1
|
Elechi JOG, Sirianni R, Conforti FL, Cione E, Pellegrino M. Food System Transformation and Gut Microbiota Transition: Evidence on Advancing Obesity, Cardiovascular Diseases, and Cancers-A Narrative Review. Foods 2023; 12:2286. [PMID: 37372497 DOI: 10.3390/foods12122286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
Food, a vital component of our daily life, is fundamental to our health and well-being, and the knowledge and practices relating to food have been passed down from countless generations of ancestors. Systems may be used to describe this extremely extensive and varied body of agricultural and gastronomic knowledge that has been gathered via evolutionary processes. The gut microbiota also underwent changes as the food system did, and these alterations had a variety of effects on human health. In recent decades, the gut microbiome has gained attention due to its health benefits as well as its pathological effects on human health. Many studies have shown that a person's gut microbiota partially determines the nutritional value of food and that diet, in turn, shapes both the microbiota and the microbiome. The current narrative review aims to explain how changes in the food system over time affect the makeup and evolution of the gut microbiota, advancing obesity, cardiovascular disease (CVD), and cancer. After a brief discussion of the food system's variety and the gut microbiota's functions, we concentrate on the relationship between the evolution of food system transformation and gut microbiota system transition linked to the increase of non-communicable diseases (NCDs). Finally, we also describe sustainable food system transformation strategies to ensure healthy microbiota composition recovery and maintain the host gut barrier and immune functions to reverse advancing NCDs.
Collapse
Affiliation(s)
- Jasper Okoro Godwin Elechi
- Department of Pharmacy and Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy
| | - Rosa Sirianni
- Department of Pharmacy and Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy
| | - Francesca Luisa Conforti
- Department of Pharmacy and Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy
| | - Erika Cione
- Department of Pharmacy and Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy
| | - Michele Pellegrino
- Department of Pharmacy and Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy
| |
Collapse
|
2
|
Bradshaw MJ, Carey J, Liu M, Bartholomew HP, Jurick WM, Hambleton S, Hendricks D, Schnittler M, Scholler M. Genetic time traveling: sequencing old herbarium specimens, including the oldest herbarium specimen sequenced from kingdom Fungi, reveals the population structure of an agriculturally significant rust. THE NEW PHYTOLOGIST 2023; 237:1463-1473. [PMID: 36385249 DOI: 10.1111/nph.18622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
Sequencing herbarium specimens can be instrumental in answering ecological, evolutionary, and taxonomic inquiries. We developed a protocol for sequencing herbarium specimens of rust fungi (Pucciniales) and proceeded to sequence specimens ranging from 4 to 211 yr old from five different genera. We then obtained sequences from an economically important biological control agent, Puccinia suaveolens, to highlight the potential of sequencing herbarium specimens in an ecological sense and to evaluate the following hypotheses: (1) The population structure of a plant pathogen changes over time, and (2) introduced pathogens are more diverse in their native range. Our efforts resulted in sequences from 87 herbarium specimens that revealed a high level of diversity with a population structure that exhibited spatial-temporal patterns. The specimens sequenced from Europe showed more diversity than the ones from North America, uncovering an invasion pattern likely related to its European native host in North America. Additionally, to the best of our knowledge, the specimen from France collected in c. 1811 is the oldest herbarium specimen sequenced from kingdom Fungi. In conclusion, sequencing old herbarium specimens is an important tool that can be extrapolated to better understand plant-microbe evolution and to evaluate old type specimens to solidify the taxonomy of plant pathogenic fungi.
Collapse
Affiliation(s)
- Michael J Bradshaw
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Julie Carey
- Biodiversity and Bioresources, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - Miao Liu
- Biodiversity and Bioresources, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - Holly P Bartholomew
- Food Quality Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA
| | - Wayne M Jurick
- Food Quality Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA
| | - Sarah Hambleton
- Biodiversity and Bioresources, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - Dylan Hendricks
- School of Environmental and Forest Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Martin Schnittler
- General Botany and Plant Systematics, Institute of Botany and Landscape Ecology, Ernst Moritz Arndt University Greifswald, 17487, Greifswald, Germany
| | - Markus Scholler
- Staatliches Museum für Naturkunde, Abteilung Biowissenschaften, D-76133, Karlsruhe, Germany
| |
Collapse
|
3
|
Warinner C. An Archaeology of Microbes. JOURNAL OF ANTHROPOLOGICAL RESEARCH 2022. [DOI: 10.1086/721976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Christina Warinner
- Department of Anthropology, Harvard University, Cambridge MA, USA 02138, and Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany 04103
| |
Collapse
|
4
|
van der Kuyl AC. Historic and Prehistoric Epidemics: An Overview of Sources Available for the Study of Ancient Pathogens. EPIDEMIOLOGIA (BASEL, SWITZERLAND) 2022; 3:443-464. [PMID: 36547255 PMCID: PMC9778136 DOI: 10.3390/epidemiologia3040034] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 12/24/2022]
Abstract
Since life on earth developed, parasitic microbes have thrived. Increases in host numbers, or the conquest of a new species, provide an opportunity for such a pathogen to enjoy, before host defense systems kick in, a similar upsurge in reproduction. Outbreaks, caused by "endemic" pathogens, and epidemics, caused by "novel" pathogens, have thus been creating chaos and destruction since prehistorical times. To study such (pre)historic epidemics, recent advances in the ancient DNA field, applied to both archeological and historical remains, have helped tremendously to elucidate the evolutionary trajectory of pathogens. These studies have offered new and unexpected insights into the evolution of, for instance, smallpox virus, hepatitis B virus, and the plague-causing bacterium Yersinia pestis. Furthermore, burial patterns and historical publications can help in tracking down ancient pathogens. Another source of information is our genome, where selective sweeps in immune-related genes relate to past pathogen attacks, while multiple viruses have left their genomes behind for us to study. This review will discuss the sources available to investigate (pre)historic diseases, as molecular knowledge of historic and prehistoric pathogens may help us understand the past and the present, and prepare us for future epidemics.
