUniversity of OklahomaNormanOK73019
| | | | - Tanvi P. Honap
- School of Life SciencesArizona State UniversityTempeAZ85287
| | | | | | - George R. Milner
- Department of AnthropologyPennsylvania State University, University ParkPA16802
| | - Cecil M. Lewis
- Department of AnthropologyUniversity of OklahomaNormanOK73019
| | - Anne C. Stone
- School of Human Evolution and Social ChangeArizona State UniversityTempeAZ85287
- Center for Bioarchaeological Research, Arizona State UniversityTempeAZ85287
- Institute of Human Origins, Arizona State UniversityTempeAZ85287
| | - Christina Warinner
- Department of AnthropologyUniversity of OklahomaNormanOK73019
- Institute of Evolutionary Medicine, University of Zurich8057 ZurichSwitzerland
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275
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Perry J, Waglechner N, Wright G. The Prehistory of Antibiotic Resistance. Cold Spring Harb Perspect Med 2016; 6:6/6/a025197. [PMID: 27252395 DOI: 10.1101/cshperspect.a025197] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Antibiotic resistance is a global problem that is reaching crisis levels. The global collection of resistance genes in clinical and environmental samples is the antibiotic "resistome," and is subject to the selective pressure of human activity. The origin of many modern resistance genes in pathogens is likely environmental bacteria, including antibiotic producing organisms that have existed for millennia. Recent work has uncovered resistance in ancient permafrost, isolated caves, and in human specimens preserved for hundreds of years. Together with bioinformatic analyses on modern-day sequences, these studies predict an ancient origin of resistance that long precedes the use of antibiotics in the clinic. Understanding the history of antibiotic resistance is important in predicting its future evolution.
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Affiliation(s)
- Julie Perry
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Nicholas Waglechner
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Gerard Wright
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Ontario L8S 4K1, Canada
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276
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Inner Workings: Ancient teeth reveal clues about microbiome evolution. Proc Natl Acad Sci U S A 2016; 113:5764-5. [PMID: 27222564 DOI: 10.1073/pnas.1606592113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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277
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Restricted diversity of dental calculus methanogens over five centuries, France. Sci Rep 2016; 6:25775. [PMID: 27166431 PMCID: PMC4863154 DOI: 10.1038/srep25775] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 04/05/2016] [Indexed: 11/08/2022] Open
Abstract
Methanogens are acknowledged archaeal members of modern dental calculus microbiota and dental pathogen complexes. Their repertoire in ancient dental calculus is poorly known. We therefore investigated archaea in one hundred dental calculus specimens collected from individuals recovered from six archaeological sites in France dated from the 14(th) to 19(th) centuries AD. Dental calculus was demonstrated by macroscopic and cone-beam observations. In 56 calculus specimens free of PCR inhibition, PCR sequencing identified Candidatus Methanobrevibacter sp. N13 in 44.6%, Methanobrevibacter oralis in 19.6%, a new Methanomassiliicoccus luminyensis-like methanogen in 12.5%, a Candidatus Nitrososphaera evergladensis-like in one and Methanoculleus bourgensis in one specimen, respectively. One Candidatus Methanobrevibacter sp. N13 dental calculus was further documented by fluorescent in situ hybridization. The prevalence of dental calculus M. oralis was significantly lower in past populations than in modern populations (P = 0.03, Chi-square test). This investigation revealed a previously unknown repertoire of archaea found in the oral cavity of past French populations as reflected in preserved dental calculus.
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278
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He Z, Zhang H, Gao S, Lercher MJ, Chen WH, Hu S. Evolview v2: an online visualization and management tool for customized and annotated phylogenetic trees. Nucleic Acids Res 2016; 44:W236-41. [PMID: 27131786 PMCID: PMC4987921 DOI: 10.1093/nar/gkw370] [Citation(s) in RCA: 396] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 04/23/2016] [Indexed: 02/06/2023] Open
Abstract
Evolview is an online visualization and management tool for customized and annotated phylogenetic trees. It allows users to visualize phylogenetic trees in various formats, customize the trees through built-in functions and user-supplied datasets and export the customization results to publication-ready figures. Its ‘dataset system’ contains not only the data to be visualized on the tree, but also ‘modifiers’ that control various aspects of the graphical annotation. Evolview is a single-page application (like Gmail); its carefully designed interface allows users to upload, visualize, manipulate and manage trees and datasets all in a single webpage. Developments since the last public release include a modern dataset editor with keyword highlighting functionality, seven newly added types of annotation datasets, collaboration support that allows users to share their trees and datasets and various improvements of the web interface and performance. In addition, we included eleven new ‘Demo’ trees to demonstrate the basic functionalities of Evolview, and five new ‘Showcase’ trees inspired by publications to showcase the power of Evolview in producing publication-ready figures. Evolview is freely available at: http://www.evolgenius.info/evolview/.
