101
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Conde-Valverde M, Martínez I, Quam RM, Rosa M, Velez AD, Lorenzo C, Jarabo P, Bermúdez de Castro JM, Carbonell E, Arsuaga JL. Neanderthals and Homo sapiens had similar auditory and speech capacities. Nat Ecol Evol 2021; 5:609-615. [PMID: 33649543 DOI: 10.1038/s41559-021-01391-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 01/12/2021] [Indexed: 01/31/2023]
Abstract
The study of audition in fossil hominins is of great interest given its relationship with intraspecific vocal communication. While the auditory capacities have been studied in early hominins and in the Middle Pleistocene Sima de los Huesos hominins, less is known about the hearing abilities of the Neanderthals. Here, we provide a detailed approach to their auditory capacities. Relying on computerized tomography scans and a comprehensive model from the field of auditory bioengineering, we have established sound power transmission through the outer and middle ear and calculated the occupied bandwidth in Neanderthals. The occupied bandwidth is directly related to the efficiency of the vocal communication system of a species. Our results show that the occupied bandwidth of Neanderthals was greater than the Sima de los Huesos hominins and similar to extant humans, implying that Neanderthals evolved the auditory capacities to support a vocal communication system as efficient as modern human speech.
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Affiliation(s)
- Mercedes Conde-Valverde
- Cátedra de Otoacústica Evolutiva y Paleoantropología (HM Hospitales-Universidad de Alcalá), Departamento de Ciencias de la Vida, Universidad de Alcalá, Madrid, Spain.
| | - Ignacio Martínez
- Cátedra de Otoacústica Evolutiva y Paleoantropología (HM Hospitales-Universidad de Alcalá), Departamento de Ciencias de la Vida, Universidad de Alcalá, Madrid, Spain.,Centro Mixto (UCM-ISCIII) de Evolución y Comportamiento Humanos, Madrid, Spain
| | - Rolf M Quam
- Cátedra de Otoacústica Evolutiva y Paleoantropología (HM Hospitales-Universidad de Alcalá), Departamento de Ciencias de la Vida, Universidad de Alcalá, Madrid, Spain.,Centro Mixto (UCM-ISCIII) de Evolución y Comportamiento Humanos, Madrid, Spain.,Department of Anthropology, Binghamton University (SUNY), Binghamton, NY, USA.,Division of Anthropology, American Museum of Natural History, New York, NY, USA
| | - Manuel Rosa
- Cátedra de Otoacústica Evolutiva y Paleoantropología (HM Hospitales-Universidad de Alcalá), Departamento de Ciencias de la Vida, Universidad de Alcalá, Madrid, Spain.,Departamento de Teoría de la Señal y Comunicaciones, Escuela Politécnica Superior, Universidad de Alcalá, Alcalá de Henares, Spain
| | - Alex D Velez
- Department of Anthropology, Binghamton University (SUNY), Binghamton, NY, USA
| | - Carlos Lorenzo
- Àrea de Prehistòria, Departament d'Història i Història de l'Art, Universitat Rovira i Virgili, Tarragona, Spain.,Institut Català de Paleoecologia Humana i Evolució Social, Tarragona, Spain
| | - Pilar Jarabo
- Departamento de Teoría de la Señal y Comunicaciones, Escuela Politécnica Superior, Universidad de Alcalá, Alcalá de Henares, Spain
| | - José María Bermúdez de Castro
- Centro Nacional de Investigación sobre la Evolución Humana (CENIEH), Burgos, Spain.,Anthropology Department, University College London, London, UK
| | - Eudald Carbonell
- Àrea de Prehistòria, Departament d'Història i Història de l'Art, Universitat Rovira i Virgili, Tarragona, Spain.,Institut Català de Paleoecologia Humana i Evolució Social, Tarragona, Spain.,Departamento de Historia, Geografía y Comunicación, Universidad de Burgos, Burgos, Spain
| | - Juan Luis Arsuaga
- Centro Mixto (UCM-ISCIII) de Evolución y Comportamiento Humanos, Madrid, Spain.,Departamento de Geodinámica, Estratigrafía y Paleontología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid, Madrid, Spain
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102
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McLean JS, Bor B, Kerns KA, Liu Q, To TT, Solden L, Hendrickson EL, Wrighton K, Shi W, He X. Acquisition and Adaptation of Ultra-small Parasitic Reduced Genome Bacteria to Mammalian Hosts. Cell Rep 2021; 32:107939. [PMID: 32698001 PMCID: PMC7427843 DOI: 10.1016/j.celrep.2020.107939] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 06/20/2020] [Accepted: 06/30/2020] [Indexed: 12/31/2022] Open
Abstract
The first cultivated representative of the enigmatic phylum Saccharibacteria (formerly TM7) was isolated from humans and revealed an ultra-small cell size (200-300 nm), a reduced genome with limited biosynthetic capabilities, and a unique parasitic lifestyle. TM7x was the only cultivated member of the candidate phyla radiation (CPR), estimated to encompass 26% of the domain Bacteria. Here we report on divergent genomes from major lineages across the Saccharibacteria phylum in humans and mammals, as well as from ancient dental calculus. These lineages are present at high prevalence within hosts. Direct imaging reveals that all groups are ultra-small in size, likely feeding off commensal bacteria. Analyses suggest that multiple acquisition events in the past led to the current wide diversity, with convergent evolution of key functions allowing Saccharibacteria from the environment to adapt to mammals. Ultra-small, parasitic CPR bacteria represent a relatively unexplored paradigm of prokaryotic interactions within mammalian microbiomes.
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Affiliation(s)
- Jeffrey S McLean
- Department of Periodontics, University of Washington, Seattle, WA 98195, USA; Department of Microbiology, University of Washington, Seattle, WA 98195, USA.
| | - Batbileg Bor
- Department of Microbiology, The Forsyth Institute, Cambridge, MA 02142, USA; Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - Kristopher A Kerns
- Department of Periodontics, University of Washington, Seattle, WA 98195, USA
| | - Quanhui Liu
- Department of Periodontics, University of Washington, Seattle, WA 98195, USA
| | - Thao T To
- Department of Periodontics, University of Washington, Seattle, WA 98195, USA
| | - Lindsey Solden
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Erik L Hendrickson
- Department of Periodontics, University of Washington, Seattle, WA 98195, USA
| | - Kelly Wrighton
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Wenyuan Shi
- Department of Microbiology, The Forsyth Institute, Cambridge, MA 02142, USA
| | - Xuesong He
- Department of Microbiology, The Forsyth Institute, Cambridge, MA 02142, USA; Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA 02115, USA
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103
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Farrer AG, Wright SL, Skelly E, Eisenhofer R, Dobney K, Weyrich LS. Effectiveness of decontamination protocols when analyzing ancient DNA preserved in dental calculus. Sci Rep 2021; 11:7456. [PMID: 33811235 PMCID: PMC8018977 DOI: 10.1038/s41598-021-86100-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 02/26/2021] [Indexed: 02/01/2023] Open
Abstract
Ancient DNA analysis of human oral microbial communities within calcified dental plaque (calculus) has revealed key insights into human health, paleodemography, and cultural behaviors. However, contamination imposes a major concern for paleomicrobiological samples due to their low endogenous DNA content and exposure to environmental sources, calling into question some published results. Decontamination protocols (e.g. an ethylenediaminetetraacetic acid (EDTA) pre-digestion or ultraviolet radiation (UV) and 5% sodium hypochlorite immersion treatments) aim to minimize the exogenous content of the outer surface of ancient calculus samples prior to DNA extraction. While these protocols are widely used, no one has systematically compared them in ancient dental calculus. Here, we compare untreated dental calculus samples to samples from the same site treated with four previously published decontamination protocols: a UV only treatment; a 5% sodium hypochlorite immersion treatment; a pre-digestion in EDTA treatment; and a combined UV irradiation and 5% sodium hypochlorite immersion treatment. We examine their efficacy in ancient oral microbiota recovery by applying 16S rRNA gene amplicon and shotgun sequencing, identifying ancient oral microbiota, as well as soil and skin contaminant species. Overall, the EDTA pre-digestion and a combined UV irradiation and 5% sodium hypochlorite immersion treatment were both effective at reducing the proportion of environmental taxa and increasing oral taxa in comparison to untreated samples. This research highlights the importance of using decontamination procedures during ancient DNA analysis of dental calculus to reduce contaminant DNA.
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Affiliation(s)
- Andrew G. Farrer
- grid.1010.00000 0004 1936 7304Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia Australia
| | - Sterling L. Wright
- grid.29857.310000 0001 2097 4281The Department of Anthropology, The Pennsylvania State University, University Park, PA USA
| | - Emily Skelly
- grid.1010.00000 0004 1936 7304Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia Australia
| | - Raphael Eisenhofer
- grid.1010.00000 0004 1936 7304Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia Australia ,grid.1010.00000 0004 1936 7304Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, South Australia Australia
| | - Keith Dobney
- grid.1013.30000 0004 1936 834XDepartment of Archaeology, University of Sydney, Sydney, NSW Australia
| | - Laura S. Weyrich
- grid.1010.00000 0004 1936 7304Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia Australia ,grid.29857.310000 0001 2097 4281The Department of Anthropology, The Pennsylvania State University, University Park, PA USA ,grid.1010.00000 0004 1936 7304Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, South Australia Australia ,grid.29857.310000 0001 2097 4281The Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA USA
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104
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Successful extraction of insect DNA from recent copal inclusions: limits and perspectives. Sci Rep 2021; 11:6851. [PMID: 33767248 PMCID: PMC7994385 DOI: 10.1038/s41598-021-86058-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 03/01/2021] [Indexed: 01/31/2023] Open
Abstract
Insects entombed in copal, the sub-fossilized resin precursor of amber, represent a potential source of genetic data for extinct and extant, but endangered or elusive, species. Despite several studies demonstrated that it is not possible to recover endogenous DNA from insect inclusions, the preservation of biomolecules in fossilized resins samples is still under debate. In this study, we tested the possibility of obtaining endogenous ancient DNA (aDNA) molecules from insects preserved in copal, applying experimental protocols specifically designed for aDNA recovery. We were able to extract endogenous DNA molecules from one of the two samples analyzed, and to identify the taxonomic status of the specimen. Even if the sample was found well protected from external contaminants, the recovered DNA was low concentrated and extremely degraded, compared to the sample age. We conclude that it is possible to obtain genomic data from resin-entombed organisms, although we discourage aDNA analysis because of the destructive method of extraction protocols and the non-reproducibility of the results.