Collapse
Affiliation(s)
- Antoinette C. van der Kuyl
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; ; Tel.: +31-205-666-778
- Amsterdam Institute for Infection and Immunity, 1100 DD Amsterdam, The Netherlands
| |
Collapse
|
5
|
Nodari R, Drancourt M, Barbieri R. Paleomicrobiology of the human digestive tract: A review. Microb Pathog 2021; 157:104972. [PMID: 34029658 DOI: 10.1016/j.micpath.2021.104972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 04/23/2021] [Accepted: 05/14/2021] [Indexed: 10/21/2022]
Abstract
The microbiota is a hot topic of research in medical microbiology, boosted by culturomics and metagenomics, with unanticipated knowledge outputs in physiology and pathology. Knowledge of the microbiota in ancient populations may therefore be of prime interest in understanding factors shaping the coevolution of the microbiota and populations. Studies on ancient human microbiomes can help us understand how the community of microorganisms presents in the oral cavity and the gut was shaped during the evolution of our species and what environmental, social or cultural changes may have changed it. This review cumulates and summarizes the discoveries in the field of the ancient human microbiota, focusing on the remains used as samples and techniques used to handle and analyze them.
Collapse
Affiliation(s)
- Riccardo Nodari
- Department of Biosciences and Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", University of Milan, Milan, 20133, Italy
| | - Michel Drancourt
- Aix-Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Rémi Barbieri
- Aix-Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France; UMR 7268, Anthropologie Bioculturelle, Droit, Ethique et Santé, Aix Marseille Univ., 11 CNRS, EFS, ADES, Marseille, France.
| |
Collapse
|
6
|
Arning N, Wilson DJ. The past, present and future of ancient bacterial DNA. Microb Genom 2020; 6:mgen000384. [PMID: 32598277 PMCID: PMC7478633 DOI: 10.1099/mgen.0.000384] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/18/2020] [Indexed: 12/12/2022] Open
Abstract
Groundbreaking studies conducted in the mid-1980s demonstrated the possibility of sequencing ancient DNA (aDNA), which has allowed us to answer fundamental questions about the human past. Microbiologists were thus given a powerful tool to glimpse directly into inscrutable bacterial history, hitherto inaccessible due to a poor fossil record. Initially plagued by concerns regarding contamination, the field has grown alongside technical progress, with the advent of high-throughput sequencing being a breakthrough in sequence output and authentication. Albeit burdened with challenges unique to the analysis of bacteria, a growing number of viable sources for aDNA has opened multiple avenues of microbial research. Ancient pathogens have been extracted from bones, dental pulp, mummies and historical medical specimens and have answered focal historical questions such as identifying the aetiological agent of the black death as Yersinia pestis. Furthermore, ancient human microbiomes from fossilized faeces, mummies and dental plaque have shown shifts in human commensals through the Neolithic demographic transition and industrial revolution, whereas environmental isolates stemming from permafrost samples have revealed signs of ancient antimicrobial resistance. Culminating in an ever-growing repertoire of ancient genomes, the quickly expanding body of bacterial aDNA studies has also enabled comparisons of ancient genomes to their extant counterparts, illuminating the evolutionary history of bacteria. In this review we summarize the present avenues of research and contextualize them in the past of the field whilst also pointing towards questions still to be answered.
Collapse
Affiliation(s)
- Nicolas Arning
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford, OX3 7LF, UK
| | - Daniel J. Wilson
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford, OX3 7LF, UK
| |
Collapse
|
7
|
Moles L, Otaegui D. The Impact of Diet on Microbiota Evolution and Human Health. Is Diet an Adequate Tool for Microbiota Modulation? Nutrients 2020; 12:nu12061654. [PMID: 32498430 PMCID: PMC7352211 DOI: 10.3390/nu12061654] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/29/2020] [Accepted: 05/31/2020] [Indexed: 02/08/2023] Open
Abstract
The human microbiome is emerging as an interesting field in research into the prevention of health problems and recovery from illness in humans. The complex ecosystem formed by the microbiota is continuously interacting with its host and the environment. Diet could be assumed to be one of the most prominent factors influencing the microbiota composition. Nevertheless, and in spite of numerous strategies proposed to modulate the human microbiota through dietary means, guidelines to achieve this goal have yet to be established. This review assesses the correlation between social and dietary changes over the course of human evolution and the adaptation of the human microbiota to those changes. In addition, it discusses the main dietary strategies for modulating the microbiota and the difficulties of putting them properly into practice.
Collapse
|
8
|
Nystrom KC. Advances in paleopathology in context: A focus on soft tissue paleopathology. INTERNATIONAL JOURNAL OF PALEOPATHOLOGY 2020; 29:16-23. [PMID: 31481317 DOI: 10.1016/j.ijpp.2019.07.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 07/11/2019] [Accepted: 07/21/2019] [Indexed: 06/10/2023]
Abstract
Skeletal and mummified remains from South America have had a significant impact on the progress of paleopathological research. In 1997, John Verano synthesized the state of paleopathological research, identifying trends and highlighting future potentials. The goal of this contribution is to consider Verano's observations on advances in soft tissue paleopathology within the context of the development of the field of mummy studies. As his article was published near the midpoint between the present and the early 1970s, when the modern form of mummy studies began to form, considering his observations in this context allows researchers the opportunity to consider how the field has progressed since the late 1990s.
Collapse
Affiliation(s)
- Kenneth C Nystrom
- Department of Anthropology, State University of New York at New Paltz, New Paltz, NY 12561, USA.
| |
Collapse
|
9
|
Toyne JM, Murphy MS, Klaus HD. An introduction to advances in Andean South American paleopathology. INTERNATIONAL JOURNAL OF PALEOPATHOLOGY 2020; 29:1-15. [PMID: 32334998 DOI: 10.1016/j.ijpp.2019.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 09/20/2019] [Accepted: 09/22/2019] [Indexed: 06/11/2023]
Abstract
In the 20 years since the publication of John Verano's foundational paper "Advances in Paleopathology of Andean South America," paleopathological and bioarchaeological investigations of human skeletal remains in the region have increased dramatically. Today, primary foci have grown to span the identification of disease, detailed reconstructions of biocultural interactions, embodied social experiences, and ancient living worlds. In this special issue, more than a dozen scholars reflect on the state of developments in the scientific analyses of ancient disease, life, and society across the region. For this introductory article, we frame the current state of Andean paleopathology by reviewing key historical contributions beginning in the last century. More recent trends since 1997 are defined via a meta-analysis of the literature. We then highlight current innovations and consider future directions of study. We then close with an overview of the papers comprising this special issue. Each article explores major theoretical, topical, and methodological advances that have transpired since 1997 and charts the course for the next two decades of work - with implications and insights that transcend the Andes and speak to key paleopathological issues around the world.