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Affiliation(s)
- Zilong He
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics (BIG), Chinese Academy of Sciences (CAS), No.7 Beitucheng West Road, Chaoyang District, 100029 Beijing, PR China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huangkai Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics (BIG), Chinese Academy of Sciences (CAS), No.7 Beitucheng West Road, Chaoyang District, 100029 Beijing, PR China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shenghan Gao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics (BIG), Chinese Academy of Sciences (CAS), No.7 Beitucheng West Road, Chaoyang District, 100029 Beijing, PR China
| | - Martin J Lercher
- Institute for Computer Science and Cluster of Excellence on Plant Sciences CEPLAS, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Wei-Hua Chen
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics (BIG), Chinese Academy of Sciences (CAS), No.7 Beitucheng West Road, Chaoyang District, 100029 Beijing, PR China BIG Data Center, Beijing Institute of Genomics (BIG), Chinese Academy of Sciences (CAS), No.7 Beitucheng West Road, Chaoyang District, 100029 Beijing, PR China
| | - Songnian Hu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics (BIG), Chinese Academy of Sciences (CAS), No.7 Beitucheng West Road, Chaoyang District, 100029 Beijing, PR China University of Chinese Academy of Sciences, Beijing 100049, China
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279
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Kato I, Vasquez AA, Moyerbrailean G, Land S, Sun J, Lin HS, Ram JL. Oral microbiome and history of smoking and colorectal cancer. ACTA ACUST UNITED AC 2016; 2:92-101. [PMID: 28111632 DOI: 10.5430/jer.v2n2p92] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND The equilibrium of oral microbiome may be altered by environmental factors, including cigarette smoking. Several recent studies also suggest that oral pathogens causing periodontal disease, such as Fusobacterium nucleatum, are involved in pathogenesis of colorectal cancer. METHODS For this study oral rinse DNA samples from 190 participants in a population-based case-control study for colorectal cancer were used to amplify a V3-V4 region of bacterial 16S rRNA gene. The amplicons were sequenced using Illumina MiSeq paired end chemistry on two runs, yielding approximately 35 million filtered reads which were assigned to bacterial phyla. RESULTS No association was found between Fusobacterium abundance or presence and colorectal cancer. However, adjusted for age and experimental batch, colorectal cancer history was associated with increased presence of genus Lactobacillus and increased relative abundance of Rothia by 28% and current smoking was associated with a 33% decrease in relative counts of Betaproteobacteria (primarily Neisseria) and 23% increase in relative abundance of Veillonellaceae family. We also found that smoking had significant effects on the 2nd component scores and 2nd coordinate distances in principal component and coordinate analyses. CONCLUSIONS It remains to be elucidated whether the observed differences can be translated into biochemical changes in oral environment, thus potentially affecting oral health.
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Affiliation(s)
- Ikuko Kato
- Department of Oncology and Pathology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Adrian A Vasquez
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Gregory Moyerbrailean
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Susan Land
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Jun Sun
- Department of Medicine, School of Medicine, University of Illinois at Chicago, IL, USA
| | - Ho-Sheng Lin
- Department of Otolaryngology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Jeffrey L Ram
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI, USA
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280
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Galvão-Moreira LV. Letter to the Editor: Toward a Multifactorial Model of Caries Formation. J Dent Res 2016; 95:597. [PMID: 26868328 DOI: 10.1177/0022034516631721] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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281
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Maixner F, Krause-Kyora B, Turaev D, Herbig A, Hoopmann MR, Hallows JL, Kusebauch U, Vigl EE, Malfertheiner P, Megraud F, O'Sullivan N, Cipollini G, Coia V, Samadelli M, Engstrand L, Linz B, Moritz RL, Grimm R, Krause J, Nebel A, Moodley Y, Rattei T, Zink A. The 5300-year-old Helicobacter pylori genome of the Iceman. Science 2016; 351:162-165. [PMID: 26744403 DOI: 10.1126/science.aad2545] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The stomach bacterium Helicobacter pylori is one of the most prevalent human pathogens. It has dispersed globally with its human host, resulting in a distinct phylogeographic pattern that can be used to reconstruct both recent and ancient human migrations. The extant European population of H. pylori is known to be a hybrid between Asian and African bacteria, but there exist different hypotheses about when and where the hybridization took place, reflecting the complex demographic history of Europeans. Here, we present a 5300-year-old H. pylori genome from a European Copper Age glacier mummy. The "Iceman" H. pylori is a nearly pure representative of the bacterial population of Asian origin that existed in Europe before hybridization, suggesting that the African population arrived in Europe within the past few thousand years.