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105
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Handsley-Davis M, Skelly E, Johnson NW, Kapellas K, Lalloo R, Kroon J, Weyrich LS. Biocultural Drivers of Salivary Microbiota in Australian Aboriginal and Torres Strait Islander Children. FRONTIERS IN ORAL HEALTH 2021; 2:641328. [PMID: 35047996 PMCID: PMC8757737 DOI: 10.3389/froh.2021.641328] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/15/2021] [Indexed: 11/13/2022] Open
Abstract
Australian Aboriginal and Torres Strait Islander children experience unacceptably high rates of dental caries compared to their non-Indigenous Australian counterparts. Dental caries significantly impacts the quality of life of children and their families, particularly in remote communities. While many socioeconomic and lifestyle factors impact caries risk, the central role of the oral microbiota in mediating dental caries has not been extensively investigated in these communities. Here, we examine factors that shape diversity and composition of the salivary microbiota in Aboriginal and Torres Strait Islander children and adolescents living in the remote Northern Peninsula Area (NPA) of Far North Queensland. We employed 16S ribosomal RNA amplicon sequencing to profile bacteria present in saliva collected from 205 individuals aged 4–17 years from the NPA. Higher average microbial diversity was generally linked to increased age and salivary pH, less frequent toothbrushing, and proxies for lower socioeconomic status (SES). Differences in microbial composition were significantly related to age, salivary pH, SES proxies, and active dental caries. Notably, a feature classified as Streptococcus sobrinus increased in abundance in children who reported less frequent tooth brushing. A specific Veillonella feature was associated with caries presence, while features classified as Actinobacillus/Haemophilus and Leptotrichia were associated with absence of caries; a Lactobacillus gasseri feature increased in abundance in severe caries. Finally, we statistically assessed the interplay between dental caries and caries risk factors in shaping the oral microbiota. These data provide a detailed understanding of biological, behavioral, and socioeconomic factors that shape the oral microbiota and may underpin caries development in this group. This information can be used in the future to improve tailored caries prevention and management options for Australian Aboriginal and Torres Strait Islander children and communities.
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Affiliation(s)
- Matilda Handsley-Davis
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- Australian Research Council Centre of Excellence in Australian Biodiversity and Heritage, University of Wollongong, Wollongong, NSW, Australia
| | - Emily Skelly
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Newell W. Johnson
- Menzies Health Institute Queensland, Griffith University, Gold Coast, QLD, Australia
- School of Dentistry and Oral Health, Griffith University, Gold Coast, QLD, Australia
- Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London, United Kingdom
- Newell W. Johnson
| | - Kostas Kapellas
- Indigenous Oral Health Unit, Australian Research Centre for Population Oral Health, Adelaide Dental School, University of Adelaide, Adelaide, SA, Australia
| | - Ratilal Lalloo
- School of Dentistry, University of Queensland, Brisbane, QLD, Australia
| | - Jeroen Kroon
- School of Dentistry and Oral Health, Griffith University, Gold Coast, QLD, Australia
| | - Laura S. Weyrich
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
- Australian Research Council Centre of Excellence in Australian Biodiversity and Heritage, University of Wollongong, Wollongong, NSW, Australia
- microARCH Laboratory, Department of Anthropology and Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, United States
- *Correspondence: Laura S. Weyrich
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106
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Fellows Yates JA, Lamnidis TC, Borry M, Andrades Valtueña A, Fagernäs Z, Clayton S, Garcia MU, Neukamm J, Peltzer A. Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager. PeerJ 2021; 9:e10947. [PMID: 33777521 PMCID: PMC7977378 DOI: 10.7717/peerj.10947] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/25/2021] [Indexed: 12/13/2022] Open
Abstract
The broadening utilisation of ancient DNA to address archaeological, palaeontological, and biological questions is resulting in a rising diversity in the size of laboratories and scale of analyses being performed. In the context of this heterogeneous landscape, we present an advanced, and entirely redesigned and extended version of the EAGER pipeline for the analysis of ancient genomic data. This Nextflow pipeline aims to address three main themes: accessibility and adaptability to different computing configurations, reproducibility to ensure robust analytical standards, and updating the pipeline to the latest routine ancient genomic practices. The new version of EAGER has been developed within the nf-core initiative to ensure high-quality software development and maintenance support; contributing to a long-term life-cycle for the pipeline. nf-core/eager will assist in ensuring that a wider range of ancient DNA analyses can be applied by a diverse range of research groups and fields.
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Affiliation(s)
- James A. Fellows Yates
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, Münich, Germany
| | - Thiseas C. Lamnidis
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Maxime Borry
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Aida Andrades Valtueña
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Zandra Fagernäs
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Stephen Clayton
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Maxime U. Garcia
- National Genomics Infrastructure, Science for Life Laboratory, Stockholm, Sweden
- Barntumörbanken, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Judith Neukamm
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
- Institute for Bioinformatics and Medical Informatics, Eberhard-Karls University Tübingen, Tübingen, Germany
| | - Alexander Peltzer
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- Quantitative Biology Center, Eberhard-Karls University Tübingen, Tübingen, Germany
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107
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Prey Size Decline as a Unifying Ecological Selecting Agent in Pleistocene Human Evolution. QUATERNARY 2021. [DOI: 10.3390/quat4010007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
We hypothesize that megafauna extinctions throughout the Pleistocene, that led to a progressive decline in large prey availability, were a primary selecting agent in key evolutionary and cultural changes in human prehistory. The Pleistocene human past is characterized by a series of transformations that include the evolution of new physiological traits and the adoption, assimilation, and replacement of cultural and behavioral patterns. Some changes, such as brain expansion, use of fire, developments in stone-tool technologies, or the scale of resource intensification, were uncharacteristically progressive. We previously hypothesized that humans specialized in acquiring large prey because of their higher foraging efficiency, high biomass density, higher fat content, and the use of less complex tools for their acquisition. Here, we argue that the need to mitigate the additional energetic cost of acquiring progressively smaller prey may have been an ecological selecting agent in fundamental adaptive modes demonstrated in the Paleolithic archaeological record. We describe several potential associations between prey size decline and specific evolutionary and cultural changes that might have been driven by the need to adapt to increased energetic demands while hunting and processing smaller and smaller game.
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108
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Palmer KS, Makarewicz CA, Tishkin AA, Tur SS, Chunag A, Diimajav E, Jamsranjav B, Buckley M. Comparing the Use of Magnetic Beads with Ultrafiltration for Ancient Dental Calculus Proteomics. J Proteome Res 2021; 20:1689-1704. [PMID: 33596076 DOI: 10.1021/acs.jproteome.0c00862] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Over the past two decades, proteomic analysis has greatly developed in application to the field of biomolecular archaeology, coinciding with advancements in LC-MS/MS instrumentation sensitivity and improvements in sample preparation methods. Recently, human dental calculus has received much attention for its well-preserved proteomes locked in mineralized dental plaque which stores information on human diets and the oral microbiome otherwise invisible to other biomolecular approaches. Maximizing proteome recovery in ancient dental calculus, available only in minute quantities and irreplaceable after destructive analysis, is of paramount importance. Here, we compare the more traditional ultrafiltration-based and acetone precipitation approaches with the newer paramagnetic bead approach in order to test the influence of demineralization acid on recovered proteome complexity obtained from specimens as well as the sequence coverages matched for significant proteins. We found that a protocol utilizing EDTA combined with paramagnetic beads increased proteome complexity, in some cases doubling the number of unique peptides and number of proteins matched, compared to protocols involving the use of HCl and either acetone precipitation or ultrafiltration. Although the increase in the number of proteins was almost exclusively of bacterial origin, a development that has implications for the study of diseases within these ancient populations, an increase in the peptide number for the dairy proteins β-lactoglobulin and casein was also observed reflecting an increase in sequence coverage for these dietary proteins of interest. We also consider structural explanations for the discrepancies observed between these two key dietary proteins preserved in archaeological dental calculus.
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Affiliation(s)
- Karren S Palmer
- School of Natural Sciences, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Cheryl A Makarewicz
- Institute for Prehistoric and Protohistoric Archaeology, Kiel University, Johanna-Mestorf Strasse 2-6, D-24118 Kiel, Germany
| | - Alexey A Tishkin
- Department of Archeology, Ethnography, and Museology, Altai State University, Lenin Prospect 61, 656049 Barnaul, Russia
| | - Svetlana S Tur
- Department of Archeology, Ethnography, and Museology, Altai State University, Lenin Prospect 61, 656049 Barnaul, Russia
| | | | - Erdenebaatar Diimajav
- Department of Archaeology and History, Ulaanbataar State University, Luvsantseveen Street, 5th khoroo, 15th khorgoolol, Bayanzurk District 13343 Ulaanbaatar, Mongolia
| | - Bayarsaikhan Jamsranjav
- National Museum of Mongolia, Ulaanbaatar Mongolia, Juulchin Street-1, Ulaanbaatar 13343, Mongolia
| | - Michael Buckley
- School of Natural Sciences, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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109
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Rampelli S, Turroni S, Mallol C, Hernandez C, Galván B, Sistiaga A, Biagi E, Astolfi A, Brigidi P, Benazzi S, Lewis CM, Warinner C, Hofman CA, Schnorr SL, Candela M. Components of a Neanderthal gut microbiome recovered from fecal sediments from El Salt. Commun Biol 2021; 4:169. [PMID: 33547403 PMCID: PMC7864912 DOI: 10.1038/s42003-021-01689-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 01/05/2021] [Indexed: 12/19/2022] Open
Abstract
A comprehensive view of our evolutionary history cannot ignore the ancestral features of our gut microbiota. To provide some glimpse into the past, we searched for human gut microbiome components in ancient DNA from 14 archeological sediments spanning four stratigraphic units of El Salt Middle Paleolithic site (Spain), including layers of unit X, which has yielded well-preserved Neanderthal occupation deposits dating around 50 kya. According to our findings, bacterial genera belonging to families known to be part of the modern human gut microbiome are abundantly represented only across unit X samples, showing that well-known beneficial gut commensals, such as Blautia, Dorea, Roseburia, Ruminococcus, Faecalibacterium and Bifidobacterium already populated the intestinal microbiome of Homo since as far back as the last common ancestor between humans and Neanderthals.