Collapse
Affiliation(s)
- J Marla Toyne
- Department of Anthropology, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL, 32803-1631, United States.
| | - Melissa S Murphy
- Anthropology Department, 12th and Lewis Streets, Laramie, WY, 82071, United States.
| | - Haagen D Klaus
- Dept. of Sociology and Anthropology, Robinson Hall B Room 305, 4400 University Dr., Mailcode 3G5, George Mason University, Fairfax, VA, 22030, United States.
| |
Collapse
|
10
|
Abstract
The trillions of microbes living in the gut—the gut microbiota—play an important role in human biology and disease. While much has been done to explore its diversity, a full understanding of our microbiomes demands an evolutionary perspective. In this review, we compare microbiomes from human populations, placing them in the context of microbes from humanity’s near and distant animal relatives. We discuss potential mechanisms to generate host-specific microbiome configurations and the consequences of disrupting those configurations. Finally, we propose that this broader phylogenetic perspective is useful for understanding the mechanisms underlying human–microbiome interactions.
Collapse
Affiliation(s)
- Emily R Davenport
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Jon G Sanders
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Se Jin Song
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, IL, USA
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA. .,Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA. .,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
| |
Collapse
|
11
|
Gut Microbiome and Putative Resistome of Inca and Italian Nobility Mummies. Genes (Basel) 2017; 8:genes8110310. [PMID: 29112136 PMCID: PMC5704223 DOI: 10.3390/genes8110310] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/20/2017] [Accepted: 10/25/2017] [Indexed: 01/09/2023] Open
Abstract
Little is still known about the microbiome resulting from the process of mummification of the human gut. In the present study, the gut microbiota, genes associated with metabolism, and putative resistome of Inca and Italian nobility mummies were characterized by using high-throughput sequencing. The Italian nobility mummies exhibited a higher bacterial diversity as compared to the Inca mummies when using 16S ribosomal (rRNA) gene amplicon sequencing, but both groups showed bacterial and fungal taxa when using shotgun metagenomic sequencing that may resemble both the thanatomicrobiome and extant human gut microbiomes. Identification of sequences associated with plants, animals, and carbohydrate-active enzymes (CAZymes) may provide further insights into the dietary habits of Inca and Italian nobility mummies. Putative antibiotic-resistance genes in the Inca and Italian nobility mummies support a human gut resistome prior to the antibiotic therapy era. The higher proportion of putative antibiotic-resistance genes in the Inca compared to Italian nobility mummies may support the hypotheses that a greater exposure to the environment may result in a greater acquisition of antibiotic-resistance genes. The present study adds knowledge of the microbiome resulting from the process of mummification of the human gut, insights of ancient dietary habits, and the preserved putative human gut resistome prior the antibiotic therapy era.
Collapse
|
12
|
Philips A, Stolarek I, Kuczkowska B, Juras A, Handschuh L, Piontek J, Kozlowski P, Figlerowicz M. Comprehensive analysis of microorganisms accompanying human archaeological remains. Gigascience 2017; 6:1-13. [PMID: 28609785 PMCID: PMC5965364 DOI: 10.1093/gigascience/gix044] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 05/09/2017] [Accepted: 06/11/2017] [Indexed: 02/01/2023] Open
Abstract
Metagenome analysis has become a common source of information about microbial communities that occupy a wide range of niches, including archaeological specimens. It has been shown that the vast majority of DNA extracted from ancient samples come from bacteria (presumably modern contaminants). However, characterization of microbial DNA accompanying human remains has never been done systematically for a wide range of different samples. We used metagenomic approaches to perform comparative analyses of microorganism communities present in 161 archaeological human remains. DNA samples were isolated from the teeth of human skeletons dated from 100 AD to 1200 AD. The skeletons were collected from 7 archaeological sites in Central Europe and stored under different conditions. The majority of identified microbes were ubiquitous environmental bacteria that most likely contaminated the host remains not long ago. We observed that the composition of microbial communities was sample-specific and not correlated with its temporal or geographical origin. Additionally, traces of bacteria and archaea typical for human oral/gut flora, as well as potential pathogens, were identified in two-thirds of the samples. The genetic material of human-related species, in contrast to the environmental species that accounted for the majority of identified bacteria, displayed DNA damage patterns comparable with endogenous human ancient DNA, which suggested that these microbes might have accompanied the individual before death. Our study showed that the microbiome observed in an individual sample is not reliant on the method or duration of sample storage. Moreover, shallow sequencing of DNA extracted from ancient specimens and subsequent bioinformatics analysis allowed both the identification of ancient microbial species, including potential pathogens, and their differentiation from contemporary species that colonized human remains more recently.
Collapse
Affiliation(s)
- Anna Philips
- European Center for Bioinformatics and Genomics, Institute of Bioorganic
Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
| | - Ireneusz Stolarek
- European Center for Bioinformatics and Genomics, Institute of Bioorganic
Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
| | - Bogna Kuczkowska
- European Center for Bioinformatics and Genomics, Institute of Bioorganic
Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
| | - Anna Juras
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty
of Biology, Adam Mickiewicz University in Poznan, Poznan, 61-614, Poland
| | - Luiza Handschuh
- European Center for Bioinformatics and Genomics, Institute of Bioorganic
Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
- Department of Hematology and Bone Marrow Transplantation, University of
Medical Sciences, Poznan, 60-569, Poland
- Institute of Technology and Chemical Engineering, Poznan University of
Technology, Poznan, 60-965, Poland
| | - Janusz Piontek
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty
of Biology, Adam Mickiewicz University in Poznan, Poznan, 61-614, Poland
| | - Piotr Kozlowski
- European Center for Bioinformatics and Genomics, Institute of Bioorganic
Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
- Institute of Technology and Chemical Engineering, Poznan University of
Technology, Poznan, 60-965, Poland
| | - Marek Figlerowicz
- European Center for Bioinformatics and Genomics, Institute of Bioorganic
Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
- Institute of Computing Science, Poznan University of Technology, Poznan,
60-965, Poland
| |
Collapse
|
13
|
Santiago-Rodriguez TM, Narganes-Storde Y, Chanlatte-Baik L, Toranzos GA, Cano RJ. Insights of the dental calculi microbiome of pre-Columbian inhabitants from Puerto Rico. PeerJ 2017; 5:e3277. [PMID: 28480145 PMCID: PMC5417066 DOI: 10.7717/peerj.3277] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 04/05/2017] [Indexed: 11/30/2022] Open
Abstract
Background The study of ancient microorganisms in mineralized dental plaque or calculi is providing insights into microbial evolution, as well as lifestyles and disease states of extinct cultures; yet, little is still known about the oral microbial community structure and function of pre-Columbian Caribbean cultures. In the present study, we investigated the dental calculi microbiome and predicted function of one of these cultures, known as the Saladoid. The Saladoids were horticulturalists that emphasized root-crop production. Fruits, as well as small marine and terrestrial animals were also part of the Saladoid diet. Methods Dental calculi samples were recovered from the archaeological site of Sorcé, in the municipal island of Vieques, Puerto Rico, characterized using 16S rRNA gene high-throughput sequencing, and compared to the microbiome of previously characterized coprolites of the same culture, as well modern plaque, saliva and stool microbiomes available from the Human Microbiome Project. Results Actinobacteria, Proteobacteria and Firmicutes comprised the majority of the Saladoid dental calculi microbiome. The Saladoid dental calculi microbiome was distinct when compared to those of modern saliva and dental plaque, but showed the presence of common inhabitants of modern oral cavities including Streptococcus sp., Veillonella dispar and Rothia mucilaginosa. Cell motility, signal transduction and biosynthesis of other secondary metabolites may be unique features of the Saladoid microbiome. Discussion Results suggest that the Saladoid dental calculi microbiome structure and function may possibly reflect a horticulturalist lifestyle and distinct dietary habits. Results also open the opportunity to further elucidate oral disease states in extinct Caribbean cultures and extinct indigenous cultures with similar lifestyles.