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Affiliation(s)
- Frank Maixner
- Institute for Mummies and the Iceman, EURAC research, Viale Druso 1, 39100 Bolzano, Italy
| | - Ben Krause-Kyora
- Institute of Clinical Molecular Biology, Kiel University, Schittenhelmstr. 12, 24105 Kiel, Germany
| | - Dmitrij Turaev
- CUBE - Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Althanstr. 14, 1090 Vienna, Austria
| | - Alexander Herbig
- Institute for Archaeological Sciences, University of Tübingen, Rümelinstr. 23, 72072 Tübingen, Germany.,Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany
| | - Michael R Hoopmann
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, USA
| | - Janice L Hallows
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, USA
| | - Ulrike Kusebauch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, USA
| | - Eduard Egarter Vigl
- Scuola Superiore Sanitaria Provinciale "Claudiana", Via Lorenz Böhler 13, 39100 Bolzano, Italy
| | - Peter Malfertheiner
- Department of Gastroenterology, Hepatology, and Infectious Diseases, Otto-von-Guericke University, Leipziger Strasse 44, 39120 Magdeburg, Germany
| | - Francis Megraud
- Université de Bordeaux, Centre National de Référence des Helicobacters et Campylobacters and INSERM U853, 146 rue Léo Saignat, 33076 Bordeaux, France
| | - Niall O'Sullivan
- Institute for Mummies and the Iceman, EURAC research, Viale Druso 1, 39100 Bolzano, Italy
| | - Giovanna Cipollini
- Institute for Mummies and the Iceman, EURAC research, Viale Druso 1, 39100 Bolzano, Italy
| | - Valentina Coia
- Institute for Mummies and the Iceman, EURAC research, Viale Druso 1, 39100 Bolzano, Italy
| | - Marco Samadelli
- Institute for Mummies and the Iceman, EURAC research, Viale Druso 1, 39100 Bolzano, Italy
| | - Lars Engstrand
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 141 83 Stockholm, Sweden
| | - Bodo Linz
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Robert L Moritz
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, USA
| | - Rudolf Grimm
- Robert Mondavi Institute for Food Science, University of California, Davis, California 95616, USA
| | - Johannes Krause
- Institute for Archaeological Sciences, University of Tübingen, Rümelinstr. 23, 72072 Tübingen, Germany.,Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany
| | - Almut Nebel
- Institute of Clinical Molecular Biology, Kiel University, Schittenhelmstr. 12, 24105 Kiel, Germany
| | - Yoshan Moodley
- Department of Zoology, University of Venda, Private Bag X5050, Thohoyandou 0950, Republic of South Africa.,Department of Integrative Biology and Evolution, Konrad Lorenz Institute for Ethology, University of Veterinary Medicine Vienna, Savoyenstr. 1a, 1160 Vienna, Austria
| | - Thomas Rattei
- CUBE - Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Althanstr. 14, 1090 Vienna, Austria
| | - Albert Zink
- Institute for Mummies and the Iceman, EURAC research, Viale Druso 1, 39100 Bolzano, Italy
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282
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Gorgé O, Bennett EA, Massilani D, Daligault J, Pruvost M, Geigl EM, Grange T. Analysis of Ancient DNA in Microbial Ecology. Methods Mol Biol 2016; 1399:289-315. [PMID: 26791510 DOI: 10.1007/978-1-4939-3369-3_17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
The development of next-generation sequencing has led to a breakthrough in the analysis of ancient genomes, and the subsequent genomic analyses of the skeletal remains of ancient humans have revolutionized the knowledge of the evolution of our species, including the discovery of a new hominin, and demonstrated admixtures with more distantly related archaic populations such as Neandertals and Denisovans. Moreover, it has also yielded novel insights into the evolution of ancient pathogens. The analysis of ancient microbial genomes allows the study of their recent evolution, presently over the last several millennia. These spectacular results have been attained despite the degradation of DNA after the death of the host, which results in very short DNA molecules that become increasingly damaged, only low quantities of which remain. The low quantity of ancient DNA molecules renders their analysis difficult and prone to contamination with modern DNA molecules, in particular via contamination from the reagents used in DNA purification and downstream analysis steps. Finally, the rare ancient molecules are diluted in environmental DNA originating from the soil microorganisms that colonize bones and teeth. Thus, ancient skeletal remains can share DNA profiles with environmental samples and identifying ancient microbial genomes among the more recent, presently poorly characterized, environmental microbiome is particularly challenging. Here, we describe the methods developed and/or in use in our laboratory to produce reliable and reproducible paleogenomic results from ancient skeletal remains that can be used to identify the presence of ancient microbiota.
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Affiliation(s)
- Olivier Gorgé
- Institut Jacques Monod, UMR 7592, CNRS, Université Paris Diderot, Batiment Buffon, 15 Rue Helene Brion, Paris, 75013, France.
| | - E Andrew Bennett
- Institut Jacques Monod, UMR 7592, CNRS, Université Paris Diderot, Batiment Buffon, 15 Rue Helene Brion, Paris, 75013, France
| | - Diyendo Massilani
- Institut Jacques Monod, UMR 7592, CNRS, Université Paris Diderot, Batiment Buffon, 15 Rue Helene Brion, Paris, 75013, France
| | - Julien Daligault
- Institut Jacques Monod, UMR 7592, CNRS, Université Paris Diderot, Batiment Buffon, 15 Rue Helene Brion, Paris, 75013, France
| | - Melanie Pruvost
- Institut Jacques Monod, UMR 7592, CNRS, Université Paris Diderot, Batiment Buffon, 15 Rue Helene Brion, Paris, 75013, France
| | - Eva-Maria Geigl
- Institut Jacques Monod, UMR 7592, CNRS, Université Paris Diderot, Batiment Buffon, 15 Rue Helene Brion, Paris, 75013, France
| | - Thierry Grange
- Institut Jacques Monod, UMR 7592, CNRS, Université Paris Diderot, Batiment Buffon, 15 Rue Helene Brion, Paris, 75013, France
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283
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Dallongeville S, Garnier N, Rolando C, Tokarski C. Proteins in Art, Archaeology, and Paleontology: From Detection to Identification. Chem Rev 2015; 116:2-79. [PMID: 26709533 DOI: 10.1021/acs.chemrev.5b00037] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Sophie Dallongeville
- Miniaturisation pour la Synthèse, l'Analyse & la Protéomique (MSAP), USR CNRS 3290, Université de Lille 1 Sciences et Technologies , 59655 Villeneuve d'Ascq Cedex, France