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Affiliation(s)
- Simone Rampelli
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, Bologna, Italy
| | - Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, Bologna, Italy
| | - Carolina Mallol
- Department of Geography and History, University of La Laguna, Campus de Guajara, La Laguna, Tenerife, Spain.,Archaeological Micromorphology and Biomarker Research Lab, University of La Laguna, Avenida Astrofísico Francisco Sánchez 2, La Laguna, Tenerife, Spain.,ICArEHB - Interdisciplinary Center for Archaeology and the Evolution of Human Behaviour, Universidade do Algarve, Campus de Gambelas, Edificio 1, Faro, Portugal
| | - Cristo Hernandez
- Department of Geography and History, University of La Laguna, Campus de Guajara, La Laguna, Tenerife, Spain
| | - Bertila Galván
- Department of Geography and History, University of La Laguna, Campus de Guajara, La Laguna, Tenerife, Spain
| | - Ainara Sistiaga
- Earth, Atmospheric and Planetary Sciences Department, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, USA.,GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Oester Voldgade 5-7, Copenhagen, Denmark
| | - Elena Biagi
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, Bologna, Italy
| | - Annalisa Astolfi
- "Giorgio Prodi" Cancer Research Center, University of Bologna, Via Massarenti 11, Bologna, Italy.,Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Via Fossato di Mortara 70, Ferrara, Italy
| | - Patrizia Brigidi
- Department of Medical and Surgical Sciences, University of Bologna, Via Massarenti 9, Bologna, Italy
| | - Stefano Benazzi
- Department of Cultural Heritage, University of Bologna, Via degli Ariani 1, Ravenna, Italy.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, Germany
| | - Cecil M Lewis
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, 101 David L. Boren Blvd, Norman, OK, USA.,Department of Anthropology, University of Oklahoma, 455W Lindsey St, Norman, OK, USA
| | - Christina Warinner
- Department of Anthropology, University of Oklahoma, 455W Lindsey St, Norman, OK, USA.,Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, Jena, Germany
| | - Courtney A Hofman
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, 101 David L. Boren Blvd, Norman, OK, USA.,Department of Anthropology, University of Oklahoma, 455W Lindsey St, Norman, OK, USA
| | - Stephanie L Schnorr
- Konrad Lorenz Institute for Evolution and Cognition Research, Martinstraße 12, Klosterneuburg, Austria. .,Department of Anthropology, University of Nevada, 4505S. Maryland Pkwy, Las Vegas, NV, USA.
| | - Marco Candela
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, Bologna, Italy.
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110
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Armbrecht L, Hallegraeff G, Bolch CJS, Woodward C, Cooper A. Hybridisation capture allows DNA damage analysis of ancient marine eukaryotes. Sci Rep 2021; 11:3220. [PMID: 33547359 PMCID: PMC7864908 DOI: 10.1038/s41598-021-82578-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 01/20/2021] [Indexed: 11/09/2022] Open
Abstract
Marine sedimentary ancient DNA (sedaDNA) is increasingly used to study past ocean ecosystems, however, studies have been severely limited by the very low amounts of DNA preserved in the subseafloor, and the lack of bioinformatic tools to authenticate sedaDNA in metagenomic data. We applied a hybridisation capture 'baits' technique to target marine eukaryote sedaDNA (specifically, phyto- and zooplankton, 'Planktonbaits1'; and harmful algal bloom taxa, 'HABbaits1'), which resulted in up to 4- and 9-fold increases, respectively, in the relative abundance of eukaryotes compared to shotgun sequencing. We further used the bioinformatic tool 'HOPS' to authenticate the sedaDNA component, establishing a new proxy to assess sedaDNA authenticity, "% eukaryote sedaDNA damage", that is positively correlated with subseafloor depth. We used this proxy to report the first-ever DNA damage profiles from a marine phytoplankton species, the ubiquitous coccolithophore Emiliania huxleyi. Our approach opens new avenues for the detailed investigation of long-term change and evolution of marine eukaryotes over geological timescales.
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Affiliation(s)
- L Armbrecht
- Australian Centre for Ancient DNA, School of Biological Sciences, Faculty of Sciences, The University of Adelaide, Adelaide, SA, Australia.
| | - G Hallegraeff
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - C J S Bolch
- Institute for Marine and Antarctic Studies, University of Tasmania, Launceston, TAS, Australia
| | - C Woodward
- Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW, Australia
| | - A Cooper
- South Australian Museum, Adelaide, SA, Australia
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111
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Mitchell KJ, Rawlence NJ. Examining Natural History through the Lens of Palaeogenomics. Trends Ecol Evol 2021; 36:258-267. [PMID: 33455740 DOI: 10.1016/j.tree.2020.10.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/05/2020] [Accepted: 10/07/2020] [Indexed: 12/20/2022]
Abstract
The many high-resolution tools that are uniquely applicable to specimens from the Quaternary period (the past ~2.5 Ma) provide an opportunity to cross-validate data and test hypotheses based on the morphology and distribution of fossils. Among these tools is palaeogenomics - the genome-scale sequencing of genetic material from ancient specimens - that can provide direct insight into ecology and evolution, potentially improving the accuracy of inferences about past ecological communities over longer timescales. Palaeogenomics has revealed instances of over- and underestimation of extinct diversity, detected cryptic faunal migration and turnover, allowed quantification of widespread sex biases and sexual dimorphism in the fossil record, revealed past hybridisation events and hybrid individuals, and has highlighted previously unrecognised routes of zoonotic disease transfer.
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Affiliation(s)
- Kieren J Mitchell
- Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia; Australian Research Council (ARC) Centre of Excellence for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.
| | - Nicolas J Rawlence
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
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112
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Michael PJ, Jones D, White N, Hane JK, Bunce M, Gibberd M. Crop-Zone Weed Mycobiomes of the South-Western Australian Grain Belt. Front Microbiol 2020; 11:581592. [PMID: 33324368 PMCID: PMC7721668 DOI: 10.3389/fmicb.2020.581592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/28/2020] [Indexed: 01/16/2023] Open
Abstract
In the absence of a primary crop host, secondary plant hosts may act as a reservoir for fungal plant pathogens of agricultural crops. Secondary hosts may potentially harbor heteroecious biotrophs (e.g., the stripe rust fungus Puccinia striiformis) or other pathogens with broad host ranges. Agricultural grain production tends toward monoculture or a limited number of crop hosts over large regions, and local weeds are a major source of potential secondary hosts. In this study, the fungal phyllospheres of 12 weed species common in the agricultural regions of Western Australia (WA) were compared through high-throughput DNA sequencing. Amplicons of D2 and ITS were sequenced on an Illumina MiSeq system using previously published primers and BLAST outputs analyzed using MEGAN. A heatmap of cumulative presence-absence for fungal taxa was generated, and variance patterns were investigated using principal components analysis (PCA) and canonical correspondence analysis (CCA). We observed the presence of several major international crop pathogens, including basidiomycete rusts of the Puccinia spp., and ascomycete phytopathogens of the Leptosphaeria and Pyrenophora genera. Unrelated to crop production, several endemic pathogen species including those infecting Eucalyptus trees were also observed, which was consistent with local native flora. We also observed that differences in latitude or climate zones appeared to influence the geographic distributions of plant pathogenic species more than the presence of compatible host species, with the exception of Brassicaceae host family. There was an increased proportion of necrotrophic Ascomycete species in warmer and drier regions of central WA, compared to an increased proportion of biotrophic Basidiomycete species in cooler and wetter regions in southern WA.
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Affiliation(s)
- Pippa J. Michael
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Darcy Jones
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Nicole White
- TRENDLab, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - James K. Hane
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Michael Bunce
- TRENDLab, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Mark Gibberd
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
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113
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Weyrich LS. The evolutionary history of the human oral microbiota and its implications for modern health. Periodontol 2000 2020; 85:90-100. [PMID: 33226710 DOI: 10.1111/prd.12353] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Numerous biological and cultural factors influence the microbial communities (microbiota) that inhabit the human mouth, including diet, environment, hygiene, physiology, health status, genetics, and lifestyle. As oral microbiota can underpin oral and systemic diseases, tracing the evolutionary history of oral microbiota and the factors that shape its origins will unlock information to mitigate disease today. Despite this, the origins of many oral microbes remain unknown, and the key factors in the past that shaped our oral microbiota are only now emerging. High throughput DNA sequencing of oral microbiota using ancient DNA and comparative anthropological methodologies has been employed to investigate oral microbiota origins, revealing a complex, rich history. Here, I review the current literature on the factors that shaped and guided oral microbiota evolution, both in Europe and globally. In Europe, oral microbiota evolution was shaped by interactions with Neandertals, the adaptation of farming, widespread integration of industrialization, and postindustrial lifestyles that emerged after World War II. Globally, evidence for a multitude of different oral microbiota histories is emerging, likely supporting dissimilarities in modern oral health across discrete human populations. I highlight how these evolutionary changes are linked to the development of modern oral diseases and discuss the remaining factors that need to be addressed to improve this embryonic field of research. I argue that understanding the evolutionary history of our oral microbiota is necessary to identify new treatment and prevention options to improve oral and systemic health in the future.