Collapse
Affiliation(s)
- Tasha M Santiago-Rodriguez
- Center for Applications in Biotechnology, California Polytechnic State University-San Luis Obispo, San Luis Obispo, CA, United States of America.,Biology Deparment, California Polytechnic State University-San Luis Obispo, San Luis Obispo, CA, United States of America.,Institute for Life Science Entrepreneurship, ATCC-Center for Translational Microbiology, Union, NJ, United States of America
| | - Yvonne Narganes-Storde
- Center for Archaeological Investigations, University of Puerto Rico, San Juan, Puerto Rico
| | - Luis Chanlatte-Baik
- Center for Archaeological Investigations, University of Puerto Rico, San Juan, Puerto Rico
| | - Gary A Toranzos
- Biology Department, University of Puerto Rico, San Juan, Puerto Rico
| | - Raul J Cano
- Center for Applications in Biotechnology, California Polytechnic State University-San Luis Obispo, San Luis Obispo, CA, United States of America.,Biology Deparment, California Polytechnic State University-San Luis Obispo, San Luis Obispo, CA, United States of America.,Institute for Life Science Entrepreneurship, ATCC-Center for Translational Microbiology, Union, NJ, United States of America
| |
Collapse
|
14
|
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.
Collapse
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.
| |
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
Abstract
The paleomicrobiology of coprolites, which are fossilized fecal materials, has already yielded data about various organisms, including micro-eukaryotes, bacteria, and archaea, thus expanding our comprehension of ancient human dietary habits, gut microbiota, and intestinal and systemic infections. This mini-review briefly describes previous works and summarizes the main techniques used in handling coprolites and the findings obtained about ancient gut microbiota. Past intestinal and systemic infections are outlined.
Collapse
|
17
|
Rivera-Perez JI, Santiago-Rodriguez TM, Toranzos GA. Paleomicrobiology: a Snapshot of Ancient Microbes and Approaches to Forensic Microbiology. Microbiol Spectr 2016; 4:10.1128/microbiolspec.EMF-0006-2015. [PMID: 27726770 PMCID: PMC5287379 DOI: 10.1128/microbiolspec.emf-0006-2015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Indexed: 01/14/2023] Open
Abstract
Paleomicrobiology, or the study of ancient microorganisms, has raised both fascination and skepticism for many years. While paleomicrobiology is not a recent field, the application of emerging techniques, such as DNA sequencing, is proving essential and has provided novel information regarding the evolution of viruses, antibiotic resistance, saprophytes, and pathogens, as well as ancient health and disease status, cultural customs, ethnic diets, and historical events. In this review, we highlight the importance of studying ancient microbial DNA, its contributions to current knowledge, and the role that forensic paleomicrobiology has played in deciphering historical enigmas. We also discuss the emerging techniques used to study the microbial composition of ancient samples as well as major concerns that accompany ancient DNA analyses.
Collapse
|
18
|
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.
Collapse
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
| | | |
Collapse
|
19
|
Santiago-Rodriguez TM, Fornaciari G, Luciani S, Dowd SE, Toranzos GA, Marota I, Cano RJ. Natural mummification of the human gut preserves bacteriophage DNA. FEMS Microbiol Lett 2015; 363:fnv219. [PMID: 26564967 DOI: 10.1093/femsle/fnv219] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2015] [Indexed: 12/23/2022] Open
Abstract
The natural mummification process of the human gut represents a unique opportunity to study the resulting microbial community structure and composition. While results are providing insights into the preservation of bacteria, fungi, pathogenic eukaryotes and eukaryotic viruses, no studies have demonstrated that the process of natural mummification also results in the preservation of bacteriophage DNA. We characterized the gut microbiome of three pre-Columbian Andean mummies, namely FI3, FI9 and FI12, and found sequences homologous to viruses. From the sequences attributable to viruses, 50.4% (mummy FI3), 1.0% (mummy FI9) and 84.4% (mummy FI12) were homologous to bacteriophages. Sequences corresponding to the Siphoviridae, Myoviridae, Podoviridae and Microviridae families were identified. Predicted putative bacterial hosts corresponded mainly to the Firmicutes and Proteobacteria, and included Bacillus, Staphylococcus, Clostridium, Escherichia, Vibrio, Klebsiella, Pseudomonas and Yersinia. Predicted functional categories associated with bacteriophages showed a representation of structural, replication, integration and entry and lysis genes. The present study suggests that the natural mummification of the human gut results in the preservation of bacteriophage DNA, representing an opportunity to elucidate the ancient phageome and to hypothesize possible mechanisms of preservation.
Collapse
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, TX 79363, USA
| | - Gary A Toranzos
- Department of Biology, University of Puerto Rico, San Juan 00932, 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
| |
Collapse
|
20
|
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.