| | - Nicolas Garnier
- SARL Laboratoire Nicolas Garnier , 63270 Vic le Comte, France
| | - Christian Rolando
- Miniaturisation pour la Synthèse, l'Analyse & la Protéomique (MSAP), USR CNRS 3290, Université de Lille 1 Sciences et Technologies , 59655 Villeneuve d'Ascq Cedex, France
| | - Caroline Tokarski
- Miniaturisation pour la Synthèse, l'Analyse & la Protéomique (MSAP), USR CNRS 3290, Université de Lille 1 Sciences et Technologies , 59655 Villeneuve d'Ascq Cedex, France
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284
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Malhi RS, Bader AC. ENGAGING NATIVE AMERICANS IN GENOMICS RESEARCH. AMERICAN ANTHROPOLOGIST 2015; 117:743-744. [PMID: 27799658 DOI: 10.1111/aman.12369] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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285
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Ziesemer KA, Mann AE, Sankaranarayanan K, Schroeder H, Ozga AT, Brandt BW, Zaura E, Waters-Rist A, Hoogland M, Salazar-García DC, Aldenderfer M, Speller C, Hendy J, Weston DA, MacDonald SJ, Thomas GH, Collins MJ, Lewis CM, Hofman C, Warinner C. Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification. Sci Rep 2015; 5:16498. [PMID: 26563586 PMCID: PMC4643231 DOI: 10.1038/srep16498] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 10/14/2015] [Indexed: 12/18/2022] Open
Abstract
To date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has been primarily accomplished through a metataxonomic approach involving targeted amplification of one or more variable regions in the 16S rRNA gene. Specifically, the V3 region (E. coli 341–534) of this gene has been suggested as an excellent candidate for ancient DNA amplification and microbial community reconstruction. However, in practice this metataxonomic approach often produces highly skewed taxonomic frequency data. In this study, we use non-targeted (shotgun metagenomics) sequencing methods to better understand skewed microbial profiles observed in four ancient dental calculus specimens previously analyzed by amplicon sequencing. Through comparisons of microbial taxonomic counts from paired amplicon (V3 U341F/534R) and shotgun sequencing datasets, we demonstrate that extensive length polymorphisms in the V3 region are a consistent and major cause of differential amplification leading to taxonomic bias in ancient microbiome reconstructions based on amplicon sequencing. We conclude that systematic amplification bias confounds attempts to accurately reconstruct microbiome taxonomic profiles from 16S rRNA V3 amplicon data generated using universal primers. Because in silico analysis indicates that alternative 16S rRNA hypervariable regions will present similar challenges, we advocate for the use of a shotgun metagenomics approach in ancient microbiome reconstructions.
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Affiliation(s)
- Kirsten A Ziesemer
- Faculty of Archaeology, Leiden University, Einsteinweg 2, 2333 CC, Leiden, the Netherlands
| | - Allison E Mann
- Department of Anthropology, University of Oklahoma, Norman, OK, USA
| | | | - Hannes Schroeder
- Faculty of Archaeology, Leiden University, Einsteinweg 2, 2333 CC, Leiden, the Netherlands.,Center for Geogenetics, University of Copenhagen, Denmark
| | - Andrew T Ozga
- Department of Anthropology, University of Oklahoma, Norman, OK, USA
| | - Bernd W Brandt
- Department of Preventive Dentistry, Academic Center for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam, the Netherlands
| | - Egija Zaura
- Department of Preventive Dentistry, Academic Center for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam, the Netherlands
| | - Andrea Waters-Rist
- Faculty of Archaeology, Leiden University, Einsteinweg 2, 2333 CC, Leiden, the Netherlands
| | - Menno Hoogland
- Faculty of Archaeology, Leiden University, Einsteinweg 2, 2333 CC, Leiden, the Netherlands
| | - Domingo C Salazar-García
- Department of Anthropology, University of Cape Town, South Africa.,Departament de Prehistòria i Arqueologia, Universitat de València, Spain.,Department of Human Evolution, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mark Aldenderfer
- School of Social Sciences, Humanities, and Arts, University of California, Merced, USA
| | | | - Jessica Hendy
- Department of Archaeology, University of York, York, UK
| | - Darlene A Weston
- Faculty of Archaeology, Leiden University, Einsteinweg 2, 2333 CC, Leiden, the Netherlands.,Department of Anthropology, University of British Columbia, Vancouver, Canada
| | | | | | | | - Cecil M Lewis
- Department of Anthropology, University of Oklahoma, Norman, OK, USA
| | - Corinne Hofman
- Faculty of Archaeology, Leiden University, Einsteinweg 2, 2333 CC, Leiden, the Netherlands
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286
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Power RC, Salazar-García DC, Wittig RM, Freiberg M, Henry AG. Dental calculus evidence of Taï Forest Chimpanzee plant consumption and life history transitions. Sci Rep 2015; 5:15161. [PMID: 26481858 PMCID: PMC4611876 DOI: 10.1038/srep15161] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 09/17/2015] [Indexed: 11/09/2022] Open
Abstract
Dental calculus (calcified dental plaque) is a source of multiple types of data on life history. Recent research has targeted the plant microremains preserved in this mineralised deposit as a source of dietary and health information for recent and past populations. However, it is unclear to what extent we can interpret behaviour from microremains. Few studies to date have directly compared the microremain record from dental calculus to dietary records, and none with long-term observation dietary records, thus limiting how we can interpret diet, food acquisition and behaviour. Here we present a high-resolution analysis of calculus microremains from wild chimpanzees (Pan troglodytes verus) of Taï National Park, Côte d’Ivoire. We test microremain assemblages against more than two decades of field behavioural observations to establish the ability of calculus to capture the composition of diet. Our results show that some microremain classes accumulate as long-lived dietary markers. Phytolith abundance in calculus can reflect the proportions of plants in the diet, yet this pattern is not true for starches. We also report microremains can record information about other dietary behaviours, such as the age of weaning and learned food processing techniques like nut-cracking.