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Affiliation(s)
- Laura S Weyrich
- Department of Anthropology and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA.,School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
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114
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Achtman M, Zhou Z. Metagenomics of the modern and historical human oral microbiome with phylogenetic studies on Streptococcus mutans and Streptococcus sobrinus. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190573. [PMID: 33012228 PMCID: PMC7702799 DOI: 10.1098/rstb.2019.0573] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/09/2020] [Indexed: 02/06/2023] Open
Abstract
We have recently developed bioinformatic tools to accurately assign metagenomic sequence reads to microbial taxa: SPARSE for probabilistic, taxonomic classification of sequence reads; EToKi for assembling and polishing genomes from short-read sequences; and GrapeTree, a graphic visualizer of genetic distances between large numbers of genomes. Together, these methods support comparative analyses of genomes from ancient skeletons and modern humans. Here, we illustrate these capabilities with 784 samples from historical dental calculus, modern saliva and modern dental plaque. The analyses revealed 1591 microbial species within the oral microbiome. We anticipated that the oral complexes of Socransky et al., which were defined in 1998, would predominate among taxa whose frequencies differed by source. However, although some species discriminated between sources, we could not confirm the existence of the complexes. The results also illustrate further functionality of our pipelines with two species that are associated with dental caries, Streptococcus mutans and Streptococcus sobrinus. They were rare in historical dental calculus but common in modern plaque, and even more common in saliva. Reconstructed draft genomes of these two species from metagenomic samples in which they were abundant were combined with modern public genomes to provide a detailed overview of their core genomic diversity. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.
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Affiliation(s)
- Mark Achtman
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
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115
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Bravo-Lopez M, Villa-Islas V, Rocha Arriaga C, Villaseñor-Altamirano AB, Guzmán-Solís A, Sandoval-Velasco M, Wesp JK, Alcantara K, López-Corral A, Gómez-Valdés J, Mejía E, Herrera A, Meraz-Moreno A, Moreno-Cabrera MDLL, Moreno-Estrada A, Nieves-Colón MA, Olvera J, Pérez-Pérez J, Iversen KH, Rasmussen S, Sandoval K, Zepeda G, Ávila-Arcos MC. Paleogenomic insights into the red complex bacteria Tannerella forsythia in Pre-Hispanic and Colonial individuals from Mexico. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190580. [PMID: 33012233 PMCID: PMC7702795 DOI: 10.1098/rstb.2019.0580] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2020] [Indexed: 12/14/2022] Open
Abstract
The 'red complex' is an aggregate of three oral bacteria (Tannerella forsythia, Porphyromonas gingivalis and Treponema denticola) responsible for severe clinical manifestation of periodontal disease. Here, we report the first direct evidence of ancient T.forsythia DNA in dentin and dental calculus samples from archaeological skeletal remains that span from the Pre-Hispanic to the Colonial period in Mexico. We recovered twelve partial ancient T. forsythia genomes and observed a distinct phylogenetic placement of samples, suggesting that the strains present in Pre-Hispanic individuals likely arrived with the first human migrations to the Americas and that new strains were introduced with the arrival of European and African populations in the sixteenth century. We also identified instances of the differential presence of genes between periods in the T. forsythia ancient genomes, with certain genes present in Pre-Hispanic individuals and absent in Colonial individuals, and vice versa. This study highlights the potential for studying ancient T. forsythia genomes to unveil past social interactions through analysis of disease transmission. Our results illustrate the long-standing relationship between this oral pathogen and its human host, while also unveiling key evidence to understand its evolutionary history in Pre-Hispanic and Colonial Mexico. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.
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Affiliation(s)
- Miriam Bravo-Lopez
- International Laboratory for Human Genome Research, National Autonomous University of México (UNAM), Querétaro, 76230, Mexico
| | - Viridiana Villa-Islas
- International Laboratory for Human Genome Research, National Autonomous University of México (UNAM), Querétaro, 76230, Mexico
| | - Carolina Rocha Arriaga
- International Laboratory for Human Genome Research, National Autonomous University of México (UNAM), Querétaro, 76230, Mexico
| | - Ana B. Villaseñor-Altamirano
- International Laboratory for Human Genome Research, National Autonomous University of México (UNAM), Querétaro, 76230, Mexico
| | - Axel Guzmán-Solís
- International Laboratory for Human Genome Research, National Autonomous University of México (UNAM), Querétaro, 76230, Mexico
| | - Marcela Sandoval-Velasco
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, 1350, Denmark
| | - Julie K. Wesp
- Department of Sociology and Anthropology, North Carolina State University, Raleigh, NC 27695, USA
| | - Keitlyn Alcantara
- Department of Anthropology, Indiana University-Bloomington, Bloomington, IN 47405, USA
| | - Aurelio López-Corral
- Department of Archeology, National Institute of Anthropology and History, Tlaxcala, 90000, Mexico
| | | | - Elizabeth Mejía
- National Institute of Anthropology and History, Querétaro, 76000, Mexico
| | - Alberto Herrera
- National Institute of Anthropology and History, Querétaro, 76000, Mexico
| | | | | | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity, Unit of Advanced Genomics (LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36824, Mexico
| | - Maria A. Nieves-Colón
- National Laboratory of Genomics for Biodiversity, Unit of Advanced Genomics (LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36824, Mexico
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85281, USA
| | - Joel Olvera
- Graduate Program of Physical Anthropology, National School of Anthropology and History, Mexico City, 14030, Mexico
| | - Julia Pérez-Pérez
- National School of Anthropology and History, Mexico City, 14030, Mexico
| | - Katrine Højholt Iversen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Karla Sandoval
- National Laboratory of Genomics for Biodiversity, Unit of Advanced Genomics (LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36824, Mexico
| | - Gabriela Zepeda
- National Institute of Anthropology and History, Guanajuato, 36250, Mexico
| | - María C. Ávila-Arcos
- International Laboratory for Human Genome Research, National Autonomous University of México (UNAM), Querétaro, 76230, Mexico
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116
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Handsley-Davis M, Jamieson L, Kapellas K, Hedges J, Weyrich LS. The role of the oral microbiota in chronic non-communicable disease and its relevance to the Indigenous health gap in Australia. BMC Oral Health 2020; 20:327. [PMID: 33198712 PMCID: PMC7670664 DOI: 10.1186/s12903-020-01308-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 10/31/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Aboriginal Australians and Torres Strait Islanders (hereafter respectfully referred to as Indigenous Australians) experience disproportionately poor health and low life expectancy compared to non-Indigenous Australians. Poor oral health is a critical, but understudied, contributor to this health gap. A considerable body of evidence links poor oral health to increased risks of other chronic non-communicable conditions, such as diabetes, cardiovascular disease, chronic kidney disease, and poor emotional wellbeing. MAIN: The oral microbiota is indisputably associated with several oral diseases that disproportionately affect Indigenous Australians. Furthermore, a growing literature suggests direct and indirect links between the oral microbiota and systemic chronic non-communicable diseases that underpin much of the Indigenous health gap in Australia. Recent research indicates that oral microbial communities are shaped by a combination of cultural and lifestyle factors and are inherited from caregivers to children. Systematic differences in oral microbiota diversity and composition have been identified between Indigenous and non-Indigenous individuals in Australia and elsewhere, suggesting that microbiota-related diseases may be distinct in Indigenous Australians. CONCLUSION: Oral microbiota research involving Indigenous Australians is a promising new area that could benefit Indigenous communities in numerous ways. These potential benefits include: (1) ensuring equity and access for Indigenous Australians in microbiota-related therapies; (2) opportunities for knowledge-sharing and collaborative research between scientists and Indigenous communities; and (3) using knowledge about the oral microbiota and chronic disease to help close the gaps in Indigenous oral and systemic health.
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Affiliation(s)
- Matilda Handsley-Davis
- Department of Molecular and Cellular Biology, University of Adelaide, Adelaide, SA, Australia.
| | - Lisa Jamieson
- Australian Research Centre for Population Oral Health (ARCPOH), University of Adelaide, Adelaide, SA, Australia
| | - Kostas Kapellas
- Australian Research Centre for Population Oral Health (ARCPOH), University of Adelaide, Adelaide, SA, Australia
| | - Joanne Hedges
- Australian Research Centre for Population Oral Health (ARCPOH), University of Adelaide, Adelaide, SA, Australia
| | - Laura S Weyrich
- Department of Molecular and Cellular Biology, University of Adelaide, Adelaide, SA, Australia.
- Department of Anthropology and Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, USA.
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117
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Hardy K. Paleomedicine and the Evolutionary Context of Medicinal Plant Use. ACTA ACUST UNITED AC 2020; 31:1-15. [PMID: 33071384 PMCID: PMC7546135 DOI: 10.1007/s43450-020-00107-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 09/23/2020] [Indexed: 12/12/2022]
Abstract
Modern human need for medicines is so extensive that it is thought to be a deep evolutionary behavior. There is abundant evidence from our Paleolithic and later prehistoric past, of survival after periodontal disease, traumas, and invasive medical treatments including trepanations and amputations, suggesting a detailed, applied knowledge of medicinal plant secondary compounds. Direct archeological evidence for use of plants in the Paleolithic is rare, but evidence is growing. An evolutionary context for early human use of medicinal plants is provided by the broad evidence for animal self-medication, in particular, of non-human primates. During the later Paleolithic, there is evidence for the use of poisonous and psychotropic plants, suggesting that Paleolithic humans built on and expanded their knowledge and use of plant secondary compounds.