Collapse
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:
| |
Collapse
|
21
|
Kim MJ, Kim YS, Oh CS, Go JH, Lee IS, Park WK, Cho SM, Kim SK, Shin DH. Anatomical confirmation of computed tomography-based diagnosis of the atherosclerosis discovered in 17th century Korean mummy. PLoS One 2015; 10:e0119474. [PMID: 25816014 PMCID: PMC4376940 DOI: 10.1371/journal.pone.0119474] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Accepted: 01/30/2015] [Indexed: 12/25/2022] Open
Abstract
In the present study on a newly discovered 17th century Korean mummy, computed tomography (CT) revealed multiple aortic calcifications within the aortic wall that were indicative of ancient atherosclerosis. The CT-based findings were confirmed by our subsequent post-factum dissection, which exhibited possible signs of the disease including ulcerated plaques, ruptured hemorrhages, and intimal thickening where the necrotic core was covered by the fibrous cap. These findings are strong indicators that the mummy suffered from aortic atherosclerosis during her lifetime. The present study is a good example of how CT images of vascular calcifications can be a useful diagnostic tool in forming at least preliminary diagnoses of ancient atherosclerosis.
Collapse
Affiliation(s)
- Myeung Ju Kim
- Department of Anatomy, Dankook University College of Medicine, Cheonan, Korea
| | - Yi-Suk Kim
- Department of Anatomy, Ewha Womans University School of Medicine, Seoul, Korea
| | - Chang Seok Oh
- Department of Anatomy, Seoul National University College of Medicine, Seoul, Korea
- Institute of Forensic Science, Seoul National University College of Medicine, Seoul, Korea
| | - Jai-Hyang Go
- Department of Pathology, Dankook University College of Medicine, Cheonan, Korea
| | - In Sun Lee
- Department of Radiology, Seoul National University Hospital, Bundang, Korea
| | - Won-Kyu Park
- Department of Wood and Paper Science, Chungbuk National University, Cheongju, Korea
| | - Seok-Min Cho
- Gaya National Research Institute of Cultural Heritage, Changwon, Korea
| | - Soon-Kwan Kim
- National Research Institute of Cultural Heritage, Cultural Heritage Science Center, Daejeon, Korea
| | - Dong Hoon Shin
- Department of Anatomy, Seoul National University College of Medicine, Seoul, Korea
- Institute of Forensic Science, Seoul National University College of Medicine, Seoul, Korea
| |
Collapse
|
22
|
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.
Collapse
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.
| |
Collapse
|
23
|
Appelt S, Armougom F, Le Bailly M, Robert C, Drancourt M. Polyphasic analysis of a middle ages coprolite microbiota, Belgium. PLoS One 2014; 9:e88376. [PMID: 24586319 PMCID: PMC3938422 DOI: 10.1371/journal.pone.0088376] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 01/06/2014] [Indexed: 11/19/2022] Open
Abstract
Paleomicrobiological investigations of a 14(th)-century coprolite found inside a barrel in Namur, Belgium were done using microscopy, a culture-dependent approach and metagenomics. Results were confirmed by ad hoc PCR--sequencing. Investigations yielded evidence for flora from ancient environment preserved inside the coprolite, indicated by microscopic observation of amoebal cysts, plant fibers, seeds, pollens and mold remains. Seventeen different bacterial species were cultured from the coprolite, mixing organisms known to originate from the environment and organisms known to be gut inhabitants. Metagenomic analyses yielded 107,470 reads, of which known sequences (31.9%) comprised 98.98% bacterial, 0.52% eukaryotic, 0.44% archaeal and 0.06% viral assigned reads. Most abundant bacterial phyla were Proteobacteria, Gemmatimonadetes, Actinobacteria and Bacteroidetes. The 16 S rRNA gene dataset yielded 132,000 trimmed reads and 673 Operational Taxonomic Units. Most abundant bacterial phyla observed in the 16 S rRNA gene dataset belonged to Proteobacteria, Firmicutes, Actinobacteria and Chlamydia. The Namur coprolite yielded typical gut microbiota inhabitants, intestinal parasites Trichuris and Ascaris and systemic pathogens Bartonella and Bordetella. This study adds knowledge to gut microbiota in medieval times.
Collapse
Affiliation(s)
- Sandra Appelt
- Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes, UM63, Centre national de la recherche scientifique 7278, IRD 198, Institut National de la Santé et de la Recherche Médicale 1095, Aix Marseille Université, Marseille, France
| | - Fabrice Armougom
- Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes, UM63, Centre national de la recherche scientifique 7278, IRD 198, Institut National de la Santé et de la Recherche Médicale 1095, Aix Marseille Université, Marseille, France
| | - Matthieu Le Bailly
- Centre national de la recherche scientifique UMR 6249 Chrono-Environnement, Franche-Comté Université, Besançon, France
| | - Catherine Robert
- Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes, UM63, Centre national de la recherche scientifique 7278, IRD 198, Institut National de la Santé et de la Recherche Médicale 1095, Aix Marseille Université, Marseille, France
| | - Michel Drancourt
- Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes, UM63, Centre national de la recherche scientifique 7278, IRD 198, Institut National de la Santé et de la Recherche Médicale 1095, Aix Marseille Université, Marseille, France
- * E-mail:
| |
Collapse
|
24
|
Anastasiou E, Mitchell PD. Palaeopathology and genes: investigating the genetics of infectious diseases in excavated human skeletal remains and mummies from past populations. Gene 2013; 528:33-40. [PMID: 23792062 DOI: 10.1016/j.gene.2013.06.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 05/23/2013] [Accepted: 06/01/2013] [Indexed: 01/11/2023]
Abstract
The aim of this paper is to review the use of genetics in palaeomicrobiology, and to highlight the importance of understanding past diseases. Palaeomicrobiology is the study of disease pathogens in skeletal and mummified remains from archaeological contexts. It has revolutionarised our understanding of health in the past by enabling a deeper knowledge of the origins and evolution of many diseases that have shaped us as a species. Bacterial diseases explored include tuberculosis, leprosy, bubonic plague, typhoid, syphilis, endemic and epidemic typhus, trench fever, and Helicobacter pylori. Viral diseases discussed include influenza, hepatitis B, human papilloma virus (HPV), human T-cell lymphotrophic virus (HTLV-1) and human immunodeficiency virus (HIV). Parasitic diseases investigated include malaria, leishmaniasis, Chagas' disease, roundworm, whipworm, pinworm, Chinese liver fluke, fleas and lice. Through a better understanding of disease origins and their evolution, we can place into context how many infectious diseases are changing over time, and so help us estimate how they may change in the future.