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Affiliation(s)
- Robert C Power
- Max Planck Research Group on Plant Foods in Hominin Dietary Ecology, Max Planck Institute for Evolutionary. Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Domingo C Salazar-García
- Department of Archaeology, University of Cape Town, Cape Town, South Africa.,Departament de Prehistòria y Arqueologia, Universitat de València, València, Spain.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Roman M Wittig
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany.,Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, Abidjan, Cote d'Ivoire
| | - Martin Freiberg
- Institute of Botany, University of Leipzig, 04103 Leipzig, Germany
| | - Amanda G Henry
- Max Planck Research Group on Plant Foods in Hominin Dietary Ecology, Max Planck Institute for Evolutionary. Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
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287
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Santiago-Rodriguez TM, Fornaciari G, Luciani S, Dowd SE, Toranzos GA, Marota I, Cano RJ. Gut Microbiome of an 11th Century A.D. Pre-Columbian Andean Mummy. PLoS One 2015; 10:e0138135. [PMID: 26422376 PMCID: PMC4589460 DOI: 10.1371/journal.pone.0138135] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 08/25/2015] [Indexed: 01/30/2023] Open
Abstract
The process of natural mummification is a rare and unique process from which little is known about the resulting microbial community structure. In the present study, we characterized the microbiome of paleofeces, and ascending, transverse and descending colon of an 11th century A.D. pre-Columbian Andean mummy by 16S rRNA gene high-throughput sequencing and metagenomics. Firmicutes were the most abundant bacterial group, with Clostridium spp. comprising up to 96.2% of the mummified gut, while Turicibacter spp. represented 89.2% of the bacteria identified in the paleofeces. Microbiome profile of the paleofeces was unique when compared to previously characterized coprolites that did not undergo natural mummification. We identified DNA sequences homologous to Clostridium botulinum, Trypanosoma cruzi and human papillomaviruses (HPVs). Unexpectedly, putative antibiotic-resistance genes including beta-lactamases, penicillin-binding proteins, resistance to fosfomycin, chloramphenicol, aminoglycosides, macrolides, sulfa, quinolones, tetracycline and vancomycin, and multi-drug transporters, were also identified. The presence of putative antibiotic-resistance genes suggests that resistance may not necessarily be associated with a selective pressure of antibiotics or contact with European cultures. Identification of pathogens and antibiotic-resistance genes in ancient human specimens will aid in the understanding of the evolution of pathogens as a way to treat and prevent diseases caused by bacteria, microbial eukaryotes and viruses.
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Affiliation(s)
| | - Gino Fornaciari
- Department of Translational Research on New Technologies in Medicine and Surgery, Division of Paleopathology, University of Pisa, Pisa, Italy
- Center for Anthropological, Paleopathological and Historical Studies of the Sardinian and Mediterranean Populations, Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Stefania Luciani
- Laboratory of Molecular Archaeo-Anthropology/ancient DNA, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Scot E. Dowd
- Molecular Research LP (MR DNA), Shallowater, Texas, United States of America
| | | | - Isolina Marota
- Laboratory of Molecular Archaeo-Anthropology/ancient DNA, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Raul J. Cano
- Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA, United States of America
- * E-mail:
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288
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Huynh H, Verneau J, Levasseur A, Drancourt M, Aboudharam G. Bacteria and archaea paleomicrobiology of the dental calculus: a review. Mol Oral Microbiol 2015. [DOI: 10.1111/omi.12118] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- H.T.T. Huynh
- Faculté d'Odontologie; Aix-Marseille Université; Marseille France
- URMITE; UMR CNRS 7278, IRD 198, INSERM 1095; Faculté de Médecine; Aix-Marseille Université; Marseille France
| | - J. Verneau
- URMITE; UMR CNRS 7278, IRD 198, INSERM 1095; Faculté de Médecine; Aix-Marseille Université; Marseille France
| | - A. Levasseur
- URMITE; UMR CNRS 7278, IRD 198, INSERM 1095; Faculté de Médecine; Aix-Marseille Université; Marseille France
| | - M. Drancourt
- URMITE; UMR CNRS 7278, IRD 198, INSERM 1095; Faculté de Médecine; Aix-Marseille Université; Marseille France
| | - G. Aboudharam
- Faculté d'Odontologie; Aix-Marseille Université; Marseille France
- URMITE; UMR CNRS 7278, IRD 198, INSERM 1095; Faculté de Médecine; Aix-Marseille Université; Marseille France
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289
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Conservation archaeogenomics: ancient DNA and biodiversity in the Anthropocene. Trends Ecol Evol 2015; 30:540-9. [PMID: 26169594 DOI: 10.1016/j.tree.2015.06.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 06/11/2015] [Accepted: 06/15/2015] [Indexed: 11/22/2022]
Abstract
There is growing consensus that we have entered the Anthropocene, a geologic epoch characterized by human domination of the ecosystems of the Earth. With the future uncertain, we are faced with understanding how global biodiversity will respond to anthropogenic perturbations. The archaeological record provides perspective on human-environment relations through time and across space. Ancient DNA (aDNA) analyses of plant and animal remains from archaeological sites are particularly useful for understanding past human-environment interactions, which can help guide conservation decisions during the environmental changes of the Anthropocene. Here, we define the emerging field of conservation archaeogenomics, which integrates archaeological and genomic data to generate baselines or benchmarks for scientists, managers, and policy-makers by evaluating climatic and human impacts on past, present, and future biodiversity.