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Affiliation(s)
- Karen Hardy
- Institució Catalana de Recerca i Estudis Avançats, Pg. Lluís Companys 23, 08010 Barcelona, Catalonia Spain.,Departament de Prehistòria, Facultat de Filosofia i Lletres, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Catalonia Spain
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118
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Schnorr SL. The soil in our microbial DNA informs about environmental interfaces across host and subsistence modalities. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190577. [PMID: 33012224 DOI: 10.1098/rstb.2019.0577] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In this study, I use microbiome datasets from global soil samples and diverse hosts to learn whether soil microbial taxa are found in host microbiomes, and whether these observations fit the narrative that environmental interaction influences human microbiomes. A major motivation for conducting host-associated microbiome research is to contribute towards understanding how the environment may influence host physiology. The microbial molecular network is considered a key vector by which environmental traits may be transmitted to the host. Research on human evolution seeks evidence that can inform about the living experiences of human ancestors. This objective is substantially enhanced by recent work on ancient biomolecules from preserved microbial tissues, such as dental calculus, faecal sediments and whole coprolites. A challenge yet is to distinguish authentic biomolecules from environmental contaminants deposited contemporaneously, primarily from soil. However, we do not have sound expectations about the soil microbial elements arriving to host-associated microbiomes in a modern context. One assumption in human microbiome research is that proximity to the natural environment should affect biodiversity or impart genetic elements. I present evidence supporting the assumption that environmental soil taxa are found among host-associated gut taxa, which can recapitulate the surrounding host habitat ecotype. Soil taxa found in gut microbiomes relate to a set of universal 'core' taxa for all soil ecotypes, demonstrating that widespread host organisms may experience a consistent pattern of external environmental cues, perhaps critical for development. Observed differentiation of soil feature diversity, abundance and composition among human communities, great apes and invertebrate hosts also indicates that lifestyle patterns are inferable from an environmental signal that is retrievable from gut microbiome amplicon data. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.
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Affiliation(s)
- Stephanie L Schnorr
- Department of Anthropology, University of Nevada, Las Vegas, NV, USA.,Konrad Lorenz Institute for Evolution and Cognition Research, Klosterneuburg, Austria
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119
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Eisenhofer R, Kanzawa-Kiriyama H, Shinoda KI, Weyrich LS. Investigating the demographic history of Japan using ancient oral microbiota. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190578. [PMID: 33012223 PMCID: PMC7702792 DOI: 10.1098/rstb.2019.0578] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
While microbial communities in the human body (microbiota) are now commonly associated with health and disease in industrialised populations, we know very little about how these communities co-evolved and changed with humans throughout history and deep prehistory. We can now examine these communities by sequencing ancient DNA preserved within calcified dental plaque (calculus), providing insights into the origins of disease and their links to human history. Here, we examine ancient DNA preserved within dental calculus samples and their associations with two major cultural periods in Japan: the Jomon period hunter–gatherers approximately 3000 years before present (BP) and the Edo period agriculturalists 400–150 BP. We investigate how human oral microbiomes have changed in Japan through time and explore the presence of microorganisms associated with oral diseases (e.g. periodontal disease, dental caries) in ancient Japanese populations. Finally, we explore oral microbial strain diversity and its potential links to ancient demography in ancient Japan by performing phylogenomic analysis of a widely conserved oral species—Anaerolineaceae oral taxon 439. This research represents, to our knowledge, the first study of ancient oral microbiomes from Japan and demonstrates that the analysis of ancient dental calculus can provide key information about the origin of non-infectious disease and its deep roots with human demography. This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.
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Affiliation(s)
- Raphael Eisenhofer
- Australian Centre for Ancient DNA, University of Adelaide, Adelaide, Australia
| | | | - Ken-Ichi Shinoda
- Department of Anthropology, National Museum of Nature and Science, Tsukuba, Japan
| | - Laura S Weyrich
- Australian Centre for Ancient DNA, University of Adelaide, Adelaide, Australia.,Department of Anthropology and the Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, USA
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120
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Jacobson DK, Honap TP, Monroe C, Lund J, Houk BA, Novotny AC, Robin C, Marini E, Lewis CM. Functional diversity of microbial ecologies estimated from ancient human coprolites and dental calculus. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190586. [PMID: 33012230 PMCID: PMC7702801 DOI: 10.1098/rstb.2019.0586] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Human microbiome studies are increasingly incorporating macroecological approaches, such as community assembly, network analysis and functional redundancy to more fully characterize the microbiome. Such analyses have not been applied to ancient human microbiomes, preventing insights into human microbiome evolution. We address this issue by analysing published ancient microbiome datasets: coprolites from Rio Zape (n = 7; 700 CE Mexico) and historic dental calculus (n = 44; 1770–1855 CE, UK), as well as two novel dental calculus datasets: Maya (n = 7; 170 BCE-885 CE, Belize) and Nuragic Sardinians (n = 11; 1400–850 BCE, Italy). Periodontitis-associated bacteria (Treponema denticola, Fusobacterium nucleatum and Eubacterium saphenum) were identified as keystone taxa in the dental calculus datasets. Coprolite keystone taxa included known short-chain fatty acid producers (Eubacterium biforme, Phascolarctobacterium succinatutens) and potentially disease-associated bacteria (Escherichia, Brachyspira). Overlap in ecological profiles between ancient and modern microbiomes was indicated by similarity in functional response diversity profiles between contemporary hunter–gatherers and ancient coprolites, as well as parallels between ancient Maya, historic UK, and modern Spanish dental calculus; however, the ancient Nuragic dental calculus shows a distinct ecological structure. We detected key ecological signatures from ancient microbiome data, paving the way to expand understanding of human microbiome evolution. This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.
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Affiliation(s)
- David K Jacobson
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, Norman, OK, USA.,Department of Anthropology, University of Oklahoma, Norman, OK, USA
| | - Tanvi P Honap
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, Norman, OK, USA.,Department of Anthropology, University of Oklahoma, Norman, OK, USA
| | - Cara Monroe
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, Norman, OK, USA
| | - Justin Lund
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, Norman, OK, USA.,Department of Anthropology, University of Oklahoma, Norman, OK, USA
| | - Brett A Houk
- Department of Sociology, Anthropology, and Social Work, Texas Tech University, Lubbock, TX, USA
| | - Anna C Novotny
- Department of Sociology, Anthropology, and Social Work, Texas Tech University, Lubbock, TX, USA
| | - Cynthia Robin
- Department of Anthropology, Northwestern University, Evanston, IL, USA
| | - Elisabetta Marini
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Sardinia, Italy
| | - Cecil M Lewis
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, Norman, OK, USA.,Department of Anthropology, University of Oklahoma, Norman, OK, USA
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121
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Brealey JC, Leitão HG, van der Valk T, Xu W, Bougiouri K, Dalén L, Guschanski K. Dental Calculus as a Tool to Study the Evolution of the Mammalian Oral Microbiome. Mol Biol Evol 2020; 37:3003-3022. [PMID: 32467975 PMCID: PMC7530607 DOI: 10.1093/molbev/msaa135] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Dental calculus, the calcified form of the mammalian oral microbial plaque biofilm, is a rich source of oral microbiome, host, and dietary biomolecules and is well preserved in museum and archaeological specimens. Despite its wide presence in mammals, to date, dental calculus has primarily been used to study primate microbiome evolution. We establish dental calculus as a valuable tool for the study of nonhuman host microbiome evolution, by using shotgun metagenomics to characterize the taxonomic and functional composition of the oral microbiome in species as diverse as gorillas, bears, and reindeer. We detect oral pathogens in individuals with evidence of oral disease, assemble near-complete bacterial genomes from historical specimens, characterize antibiotic resistance genes, reconstruct components of the host diet, and recover host genetic profiles. Our work demonstrates that metagenomic analyses of dental calculus can be performed on a diverse range of mammalian species, which will allow the study of oral microbiome and pathogen evolution from a comparative perspective. As dental calculus is readily preserved through time, it can also facilitate the quantification of the impact of anthropogenic changes on wildlife and the environment.
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Affiliation(s)
- Jaelle C Brealey
- Department of Ecology and Genetics, Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Henrique G Leitão
- Department of Ecology and Genetics, Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Tom van der Valk
- Department of Ecology and Genetics, Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Wenbo Xu
- Department of Ecology and Genetics, Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Katia Bougiouri
- Department of Ecology and Genetics, Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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122
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Identification of ancient viruses from metagenomic data of the Jomon people. J Hum Genet 2020; 66:287-296. [PMID: 32994538 DOI: 10.1038/s10038-020-00841-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/20/2020] [Accepted: 09/05/2020] [Indexed: 11/08/2022]
Abstract
Ancient DNA studies provide genomic information about the origins, population structures, and physical characteristics of ancient humans that cannot be solely examined by archeological studies. The DNAs extracted from ancient human bones, teeth, or tissues are often contaminated with coexisting bacterial and viral genomes that contain DNA from ancient microbes infecting those of ancient humans. Information on ancient viral genomes is useful in making inferences about the viral evolution. Here, we have utilized metagenomic sequencing data from the dental pulp of five Jomon individuals, who lived on the Japanese archipelago more than 3000 years ago; this is to detect ancient viral genomes. We conducted de novo assembly of the non-human reads where we have obtained 277,387 contigs that were longer than 1000 bp. These contigs were subjected to homology searches against a collection of modern viral genome sequences. We were able to detect eleven putative ancient viral genomes. Among them, we reconstructed the complete sequence of the Siphovirus contig89 (CT89) viral genome. The Jomon CT89-like sequence was determined to contain 59 open reading frames, among which five genes known to encode phage proteins were under strong purifying selection. The host of CT89 was predicted to be Schaalia meyeri, a bacterium residing in the human oral cavity. Finally, the CT89 phylogenetic tree showed two clusters, from both of which the Jomon sequence was separated. Our results suggest that metagenomic information from the dental pulp of the Jomon people is essential in retrieving ancient viral genomes used to examine their evolution.