Collapse
Affiliation(s)
- Evilena Anastasiou
- Division of Biological Anthropology, Department of Archaeology and Anthropology, University of Cambridge, The Henry Wellcome Building, Fitzwilliam Street, Cambridge CB2 1QH, UK
| | | |
Collapse
|
25
|
Jurado V, Porca E, Pastrana MP, Cuezva S, Fernandez-Cortes A, Saiz-Jimenez C. Microbiological study of bulls of indulgence of the 15th-16th centuries. THE SCIENCE OF THE TOTAL ENVIRONMENT 2010; 408:3711-5. [PMID: 20595060 DOI: 10.1016/j.scitotenv.2010.05.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2010] [Revised: 05/05/2010] [Accepted: 05/06/2010] [Indexed: 05/25/2023]
Abstract
During the restoration of the church of "San Esteban" in Cuéllar (Segovia, Spain) a few sepulchres were opened. Among them was that of Doña Isabel de Zuazo, from the 16th century. Together with the corpse was found a series of printed documents from the 15th-16th centuries, most of which were bulls of indulgence. A microbiological study of the documents was carried out using techniques of isolation and molecular microbiology, together with scanning electron microscopy. Most of the identified bacteria were highly suggestive of a human origin, particularly the predominance of Clostridium species consistent with the flora of the human intestinal tract. Our results demonstrate that appreciable post-mortem migration of bacteria has taken place from the corpse to the historic documents. This can be explained considering that the documents were found on pelvic region, and were contaminated by body fluids and putrefaction.
Collapse
Affiliation(s)
- V Jurado
- Instituto de Recursos Naturales y Agrobiología, CSIC, Apartado 1052, 41080 Sevilla, Spain
| | | | | | | | | | | |
Collapse
|
26
|
Olivieri C, Ermini L, Rizzi E, Corti G, Bonnal R, Luciani S, Marota I, De Bellis G, Rollo F. Characterization of nucleotide misincorporation patterns in the iceman's mitochondrial DNA. PLoS One 2010; 5:e8629. [PMID: 20072618 PMCID: PMC2799664 DOI: 10.1371/journal.pone.0008629] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2009] [Accepted: 12/15/2009] [Indexed: 12/03/2022] Open
Abstract
Background The degradation of DNA represents one of the main issues in the genetic analysis of archeological specimens. In the recent years, a particular kind of post-mortem DNA modification giving rise to nucleotide misincorporation (“miscoding lesions”) has been the object of extensive investigations. Methodology/Principal Findings To improve our knowledge regarding the nature and incidence of ancient DNA nucleotide misincorporations, we have utilized 6,859 (629,975 bp) mitochondrial (mt) DNA sequences obtained from the 5,350–5,100-years-old, freeze-desiccated human mummy popularly known as the Tyrolean Iceman or Ötzi. To generate the sequences, we have applied a mixed PCR/pyrosequencing procedure allowing one to obtain a particularly high sequence coverage. As a control, we have produced further 8,982 (805,155 bp) mtDNA sequences from a contemporary specimen using the same system and starting from the same template copy number of the ancient sample. From the analysis of the nucleotide misincorporation rate in ancient, modern, and putative contaminant sequences, we observed that the rate of misincorporation is significantly lower in modern and putative contaminant sequence datasets than in ancient sequences. In contrast, type 2 transitions represent the vast majority (85%) of the observed nucleotide misincorporations in ancient sequences. Conclusions/Significance This study provides a further contribution to the knowledge of nucleotide misincorporation patterns in DNA sequences obtained from freeze-preserved archeological specimens. In the Iceman system, ancient sequences can be clearly distinguished from contaminants on the basis of nucleotide misincorporation rates. This observation confirms a previous identification of the ancient mummy sequences made on a purely phylogenetical basis. The present investigation provides further indication that the majority of ancient DNA damage is reflected by type 2 (cytosine→thymine/guanine→adenine) transitions and that type 1 transitions are essentially PCR artifacts.
Collapse
Affiliation(s)
- Cristina Olivieri
- Laboratorio di Archeo-Antropologia molecolare/DNA Antico, Dipartimento di Biologia Molecolare, Cellulare e Animale, University of Camerino, Camerino, Italy
| | - Luca Ermini
- Institute of Cellular Medicine, University of Newcastle, Newcastle, United Kingdom
| | - Ermanno Rizzi
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Milano, Italy
| | - Giorgio Corti
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Milano, Italy
| | - Raoul Bonnal
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Milano, Italy
| | - Stefania Luciani
- Laboratorio di Archeo-Antropologia molecolare/DNA Antico, Dipartimento di Biologia Molecolare, Cellulare e Animale, University of Camerino, Camerino, Italy
| | - Isolina Marota
- Laboratorio di Archeo-Antropologia molecolare/DNA Antico, Dipartimento di Biologia Molecolare, Cellulare e Animale, University of Camerino, Camerino, Italy
| | - Gianluca De Bellis
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Milano, Italy
| | - Franco Rollo
- Laboratorio di Archeo-Antropologia molecolare/DNA Antico, Dipartimento di Biologia Molecolare, Cellulare e Animale, University of Camerino, Camerino, Italy
- * E-mail:
| |
Collapse
|
27
|
|
28
|
Luciani S, Fornaciari G, Rickards O, Labarga CM, Rollo F. Molecular characterization of a pre-Columbian mummy and in situ coprolite. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2006; 129:620-9. [PMID: 16342258 DOI: 10.1002/ajpa.20314] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The history of Homo sapiens dispersal around the world and inherent interpopulation contacts and conflicts has given rise to several transitions in his relationships with the natural world, with the final result of changes in the patterns of infectious disease (McMichael [2001] Ecosystem Health 7:107-115). Of particular interest, in this context, is the contact between Amerindians and Europeans that started at the end of the 15th century, and the resulting exchange of microbes. We successfully recovered ancient DNA from a pre-Columbian mummy from Cuzco (Peru), radiocarbon-dated to 980-1170 AD, for which consistent mtDNA amplifications and sequences were obtained. The analysis of mtDNA revealed that the mummy's haplogroup was characteristic of Native American populations. We also investigated a sample of feces directly isolated from the intestines of the mummy, using a polymerase chain reaction system designed to detect the broadest spectrum of bacterial DNAs. The analysis of results, following a criterion of "paleoecological consistency" (Rollo and Marota [1998] Philos. Trans. R. Soc. Lond. [Biol.] 354: 111-119), demonstrated that some vestiges of the original microbial flora of the feces were preserved. In particular, we were able to identify the DNA of Haemophylus parainfluenzae, thus suggesting that this recently recognized pathogen was present in precontact Native Americans.