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290
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Orlando L, Gilbert MTP, Willerslev E. Reconstructing ancient genomes and epigenomes. Nat Rev Genet 2015; 16:395-408. [PMID: 26055157 DOI: 10.1038/nrg3935] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Research involving ancient DNA (aDNA) has experienced a true technological revolution in recent years through advances in the recovery of aDNA and, particularly, through applications of high-throughput sequencing. Formerly restricted to the analysis of only limited amounts of genetic information, aDNA studies have now progressed to whole-genome sequencing for an increasing number of ancient individuals and extinct species, as well as to epigenomic characterization. Such advances have enabled the sequencing of specimens of up to 1 million years old, which, owing to their extensive DNA damage and contamination, were previously not amenable to genetic analyses. In this Review, we discuss these varied technical challenges and solutions for sequencing ancient genomes and epigenomes.
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Affiliation(s)
- Ludovic Orlando
- 1] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen 1350C, Denmark. [2] Université de Toulouse, University Paul Sabatier (UPS), Laboratoire AMIS, CNRS UMR 5288, 37 allées Jules Guesde, 31000 Toulouse, France
| | - M Thomas P Gilbert
- 1] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen 1350C, Denmark. [2] Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6102, Australia
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen 1350C, Denmark
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291
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Metagenome Sequencing of the Hadza Hunter-Gatherer Gut Microbiota. Curr Biol 2015; 25:1682-93. [PMID: 25981789 DOI: 10.1016/j.cub.2015.04.055] [Citation(s) in RCA: 232] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 04/09/2015] [Accepted: 04/29/2015] [Indexed: 12/21/2022]
Abstract
Through human microbiome sequencing, we can better understand how host evolutionary and ontogenetic history is reflected in the microbial function. However, there has been no information on the gut metagenome configuration in hunter-gatherer populations, posing a gap in our knowledge of gut microbiota (GM)-host mutualism arising from a lifestyle that describes over 90% of human evolutionary history. Here, we present the first metagenomic analysis of GM from Hadza hunter-gatherers of Tanzania, showing a unique enrichment in metabolic pathways that aligns with the dietary and environmental factors characteristic of their foraging lifestyle. We found that the Hadza GM is adapted for broad-spectrum carbohydrate metabolism, reflecting the complex polysaccharides in their diet. Furthermore, the Hadza GM is equipped for branched-chain amino acid degradation and aromatic amino acid biosynthesis. Resistome functionality demonstrates the existence of antibiotic resistance genes in a population with little antibiotic exposure, indicating the ubiquitous presence of environmentally derived resistances. Our results demonstrate how the functional specificity of the GM correlates with certain environment and lifestyle factors and how complexity from the exogenous environment can be balanced by endogenous homeostasis. The Hadza gut metagenome structure allows us to appreciate the co-adaptive functional role of the GM in complementing the human physiology, providing a better understanding of the versatility of human life and subsistence.
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292
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Clemente JC, Pehrsson EC, Blaser MJ, Sandhu K, Gao Z, Wang B, Magris M, Hidalgo G, Contreras M, Noya-Alarcón Ó, Lander O, McDonald J, Cox M, Walter J, Oh PL, Ruiz JF, Rodriguez S, Shen N, Song SJ, Metcalf J, Knight R, Dantas G, Dominguez-Bello MG. The microbiome of uncontacted Amerindians. SCIENCE ADVANCES 2015; 1:e1500183. [PMID: 26229982 PMCID: PMC4517851 DOI: 10.1126/sciadv.1500183] [Citation(s) in RCA: 510] [Impact Index Per Article: 56.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Most studies of the human microbiome have focused on westernized people with life-style practices that decrease microbial survival and transmission, or on traditional societies that are currently in transition to westernization. We characterize the fecal, oral, and skin bacterial microbiome and resistome of members of an isolated Yanomami Amerindian village with no documented previous contact with Western people. These Yanomami harbor a microbiome with the highest diversity of bacteria and genetic functions ever reported in a human group. Despite their isolation, presumably for >11,000 years since their ancestors arrived in South America, and no known exposure to antibiotics, they harbor bacteria that carry functional antibiotic resistance (AR) genes, including those that confer resistance to synthetic antibiotics and are syntenic with mobilization elements. These results suggest that westernization significantly affects human microbiome diversity and that functional AR genes appear to be a feature of the human microbiome even in the absence of exposure to commercial antibiotics. AR genes are likely poised for mobilization and enrichment upon exposure to pharmacological levels of antibiotics. Our findings emphasize the need for extensive characterization of the function of the microbiome and resistome in remote nonwesternized populations before globalization of modern practices affects potentially beneficial bacteria harbored in the human body.