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Boethius A, Hollund H, Linderholm J, Vanhanen S, Kjällquist M, Magnell O, Apel J. Quantifying archaeo-organic degradation - A multiproxy approach to understand the accelerated deterioration of the ancient organic cultural heritage at the Swedish Mesolithic site Ageröd. PLoS One 2020; 15:e0239588. [PMID: 32966345 PMCID: PMC7511028 DOI: 10.1371/journal.pone.0239588] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/10/2020] [Indexed: 11/19/2022] Open
Abstract
Despite a growing body of evidence concerning accelerated organic degradation at archaeological sites, there have been few follow-up investigations to examine the status of the remaining archaeological materials in the ground. To address the question of archaeo-organic preservation, we revisited the Swedish, Mesolithic key-site Ageröd and could show that the bone material had been subjected to an accelerated deterioration during the last 75 years, which had destroyed the bones in the areas where they had previously been best preserved. To understand why this has happened and to quantify and qualify the extent of the organic degradation, we here analyse the soil chemistry, bone histology, collagen preservation and palaeobotany at the site. Our results show that the soil at Ageröd is losing, or has already lost, its preservative and buffering qualities, and that pH-values in the still wet areas of the site have dropped to levels where no bone preservation is possible. Our results suggest that this acidification process is enhanced by the release of sulphuric acid as pyrite in the bones oxidizes. While we are still able to find well-preserved palaeobotanical remains, they are also starting to corrode through re-introduced oxygen into the archaeological layers. While some areas of the site have been more protected through redeposited soil on top of the archaeological layers, all areas of Ageröd are rapidly deteriorating. Lastly, while it is still possible to perform molecular analyses on the best-preserved bones from the most protected areas, this opportunity will likely be lost within a few decades. In conclusion, we find that if we, as a society, wish to keep this valuable climatic, environmental and cultural archive, both at Ageröd and elsewhere, the time to act is now and if we wait we will soon be in a situation where this record will be irretrievably lost forever.
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Affiliation(s)
- Adam Boethius
- Department of Archaeology and Ancient History, Lund University, Lund, Sweden
- * E-mail:
| | - Hege Hollund
- Museum of Archaeology, University of Stavanger, Stavanger, Norway
| | - Johan Linderholm
- Department of Historical, Philosophical and Religious Studies, Umeå University, Umeå, Sweden
| | | | | | - Ola Magnell
- The Archaeologists, National Historical Museums, Lund, Sweden
| | - Jan Apel
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
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124
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Assessment of Cardiotoxicity With Stem Cell-based Strategies. Clin Ther 2020; 42:1892-1910. [PMID: 32938533 DOI: 10.1016/j.clinthera.2020.08.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/20/2020] [Accepted: 08/25/2020] [Indexed: 02/08/2023]
Abstract
PURPOSE Adverse cardiovascular drug effects pose a substantial medical risk and represent a common cause of drug withdrawal from the market. Thus, current in vitro assays and in vivo animal models still have shortcomings in assessing cardiotoxicity. A human model for more accurate preclinical cardiotoxicity assessment is highly desirable. Current differentiation protocols allow for the generation of human pluripotent stem cell-derived cardiomyocytes in basically unlimited numbers and offer the opportunity to study drug effects on human cardiomyocytes. The purpose of this review is to provide a brief overview of the current approaches to translate studies with pluripotent stem cell-derived cardiomyocytes from basic science to preclinical risk assessment. METHODS A review of the literature was performed to gather data on the pathophysiology of cardiotoxicity, the current cardiotoxicity screening assays, stem cell-derived cardiomyocytes, and their application in cardiotoxicity screening. FINDINGS There is increasing evidence that stem cell-derived cardiomyocytes predict arrhythmogenicity with high accuracy. Cardiomyocyte immaturity represents the major limitation so far. However, strategies are being developed to overcome this hurdle, such as tissue engineering. In addition, stem cell-based strategies offer the possibility to assess structural drug toxicity (eg, by anticancer drugs) on complex models that more closely mirror the structure of the heart and contain endothelial cells and fibroblasts. IMPLICATIONS Pluripotent stem cell-derived cardiomyocytes have the potential to substantially change how preclinical cardiotoxicity screening is performed. To which extent they will replace or complement current approaches is being evaluated.
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125
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Breyl M. Triangulating Neanderthal cognition: A tale of not seeing the forest for the trees. WILEY INTERDISCIPLINARY REVIEWS. COGNITIVE SCIENCE 2020; 12:e1545. [PMID: 32918796 DOI: 10.1002/wcs.1545] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/09/2020] [Accepted: 08/13/2020] [Indexed: 01/20/2023]
Abstract
The inference of Neanderthal cognition, including their cultural and linguistic capabilities, has persisted as a fiercely debated research topic for decades. This lack of consensus is substantially based on inherent uncertainties in reconstructing prehistory out of indirect evidence as well as other methodological limitations. Further factors include systemic difficulties within interdisciplinary discourse, data artifacts, historic research biases, and the sheer scope of the relevant research. Given the degrees of freedom in interpretation ensuing from these complications, any attempt to find approximate answers to the yet unsettled pertinent discourse may not rest on single studies, but instead a careful and comprehensive interdisciplinary synthesis of findings. Triangulating Neanderthals' cognition by considering the plethora of data, diverse perspectives and aforementioned complexities present within the literature constitutes the currently most reliable pathway to tentative conclusions. While some uncertainties remain, such an approach paints the picture of an extensive shared humanity between anatomically modern humans and Neanderthals. This article is categorized under: Cognitive Biology > Evolutionary Roots of Cognition Linguistics > Evolution of Language.
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Affiliation(s)
- Michael Breyl
- Germanistik, Komparatistik, Nordistik, Deutsch als Fremdsprache, Ludwig-Maximilians-University of Munich (LMU), Munich, Germany
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126
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Oxilia G, Bortolini E, Badino F, Bernardini F, Gazzoni V, Lugli F, Romandini M, Radini A, Terlato G, Marciani G, Silvestrini S, Menghi Sartorio JC, Thun Hohenstein U, Fiorenza L, Kullmer O, Tuniz C, Moggi Cecchi J, Talamo S, Fontana F, Peresani M, Benazzi S, Cristiani E. Exploring late Paleolithic and Mesolithic diet in the Eastern Alpine region of Italy through multiple proxies. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 174:232-253. [PMID: 32914870 PMCID: PMC7918647 DOI: 10.1002/ajpa.24128] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 06/30/2020] [Accepted: 07/09/2020] [Indexed: 11/30/2022]
Abstract
Objectives The analysis of prehistoric human dietary habits is key for understanding the effects of paleoenvironmental changes on the evolution of cultural and social human behaviors. In this study, we compare results from zooarchaeological, stable isotope and dental calculus analyses as well as lower second molar macrowear patterns to gain a broader understanding of the diet of three individuals who lived between the end of the Late Pleistocene and the Early Holocene (ca., 17–8 ky cal BP) in the Eastern Alpine region of Italy. Materials and methods We analyze individuals buried at the sites of Riparo Tagliente (Verona), Riparo Villabruna, and Mondeval de Sora (Belluno). The three burials provide a unique dataset for diachronically exploring the influence of climatic changes on human subsistence strategies. Results Isotopic results indicate that all individuals likely relied on both terrestrial and freshwater animal proteins. Even though dental calculus analysis was, in part, hindered by the amount of mineral deposit available on the teeth, tooth macrowear study suggests that the dietary habits of the individuals included plant foods. Moreover, differences in macrowear patterns of lower second molars have been documented between Neanderthals and modern humans in the present sample, due to a prevalence of Buccal wear among the former as opposed to higher values of Lingual wear in modern human teeth. Discussion Isotopic analyses have emphasized the contribution of animal proteins in the diet of the three foragers from the Eastern Alpine region. The possible intake of carbohydrate‐rich plant foods, suggested by the retrieval of plant remains in dental calculus, is supported by the signal of macrowear analysis. Moreover, the latter method indicates that the distribution of macrowear in lower second molars (M2s) allows us to discriminate between Neanderthals and modern humans within the present reference sample. Overall, our results show these three prehistoric hunter‐gatherers were well adapted to the environment in which they lived exploiting many natural resources.