Collapse
MESH Headings
- Base Sequence
- DNA, Bacterial/analysis
- DNA, Bacterial/genetics
- DNA, Bacterial/history
- DNA, Mitochondrial/analysis
- DNA, Mitochondrial/chemistry
- DNA, Mitochondrial/history
- Feces/microbiology
- Haemophilus Infections/history
- Haemophilus Infections/microbiology
- Haemophilus parainfluenzae/genetics
- Haemophilus parainfluenzae/isolation & purification
- Haplotypes
- History, Medieval
- Humans
- Indians, South American/classification
- Indians, South American/genetics
- Indians, South American/history
- Molecular Sequence Data
- Mummies/microbiology
- Peru
- Phylogeny
- Polymerase Chain Reaction
- Sequence Alignment
- Sequence Analysis, DNA/methods
Collapse
Affiliation(s)
- Stefania Luciani
- Laboratorio di Archeo-Antropologia Molecolare/DNA Antico, UNICAM, I-62032 Camerino, Italy
| | | | | | | | | |
Collapse
|
29
|
Iñiguez AM, Araújo A, Ferreira LF, Vicente ACP. Analysis of ancient DNA from coprolites: a perspective with random amplified polymorphic DNA-polymerase chain reaction approach. Mem Inst Oswaldo Cruz 2003; 98 Suppl 1:63-5. [PMID: 12687765 DOI: 10.1590/s0074-02762003000900012] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The aim of this work was to determine approaches that would improve the quality of ancient DNA (aDNA) present in coprolites to enhance the possibility of success in retrieving specific sequence targets. We worked with coprolites from South American archaeological sites in Brazil and Chile dating up to 7,000 years ago. Using established protocols for aDNA extraction we obtained samples showing high degradation as usually happens with this kind of material. The reconstructive polymerization pretreatment was essential to overcome the DNA degradation and the serial dilutions helped with to prevent polymerase chain reaction (PCR) inhibitors. Moreover, the random amplified polymorphic DNA-PCR has been shown to be a reliable technique for further experiments to recover specific aDNA sequences.
Collapse
Affiliation(s)
- Alena M Iñiguez
- Laboratório de Genética Molecular de Microorganismos, Departamento de Genética, Instituto Oswaldo Cruz-Fiocruz, Av. Brasil 4365, 21045-900 Rio de Janeiro, RJ, Brasil.
| | | | | | | |
Collapse
|
30
|
Baker GC, Tow LA, Cowan DA. PCR-based detection of non-indigenous microorganisms in 'pristine' environments. J Microbiol Methods 2003; 53:157-64. [PMID: 12654487 DOI: 10.1016/s0167-7012(03)00021-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
PCR-based technologies are widely employed for the detection of specific microorganisms, and may be applied to the identification of non-indigenous microorganisms in 'pristine' environments. For 'pristine' environments such as those found on the Antarctic continent, the application of these methods to the assessment of environmental contamination from human activities must be treated with caution. Issues such as the possibility of non-human dispersal of organisms, stability and survival of non-indigenous organisms in vivo, the sensitivity, reproducibility and specificity of the PCR process (and particularly primer design) and the sampling regime employed must all be considered in detail. We conclude that despite these limitations, PCR and related technologies offer enormous scope for assessment of both natural and non-indigenous microbial distributions.
Collapse
Affiliation(s)
- Gillian C Baker
- Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville, Cape Town, South Africa.
| | | | | |
Collapse
|
31
|
Marota I, Basile C, Ubaldi M, Rollo F. DNA decay rate in papyri and human remains from Egyptian archaeological sites. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2002; 117:310-8. [PMID: 11920366 DOI: 10.1002/ajpa.10045] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The writing sheets made with strips from the stem (caulis) of papyri (Cyperus papyrus) are one of the most ingenious products of ancient technology. We extracted DNA from samples of modern papyri varying in age from 0-100 years BP and from ancient specimens from Egypt, with an age-span from 1,300-3,200 years BP. The copy number of the plant chloroplast DNA in the sheets was determined using a competitive PCR system designed on the basis of a short (90 bp) tract of the chloroplast's ribulose bisphosphate carboxylase large subunit (rbcL) gene sequence. The results allowed us to establish that the DNA half-life in papyri is about 19-24 years. This means that the last DNA fragments will vanish within no more than 532-672 years from the sheets being manufactured. In a parallel investigation, we checked the archaeological specimens for the presence of residual DNA and determined the extent of racemization of aspartic (Asp) acid in both modern and ancient specimens, as a previous report (Poinar et al. [1996], Science 272:864-866) showed that racemization of aspartic acid and DNA decay are linked. The results confirmed the complete loss of authentic DNA, even in the less ancient (8th century AD) papyri. On the other hand, when the regression for Asp racemization rates in papyri was compared with that for human and animal remains from Egyptian archaeological sites, it proved, quite surprisingly, that the regressions are virtually identical. Our study provides an indirect argument against the reliability of claims about the recovery of authentic DNA from Egyptian mummies and bone remains.
Collapse
Affiliation(s)
- Isolina Marota
- Laboratorio di Archeo-Antropologia Molecolare/DNA Antico, Dipartimento di Biologia Molecolare, Cellulare e Animale, Università di Camerino, I-62032 Camerino, Italy
| | | | | | | |
Collapse
|
32
|
Abstract
Molecular-phylogenetic methods have revolutionized the analysis of complex microbial communities. Polymerase chain reaction amplification and phylogenetic analysis of small-subunit ribosomal RNA gene sequences allow microbes to be identified objectively, even in the absence of cultivation. Furthermore, the sequence information obtained by these means can be used to design sequence-based tools for identifying, tracking, and diagnosing the presence of microbes in complex samples. In this article, we summarize this approach and review its application to the study of the human gastrointestinal microbiota. Although just beginning, molecular-phylogenetic surveys of human gut microbes have revealed that most microbes identified in the gastrointestinal tract represent novel, previously undescribed species. A full description of the microbial constituents of the human gut will set the groundwork for interpreting how the gastrointestinal microbiota influence the health of the host.