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Affiliation(s)
- Jose C. Clemente
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Erica C. Pehrsson
- Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Martin J. Blaser
- Laboratory Service, VA Medical Center, New York, NY 10010, USA
- New York University School of Medicine, New York, NY 10016, USA
| | - Kuldip Sandhu
- New York University School of Medicine, New York, NY 10016, USA
| | - Zhan Gao
- New York University School of Medicine, New York, NY 10016, USA
| | - Bin Wang
- Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Magda Magris
- Amazonic Center for Research and Control of Tropical Diseases (CAICET), Puerto Ayacucho 7101, Venezuela
| | - Glida Hidalgo
- Amazonic Center for Research and Control of Tropical Diseases (CAICET), Puerto Ayacucho 7101, Venezuela
| | - Monica Contreras
- Venezuelan Institute for Scientific Research, Caracas 1020-A, Venezuela
| | - Óscar Noya-Alarcón
- Amazonic Center for Research and Control of Tropical Diseases (CAICET), Puerto Ayacucho 7101, Venezuela
| | - Orlana Lander
- Sección de Ecología Parasitaria, Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas 1051, Venezuela
| | | | - Mike Cox
- Anaerobe Systems, Morgan Hill, CA 95037, USA
| | - Jens Walter
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68583, USA
| | - Phaik Lyn Oh
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68583, USA
| | - Jean F. Ruiz
- Department of Biology, University of Puerto Rico, Rio Piedras 00931, Puerto Rico
| | - Selena Rodriguez
- Department of Biology, University of Puerto Rico, Rio Piedras 00931, Puerto Rico
| | - Nan Shen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Se Jin Song
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
| | - Jessica Metcalf
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
| | - Rob Knight
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
- Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA
| | - Gautam Dantas
- Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - M. Gloria Dominguez-Bello
- New York University School of Medicine, New York, NY 10016, USA
- Venezuelan Institute for Scientific Research, Caracas 1020-A, Venezuela
- Department of Biology, University of Puerto Rico, Rio Piedras 00931, Puerto Rico
- Corresponding author. E-mail:
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293
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Liu G, Tang CM, Exley RM. Non-pathogenic Neisseria: members of an abundant, multi-habitat, diverse genus. MICROBIOLOGY-SGM 2015; 161:1297-1312. [PMID: 25814039 DOI: 10.1099/mic.0.000086] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The genus Neisseria contains the important pathogens Neisseria meningitidis and Neisseria gonorrhoeae. These Gram-negative coccoid bacteria are generally thought to be restricted to humans and inhabit mucosal surfaces in the upper respiratory and genito-urinary tracts. While the meningococcus and gonococcus have been widely studied, far less attention has been paid to other Neisseria species. Here we review current knowledge of the distribution of commensal Neisseria in humans and other hosts. Analysis of the microbiome has revealed that Neisseria is an abundant member of the oropharyngeal flora, and we review its potential impact on health and disease. Neisseria also exhibit remarkable diversity, exhibiting both coccoid and rod-shaped morphologies, as well as environmental strains which are capable of degrading complex organic molecules.
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Affiliation(s)
- Guangyu Liu
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Christoph M Tang
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Rachel M Exley
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
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294
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Nobbs AH, Jenkinson HF. Interkingdom networking within the oral microbiome. Microbes Infect 2015; 17:484-92. [PMID: 25805401 DOI: 10.1016/j.micinf.2015.03.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 03/10/2015] [Accepted: 03/13/2015] [Indexed: 02/07/2023]
Abstract
Different sites within the oropharynx harbour unique microbial communities. Co-evolution of microbes and host has resulted in complex interkingdom circuitries. Metabolic signalling is crucial to these processes, and novel microbial communication factors are progressively being discovered. Resolving interkingdom networks will lead to better understanding of oral health or disease aetiology.
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Affiliation(s)
- Angela H Nobbs
- School of Oral and Dental Sciences, University of Bristol, Bristol BS1 2LY, United Kingdom
| | - Howard F Jenkinson
- School of Oral and Dental Sciences, University of Bristol, Bristol BS1 2LY, United Kingdom.
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295
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Appels R, Nystrom J, Webster H, Keeble-Gagnere G. Discoveries and advances in plant and animal genomics. Funct Integr Genomics 2015; 15:121-9. [PMID: 25763751 PMCID: PMC4361718 DOI: 10.1007/s10142-015-0434-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 02/17/2015] [Accepted: 02/19/2015] [Indexed: 12/04/2022]
Abstract
Plant and animal genomics is a broad area of research with respect to the biological issues covered because it continues to deal with the structure and function of genetic material underpinning all organisms. This mini-review utilizes the plenary lectures from the Plant and Animal Genome Conference as a basis for summarizing the trends in the genome-level studies of organisms.
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Affiliation(s)
- Rudi Appels
- School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Murdoch, Perth, Australia, 6150,
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296
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Castro-Nallar E, Hasan NA, Cebula TA, Colwell RR, Robison RA, Johnson WE, Crandall KA. Concordance and discordance of sequence survey methods for molecular epidemiology. PeerJ 2015; 3:e761. [PMID: 25737810 PMCID: PMC4338773 DOI: 10.7717/peerj.761] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 01/21/2015] [Indexed: 12/23/2022] Open
Abstract
The post-genomic era is characterized by the direct acquisition and analysis of genomic data with many applications, including the enhancement of the understanding of microbial epidemiology and pathology. However, there are a number of molecular approaches to survey pathogen diversity, and the impact of these different approaches on parameter estimation and inference are not entirely clear. We sequenced whole genomes of bacterial pathogens, Burkholderia pseudomallei, Yersinia pestis, and Brucella spp. (60 new genomes), and combined them with 55 genomes from GenBank to address how different molecular survey approaches (whole genomes, SNPs, and MLST) impact downstream inferences on molecular evolutionary parameters, evolutionary relationships, and trait character associations. We selected isolates for sequencing to represent temporal, geographic origin, and host range variability. We found that substitution rate estimates vary widely among approaches, and that SNP and genomic datasets yielded different but strongly supported phylogenies. MLST yielded poorly supported phylogenies, especially in our low diversity dataset, i.e., Y. pestis. Trait associations showed that B. pseudomallei and Y. pestis phylogenies are significantly associated with geography, irrespective of the molecular survey approach used, while Brucella spp. phylogeny appears to be strongly associated with geography and host origin. We contrast inferences made among monomorphic (clonal) and non-monomorphic bacteria, and between intra- and inter-specific datasets. We also discuss our results in light of underlying assumptions of different approaches.