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Affiliation(s)
- Gregorio Oxilia
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy.,DANTE Diet and Ancient Technology Laboratory, Department of Oral and Maxillo Facial Sciences Sapienza University, Rome, Italy
| | - Eugenio Bortolini
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Federica Badino
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy.,C.N.R. - Istituto di Geologia Ambientale e Geoingegneria, Milan, Italy
| | - Federico Bernardini
- Centro Fermi, Museo Storico della Fisica e Centro di Studi e Ricerche Enrico Fermi, Rome, Italy.,Multidisciplinary Laboratory, The Abdus Salam International Centre for Theoretical Physics, Trieste, Italy
| | - Valentina Gazzoni
- Department of Humanities-Section of Prehistoric and Anthropological Sciences, University of Ferrara, Ferrara, Italy
| | - Federico Lugli
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy.,Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Matteo Romandini
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy.,Department of Humanities-Section of Prehistoric and Anthropological Sciences, University of Ferrara, Ferrara, Italy
| | - Anita Radini
- DANTE Diet and Ancient Technology Laboratory, Department of Oral and Maxillo Facial Sciences Sapienza University, Rome, Italy
| | - Gabriele Terlato
- Department of Humanities-Section of Prehistoric and Anthropological Sciences, University of Ferrara, Ferrara, Italy
| | - Giulia Marciani
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Sara Silvestrini
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Jessica C Menghi Sartorio
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy.,Department of Humanities-Section of Prehistoric and Anthropological Sciences, University of Ferrara, Ferrara, Italy
| | - Ursula Thun Hohenstein
- Department of Humanities-Section of Prehistoric and Anthropological Sciences, University of Ferrara, Ferrara, Italy
| | - Luca Fiorenza
- Monash Biomedicine Discovery Institute, Department of Anatomy and Developmental Biology, Monash University, Melbourne, Victoria, Australia.,Earth Sciences, University of New England, Armidale, New South Wales, Australia
| | - Ottmar Kullmer
- Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany.,Department of Paleobiology and Environment, Institute of Ecology, Evolution, and Diversity, Johann Wolfgang Goethe University, Frankfurt, Germany
| | - Claudio Tuniz
- Centro Fermi, Museo Storico della Fisica e Centro di Studi e Ricerche Enrico Fermi, Rome, Italy.,Multidisciplinary Laboratory, The Abdus Salam International Centre for Theoretical Physics, Trieste, Italy.,Centre for Archaeological Science, University of Wollongong, Wollongong, New South Wales, Australia
| | | | - Sahra Talamo
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Department of Chemistry "G. Ciamician", University of Bologna, Bologna, Italy
| | - Federica Fontana
- Department of Humanities-Section of Prehistoric and Anthropological Sciences, University of Ferrara, Ferrara, Italy
| | - Marco Peresani
- C.N.R. - Istituto di Geologia Ambientale e Geoingegneria, Milan, Italy.,Department of Humanities-Section of Prehistoric and Anthropological Sciences, University of Ferrara, Ferrara, Italy
| | - Stefano Benazzi
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Emanuela Cristiani
- DANTE Diet and Ancient Technology Laboratory, Department of Oral and Maxillo Facial Sciences Sapienza University, Rome, Italy
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127
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Neukamm J, Pfrengle S, Molak M, Seitz A, Francken M, Eppenberger P, Avanzi C, Reiter E, Urban C, Welte B, Stockhammer PW, Teßmann B, Herbig A, Harvati K, Nieselt K, Krause J, Schuenemann VJ. 2000-year-old pathogen genomes reconstructed from metagenomic analysis of Egyptian mummified individuals. BMC Biol 2020; 18:108. [PMID: 32859198 PMCID: PMC7456089 DOI: 10.1186/s12915-020-00839-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 07/29/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Recent advances in sequencing have facilitated large-scale analyses of the metagenomic composition of different samples, including the environmental microbiome of air, water, and soil, as well as the microbiome of living humans and other animals. Analyses of the microbiome of ancient human samples may provide insights into human health and disease, as well as pathogen evolution, but the field is still in its very early stages and considered highly challenging. RESULTS The metagenomic and pathogen content of Egyptian mummified individuals from different time periods was investigated via genetic analysis of the microbial composition of various tissues. The analysis of the dental calculus' microbiome identified Red Complex bacteria, which are correlated with periodontal diseases. From bone and soft tissue, genomes of two ancient pathogens, a 2200-year-old Mycobacterium leprae strain and a 2000-year-old human hepatitis B virus, were successfully reconstructed. CONCLUSIONS The results show the reliability of metagenomic studies on Egyptian mummified individuals and the potential to use them as a source for the extraction of ancient pathogen DNA.
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Affiliation(s)
- Judith Neukamm
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany.,Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076, Tübingen, Germany
| | - Saskia Pfrengle
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany
| | - Martyna Molak
- Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679, Warsaw, Poland.,Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097, Warsaw, Poland
| | - Alexander Seitz
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076, Tübingen, Germany
| | - Michael Francken
- Senckenberg Centre for Human Evolution and Paleoenvironments, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany.,Paleoanthropology, Dept. of Geosciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany
| | - Partick Eppenberger
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Charlotte Avanzi
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, USA
| | - Ella Reiter
- Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany
| | - Christian Urban
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Beatrix Welte
- Institute of Pre- and Protohistory and Medieval Archaeology, Department of Early Prehistory and Quaternary Ecology, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany
| | - Philipp W Stockhammer
- Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig Maximilian University Munich, 80799, Munich, Germany.,Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany
| | - Barbara Teßmann
- Berlin Society of Anthropology, Ethnology and Prehistory, 10117, Berlin, Germany.,Museum of Prehistory and Early History, SMPK Berlin, 10117, Berlin, Germany
| | - Alexander Herbig
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany
| | - Katerina Harvati
- Senckenberg Centre for Human Evolution and Paleoenvironments, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany.,Paleoanthropology, Dept. of Geosciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany.,DFG Centre for Advanced Studies Words, Bones, Genes, Tools: Tracking Linguistic, Cultural and Biological Trajectories of the Human Past, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany
| | - Kay Nieselt
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076, Tübingen, Germany
| | - Johannes Krause
- Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany. .,Senckenberg Centre for Human Evolution and Paleoenvironments, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany. .,Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745, Jena, Germany.
| | - Verena J Schuenemann
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland. .,Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany. .,Senckenberg Centre for Human Evolution and Paleoenvironments, University of Tübingen, Rümelinstrasse 19-23, 72070, Tübingen, Germany.
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128
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Chessa D, Murgia M, Sias E, Deligios M, Mazzarello V, Fiamma M, Rovina D, Carenti G, Ganau G, Pintore E, Fiori M, Kay GL, Ponzeletti A, Cappuccinelli P, Kelvin DJ, Wain J, Rubino S. Metagenomics and microscope revealed T. trichiura and other intestinal parasites in a cesspit of an Italian nineteenth century aristocratic palace. Sci Rep 2020; 10:12656. [PMID: 32728085 PMCID: PMC7391740 DOI: 10.1038/s41598-020-69497-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 07/08/2020] [Indexed: 11/09/2022] Open
Abstract
This study evidenced the presence of parasites in a cesspit of an aristocratic palace of nineteenth century in Sardinia (Italy) by the use of classical paleoparasitological techniques coupled with next-generation sequencing. Parasite eggs identified by microscopy included helminth genera pathogenic for humans and animals: the whipworm Trichuris sp., the roundworm Ascaris sp., the flatworm Dicrocoelium sp. and the fish tapeworm Diphyllobothrium sp. In addition, 18S rRNA metabarcoding and metagenomic sequencing analysis allowed the first description in Sardinia of aDNA of the human specific T. trichiura species and Ascaris genus. Their presence is important for understanding the health conditions, hygiene habits, agricultural practices and the diet of the local inhabitants in the period under study.
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Affiliation(s)
- Daniela Chessa
- Department of Biomedical Science, University of Sassari, V. le San Pietro 43/B, 07100, Sassari, Italy
| | - Manuela Murgia
- Department of Biomedical Science, University of Sassari, V. le San Pietro 43/B, 07100, Sassari, Italy.
| | - Emanuela Sias
- Department of Biomedical Science, University of Sassari, V. le San Pietro 43/B, 07100, Sassari, Italy
| | - Massimo Deligios
- Department of Biomedical Science, University of Sassari, V. le San Pietro 43/B, 07100, Sassari, Italy
| | - Vittorio Mazzarello
- Department of Biomedical Science, University of Sassari, V. le San Pietro 43/B, 07100, Sassari, Italy
| | - Maura Fiamma
- Department of Biomedical Science, University of Sassari, V. le San Pietro 43/B, 07100, Sassari, Italy
| | - Daniela Rovina
- Superintendence Archaeology of Sardinia, 07100, Sassari, Italy
| | - Gabriele Carenti
- Department of Nature and Environmental Sciences, University of Sassari, 07100, Sassari, Italy
| | - Giulia Ganau
- Department of Biomedical Science, University of Sassari, V. le San Pietro 43/B, 07100, Sassari, Italy
| | - Elisabetta Pintore
- Department of Veterinary Medicine, University of Sassari, 07100, Sassari, Italy
| | | | - Gemma L Kay
- Bob Champion Research and Educational Building, University of East Anglia, Norwich Research Park, Norwich, UK
- The Quadram Institute, Norwich Research Park, Norwich, UK
| | | | - Piero Cappuccinelli
- Department of Biomedical Science, University of Sassari, V. le San Pietro 43/B, 07100, Sassari, Italy
| | - David J Kelvin
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
| | - John Wain
- Bob Champion Research and Educational Building, University of East Anglia, Norwich Research Park, Norwich, UK
- The Quadram Institute, Norwich Research Park, Norwich, UK
| | - Salvatore Rubino
- Department of Biomedical Science, University of Sassari, V. le San Pietro 43/B, 07100, Sassari, Italy
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129
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Oelze VM, Wittig RM, Lemoine S, Kühl HS, Boesch C. How isotopic signatures relate to meat consumption in wild chimpanzees: A critical reference study from Taï National Park, Côte d'Ivoire. J Hum Evol 2020; 146:102817. [PMID: 32683168 DOI: 10.1016/j.jhevol.2020.102817] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/21/2020] [Accepted: 04/21/2020] [Indexed: 11/27/2022]
Abstract
The roots of human hunting and meat eating lie deep in our evolutionary past shared with chimpanzees (Pan troglodytes). From the few habituated wild populations, we know that there is considerable variation in the extent to which chimpanzees consume meat. Expanding our knowledge of meat eating frequencies to more, yet unhabituated, populations requires noninvasive, indirect quantitative techniques. We here evaluate the use of stable isotopes to reconstruct meat-eating behavior in wild chimpanzees. We present hair isotope data (n = 260) of two western chimpanzee (P. troglodytes verus) groups from Taï forest (Côte d'Ivoire) and relate them to directly observed amounts of meat consumed, sex/female reproductive state, and group, while controlling for differences between individuals, seasons, and observation efforts. Succeeding seven months of hunting observations, we collected hair of 25 individuals for sequential analysis of δ15N and δ13C. Hunting success in the 7-month study period varied between the groups, with 25 successful hunts in the East group and only 8 in the North group. However, our models only found a direct relationship between amounts of meat consumed and variation within individual hair δ15N values in the East group, but not in the North group and not when comparing between individuals or groups. Although on average East group individuals consumed more than double the amount of meat than North group individuals, their δ15N values were significantly lower, suggesting that differences in microhabitat are substantial between group territories. The effect of sex/female reproductive state was significant in δ15N and δ13C, suggesting it related to access to food or feeding preferences. We conclude that several factors additional to diet are influencing and thus obscuring the isotope ratios in wild chimpanzee hair, particularly when comparing between sexes and social groups.