Collapse
Affiliation(s)
- D N Frank
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
| | | |
Collapse
|
33
|
Affiliation(s)
- Dennis H. O'Rourke
- Laboratory of Biological Anthropology, University of Utah, Salt Lake City, Utah 84112-0060; e-mail:
| | - M. Geoffrey Hayes
- Laboratory of Biological Anthropology, University of Utah, Salt Lake City, Utah 84112-0060; e-mail:
| | - Shawn W. Carlyle
- Laboratory of Biological Anthropology, University of Utah, Salt Lake City, Utah 84112-0060; e-mail:
| |
Collapse
|
34
|
Cano RJ, Tiefenbrunner F, Ubaldi M, Del Cueto C, Luciani S, Cox T, Orkand P, Künzel KH, Rollo F. Sequence analysis of bacterial DNA in the colon and stomach of the Tyrolean Iceman. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2000; 112:297-309. [PMID: 10861348 DOI: 10.1002/1096-8644(200007)112:3<297::aid-ajpa2>3.0.co;2-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The male human body found in an Alpine glacier on September 19, 1991 ("Tyrolean Iceman") has, for the first time in history, given scientists a chance to perform detailed anatomical, histological, and molecular investigations on the organs of a person from the Neolithic Age (5350-5100 B.P.). In the present study, tissue samples aseptically taken from the stomach and the colon of the mummy were utilized for DNA extraction, and the DNA was PCR-amplified, using primer pairs designed to bind to fragments of the 16s ribosomal RNA gene (16s rDNA) of a broad range of bacteria. The PCR products were cloned in plasmid vectors, and the recombinant clones (amplicons) were sequenced. The sequence data were finally used for scanning data libraries containing the corresponding sequences of present-day bacteria, to infer the putative ecophysiology of the ancient ones. The same procedure was repeated on some fragments of grass from the clothing found near the corpse. These fragments were taken as a control of the microbiological situation of the glacier. The results show that the flora of the Iceman's stomach is entirely composed of Burkholderia pickettii, an organism commonly found in aquatic habitats. The colon, on the other hand, contains several members of the fecal flora of humans, such as Clostridium perfringens, C. ghonii, C. sordellii, Eubacterium tenue, and Bacteroides sp. The Iceman's colon, however, was found to contain, rather unexpectedly, also some members of the genus Vibrio. The results are discussed in light of what is known about the preservation of microbial DNA at the Iceman's site and of previous parasitological studies performed on the Iceman himself and on human coprolites.
Collapse
Affiliation(s)
- R J Cano
- Environmental Biotechnology Institute, California Polytechnic State University, San Luis Obispo, California 93407, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Rollo F, Luciani S, Canapa A, Marota I. Analysis of bacterial DNA in skin and muscle of the Tyrolean iceman offers new insight into the mummification process. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2000; 111:211-9. [PMID: 10640948 DOI: 10.1002/(sici)1096-8644(200002)111:2<211::aid-ajpa7>3.0.co;2-m] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
About 80 sequences (16s ribosomal RNA gene) of bacterial DNA in samples of skin and muscle taken directly from the Tyrolean iceman (3350-3100 years B.C.) or recovered during the 1992 archaeological expedition at the Alpine site were analyzed to obtain clues to the natural mummification process that allowed the corpse of the Neolithic shepherd/hunter to be preserved for more than 5,000 years. The investigation was made more complex by the fact that the surface of the mummy had been swabbed with phenol soon after the discovery (September 19, 1991). Our results show that no trace of microbial DNA is left on the actual surface of the body, while the untreated skin still bears the remains of large numbers of bacteria belonging to the genera Sphingomonas, Afipia, Curtobacterium, Microbacterium, Agromyces, and others. Compared to the untreated skin, the iceman's muscle is also very rich in bacterial DNA. However, this DNA comes, with few exceptions, from the species Clostridium algidicarnis. The sharp difference in the bacterial DNA composition of skin and muscle suggests that the remains of the original cadaveric microflora of the latter have not disappeared during the iceman's taphonomic history. On the other hand, the massive presence of C. algidicarnis, a cold-adapted sporigenous, the DNA of which was previously (Ubaldi et al. [1998] Am. J. Phys. Anthropol. 107:285-295) found in the soft tissue of a naturally desiccated Andean mummy, indicates that the hypothesis that the iceman's corpse underwent rapid dehydration by the effect of a warm wind (föhn) is no longer plausible. The results best fit with the hypothesis (Bereuter et al. [1997] Chem. Eur. J. 7:1032-1038) that the body was first covered by snow and ice, and then underwent thawing and, finally, desiccation.
Collapse
Affiliation(s)
- F Rollo
- Dipartimento di Biologia Molecolare, Cellulare e Animale, Università di Camerino, I-62032, Camerino, Italy.
| | | | | | | |
Collapse
|
36
|
Rollo F, Marota I. How microbial ancient DNA, found in association with human remains, can be interpreted. Philos Trans R Soc Lond B Biol Sci 1999; 354:111-9. [PMID: 10091251 PMCID: PMC1692447 DOI: 10.1098/rstb.1999.0364] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The analysis of the DNA of ancient micro-organisms in archaeological and palaeontological human remains can contribute to the understanding of issues as different as the spreading of a new disease, a mummification process or the effect of diets on historical human populations. The quest for this type of DNA, however, can represent a particularly demanding task. This is mainly due to the abundance and diffusion of bacteria, fungi, yeasts, algae and protozoans in the most diverse environments of the present-day biosphere and the resulting difficulty in distinguishing between ancient and modern DNA. Nevertheless, at least under some special circumstances, by using rigorous protocols, which include an archaeometric survey of the specimens and evaluation of the palaeoecological consistency of the results of DNA sequence analysis, glimpses of the composition of the original microbial flora (e.g. colonic flora) can be caught in ancient human remains. Potentials and pitfalls of this research field are illustrated by the results of research works performed on prehistoric, pre-Columbian and Renaissance human mummies.
Collapse
Affiliation(s)
- F Rollo
- Dipartimento di Biologia Molecolare, Cellulare e Animale, Università di Camerino, Italy.
| | | |
Collapse
|