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Affiliation(s)
| | - Nur A. Hasan
- CosmosID, College Park, MD, USA
- University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, MD, USA
| | - Thomas A. Cebula
- CosmosID, College Park, MD, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Rita R. Colwell
- CosmosID, College Park, MD, USA
- University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, MD, USA
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Richard A. Robison
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, USA
| | - W. Evan Johnson
- Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA
| | - Keith A. Crandall
- Computational Biology Institute, George Washington University, Ashburn, VA, USA
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297
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Warinner C, Speller C, Collins MJ, Lewis CM. Ancient human microbiomes. J Hum Evol 2015; 79:125-36. [PMID: 25559298 PMCID: PMC4312737 DOI: 10.1016/j.jhevol.2014.10.016] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 07/06/2014] [Accepted: 10/29/2014] [Indexed: 12/20/2022]
Abstract
Very recently, we discovered a vast new microbial self: the human microbiome. Our native microbiota interface with our biology and culture to influence our health, behavior, and quality of life, and yet we know very little about their origin, evolution, or ecology. With the advent of industrialization, globalization, and modern sanitation, it is intuitive that we have changed our relationship with microbes, but we have little information about the ancestral state of our microbiome, and we therefore lack a foundation for characterizing this change. High-throughput sequencing has opened up new opportunities in the field of paleomicrobiology, allowing us to investigate the evolution of the complex microbial ecologies that inhabit our bodies. By focusing on recent coprolite and dental calculus research, we explore how emerging research on ancient human microbiomes is changing the way we think about ancient disease and how archaeological studies can contribute to a medical understanding of health and nutrition today.
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Affiliation(s)
- Christina Warinner
- Department of Anthropology, University of Oklahoma, 101 David L. Boren Blvd., Norman, OK 73019, USA
| | - Camilla Speller
- Department of Archaeology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Matthew J Collins
- Department of Archaeology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Cecil M Lewis
- Department of Anthropology, University of Oklahoma, 101 David L. Boren Blvd., Norman, OK 73019, USA.
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298
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Warinner C, Speller C, Collins MJ. A new era in palaeomicrobiology: prospects for ancient dental calculus as a long-term record of the human oral microbiome. Philos Trans R Soc Lond B Biol Sci 2015; 370:20130376. [PMID: 25487328 PMCID: PMC4275884 DOI: 10.1098/rstb.2013.0376] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The field of palaeomicrobiology is dramatically expanding thanks to recent advances in high-throughput biomolecular sequencing, which allows unprecedented access to the evolutionary history and ecology of human-associated and environmental microbes. Recently, human dental calculus has been shown to be an abundant, nearly ubiquitous, and long-term reservoir of the ancient oral microbiome, preserving not only microbial and host biomolecules but also dietary and environmental debris. Modern investigations of native human microbiota have demonstrated that the human microbiome plays a central role in health and chronic disease, raising questions about changes in microbial ecology, diversity and function through time. This paper explores the current state of ancient oral microbiome research and discusses successful applications, methodological challenges and future possibilities in elucidating the intimate evolutionary relationship between humans and their microbes.
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299
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Der Sarkissian C, Allentoft ME, Ávila-Arcos MC, Barnett R, Campos PF, Cappellini E, Ermini L, Fernández R, da Fonseca R, Ginolhac A, Hansen AJ, Jónsson H, Korneliussen T, Margaryan A, Martin MD, Moreno-Mayar JV, Raghavan M, Rasmussen M, Velasco MS, Schroeder H, Schubert M, Seguin-Orlando A, Wales N, Gilbert MTP, Willerslev E, Orlando L. Ancient genomics. Philos Trans R Soc Lond B Biol Sci 2015; 370:20130387. [PMID: 25487338 PMCID: PMC4275894 DOI: 10.1098/rstb.2013.0387] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when testing specific hypotheses related to the past.
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Affiliation(s)
- Clio Der Sarkissian
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Morten E Allentoft
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - María C Ávila-Arcos
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Ross Barnett
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Paula F Campos
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Enrico Cappellini
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Luca Ermini
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Ruth Fernández
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Rute da Fonseca
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Aurélien Ginolhac
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Anders J Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Hákon Jónsson
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Thorfinn Korneliussen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Ashot Margaryan
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Michael D Martin
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - J Víctor Moreno-Mayar
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Maanasa Raghavan
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Morten Rasmussen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Marcela Sandoval Velasco
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Hannes Schroeder
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Nathan Wales
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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300
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Ancient pathogen genomics: insights into timing and adaptation. J Hum Evol 2014; 79:137-49. [PMID: 25532802 DOI: 10.1016/j.jhevol.2014.11.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 09/08/2014] [Accepted: 11/05/2014] [Indexed: 12/15/2022]
Abstract
Disease is a major cause of natural selection affecting human evolution, whether through a sudden pandemic or persistent morbidity and mortality. Recent contributions in the field of ancient pathogen genomics have advanced our understanding of the antiquity and nature of human-pathogen interactions through time. Technical advancements have facilitated the recovery, enrichment, and high-throughput sequencing of pathogen and parasite DNA from archived and archaeological remains. These time-stamped genomes are crucial for calibrating molecular clocks to infer the timing of evolutionary events, while providing finer-grain resolution to phylogenetic reconstructions and complex biogeographical patterns. Additionally, genome scale data allow better identification of substitutions linked to adaptations of the pathogen to their human hosts. As methodology continues to improve, ancient genomes of humans and their diverse microbiomes from a range of eras and archaeological contexts will enable population-level ancient analyses in the near future and a better understanding of their co-evolutionary history.
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