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Affiliation(s)
- Vicky M Oelze
- Anthropology Department, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA; Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, 04103, Germany.
| | - Roman M Wittig
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, 04103, Germany; Taï Chimpanzee Project, CSRS, Abidjan, Ivory Coast
| | - Sylvain Lemoine
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, 04103, Germany; Taï Chimpanzee Project, CSRS, Abidjan, Ivory Coast
| | - Hjalmar S Kühl
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, 04103, Germany
| | - Christophe Boesch
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, 04103, Germany
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130
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Redford KE, Abbott GW. The ubiquitous flavonoid quercetin is an atypical KCNQ potassium channel activator. Commun Biol 2020; 3:356. [PMID: 32641720 PMCID: PMC7343821 DOI: 10.1038/s42003-020-1089-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 06/18/2020] [Indexed: 12/11/2022] Open
Abstract
Many commonly consumed plants are used as folk medicines, often with unclear molecular mechanisms. Recent studies uncovered the ubiquitous and influential KCNQ family of voltage-gated potassium (Kv) channels as a therapeutic target for several medicinal plant compounds. Capers - immature flower buds of Capparis spinosa - have been consumed for food and medicinal purposes for millennia. Here, we show that caper extract hyperpolarizes cells expressing KCNQ1 or KCNQ2/3 Kv channels. Capers are the richest known natural source of quercetin, the most consumed dietary flavonoid. Quercetin potentiated KCNQ1/KCNE1, KCNQ2/3 and KCNQ4 currents but, unusually, not KCNQ5. Strikingly, quercetin augmented both activation and inactivation of KCNQ1, via a unique KCNQ activation mechanism involving sites atop the voltage sensor and in the pore. The findings uncover a novel potential molecular basis for therapeutic effects of quercetin-rich foods and a new chemical space for atypical modes of KCNQ channel modulation. Kaitlyn E. Redford and Geoffrey W. Abbott show that quercetin, a flavonoid highly expressed in capers, potentiates KCNQ currents to varying degrees depending on the subunit composition of the channel complex. By combining in silico docking, mutagenesis, and electrophysiology they show that this flavonoid can bind KCNQ channels atop the voltage sensor and within the pore module, highlighting an atypical mode of channel modulation.
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Affiliation(s)
- Kaitlyn E Redford
- Bioelectricity Laboratory, Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, USA
| | - Geoffrey W Abbott
- Bioelectricity Laboratory, Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, USA.
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131
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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.
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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
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132
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Weiß CL, Gansauge MT, Aximu-Petri A, Meyer M, Burbano HA. Mining ancient microbiomes using selective enrichment of damaged DNA molecules. BMC Genomics 2020; 21:432. [PMID: 32586278 PMCID: PMC7318760 DOI: 10.1186/s12864-020-06820-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 06/11/2020] [Indexed: 12/17/2022] Open
Abstract
Background The identification of bona fide microbial taxa in microbiomes derived from ancient and historical samples is complicated by the unavoidable mixture between DNA from ante- and post-mortem microbial colonizers. One possibility to distinguish between these sources of microbial DNA is querying for the presence of age-associated degradation patterns typical of ancient DNA (aDNA). The presence of uracils, resulting from cytosine deamination, has been detected ubiquitously in aDNA retrieved from diverse sources, and used as an authentication criterion. Here, we employ a library preparation method that separates molecules that carry uracils from those that do not for a set of samples that includes Neandertal remains, herbarium specimens and archaeological plant remains. Results We show that sequencing DNA libraries enriched in molecules carrying uracils effectively amplifies age associated degradation patterns in microbial mixtures of ancient and historical origin. This facilitates the discovery of authentic ancient microbial taxa in cases where degradation patterns are difficult to detect due to large sequence divergence in microbial mixtures. Additionally, the relative enrichment of taxa in the uracil enriched fraction can help to identify bona fide ancient microbial taxa that could be missed using a more targeted approach. Conclusions Our experiments show, that in addition to its use in enriching authentic endogenous DNA of organisms of interest, the selective enrichment of damaged DNA molecules can be a valuable tool in the discovery of ancient microbial taxa.
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Affiliation(s)
- Clemens L Weiß
- Department of Molecular Biology, Research Group for Ancient Genomics and Evolution, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany.,Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Marie-Theres Gansauge
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Ayinuer Aximu-Petri
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Hernán A Burbano
- Department of Molecular Biology, Research Group for Ancient Genomics and Evolution, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany. .,Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK.
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133
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Arriola LA, Cooper A, Weyrich LS. Palaeomicrobiology: Application of Ancient DNA Sequencing to Better Understand Bacterial Genome Evolution and Adaptation. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00040] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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134
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Giffin K, Lankapalli AK, Sabin S, Spyrou MA, Posth C, Kozakaitė J, Friedrich R, Miliauskienė Ž, Jankauskas R, Herbig A, Bos KI. A treponemal genome from an historic plague victim supports a recent emergence of yaws and its presence in 15 th century Europe. Sci Rep 2020; 10:9499. [PMID: 32528126 PMCID: PMC7290034 DOI: 10.1038/s41598-020-66012-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 03/30/2020] [Indexed: 12/30/2022] Open
Abstract
Developments in techniques for identification of pathogen DNA in archaeological samples can expand our resolution of disease detection. Our application of a non-targeted molecular screening tool for the parallel detection of pathogens in historical plague victims from post-medieval Lithuania revealed the presence of more than one active disease in one individual. In addition to Yersinia pestis, we detected and genomically characterized a septic infection of Treponema pallidum pertenue, a subtype of the treponemal disease family recognised as the cause of the tropical disease yaws. Our finding in northern Europe of a disease that is currently restricted to equatorial regions is interpreted within an historical framework of intercontinental trade and potential disease movements. Through this we offer an alternative hypothesis for the history and evolution of the treponemal diseases, and posit that yaws be considered an important contributor to the sudden epidemic of late 15th century Europe that is widely ascribed to syphilis.
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Affiliation(s)
- Karen Giffin
- Max Planck Institute for the Science of Human History, Jena, Germany
| | | | - Susanna Sabin
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Maria A Spyrou
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Cosimo Posth
- Max Planck Institute for the Science of Human History, Jena, Germany.,Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Rümelinstraße 23, 72070, Tübingen, Germany
| | | | | | | | | | - Alexander Herbig
- Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Kirsten I Bos
- Max Planck Institute for the Science of Human History, Jena, Germany.
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135
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Fitak RR, Antonides JD, Baitchman EJ, Bonaccorso E, Braun J, Kubiski S, Chiu E, Fagre AC, Gagne RB, Lee JS, Malmberg JL, Stenglein MD, Dusek RJ, Forgacs D, Fountain-Jones NM, Gilbertson MLJ, Worsley-Tonks KEL, Funk WC, Trumbo DR, Ghersi BM, Grimaldi W, Heisel SE, Jardine CM, Kamath PL, Karmacharya D, Kozakiewicz CP, Kraberger S, Loisel DA, McDonald C, Miller S, O'Rourke D, Ott-Conn CN, Páez-Vacas M, Peel AJ, Turner WC, VanAcker MC, VandeWoude S, Pecon-Slattery J. The Expectations and Challenges of Wildlife Disease Research in the Era of Genomics: Forecasting with a Horizon Scan-like Exercise. J Hered 2020; 110:261-274. [PMID: 31067326 DOI: 10.1093/jhered/esz001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 01/08/2019] [Indexed: 12/14/2022] Open
Abstract
The outbreak and transmission of disease-causing pathogens are contributing to the unprecedented rate of biodiversity decline. Recent advances in genomics have coalesced into powerful tools to monitor, detect, and reconstruct the role of pathogens impacting wildlife populations. Wildlife researchers are thus uniquely positioned to merge ecological and evolutionary studies with genomic technologies to exploit unprecedented "Big Data" tools in disease research; however, many researchers lack the training and expertise required to use these computationally intensive methodologies. To address this disparity, the inaugural "Genomics of Disease in Wildlife" workshop assembled early to mid-career professionals with expertise across scientific disciplines (e.g., genomics, wildlife biology, veterinary sciences, and conservation management) for training in the application of genomic tools to wildlife disease research. A horizon scanning-like exercise, an activity to identify forthcoming trends and challenges, performed by the workshop participants identified and discussed 5 themes considered to be the most pressing to the application of genomics in wildlife disease research: 1) "Improving communication," 2) "Methodological and analytical advancements," 3) "Translation into practice," 4) "Integrating landscape ecology and genomics," and 5) "Emerging new questions." Wide-ranging solutions from the horizon scan were international in scope, itemized both deficiencies and strengths in wildlife genomic initiatives, promoted the use of genomic technologies to unite wildlife and human disease research, and advocated best practices for optimal use of genomic tools in wildlife disease projects. The results offer a glimpse of the potential revolution in human and wildlife disease research possible through multi-disciplinary collaborations at local, regional, and global scales.
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Affiliation(s)
| | - Jennifer D Antonides
- Department of Forestry & Natural Resources, Purdue University, West Lafayette, IN
| | - Eric J Baitchman
- The Zoo New England Division of Animal Health and Conservation, Boston, MA
| | - Elisa Bonaccorso
- The Instituto BIOSFERA and Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, vía Interoceánica y Diego de Robles, Quito, Ecuador
| | - Josephine Braun
- The Institute for Conservation Research, San Diego Zoo Global, Escondido, CA
| | - Steven Kubiski
- The Institute for Conservation Research, San Diego Zoo Global, Escondido, CA
| | - Elliott Chiu
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO
| | - Anna C Fagre
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO
| | - Roderick B Gagne
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO
| | - Justin S Lee
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO
| | - Jennifer L Malmberg
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO
| | - Mark D Stenglein
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO
| | - Robert J Dusek
- The U. S. Geological Survey, National Wildlife Health Center, Madison, WI
| | - David Forgacs
- The Interdisciplinary Graduate Program of Genetics, Texas A&M University, College Station, TX
| | | | - Marie L J Gilbertson
- The Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN
| | | | - W Chris Funk
- The Department of Biology, Colorado State University, Fort Collins, CO
| | - Daryl R Trumbo
- The Department of Biology, Colorado State University, Fort Collins, CO
| | | | | | - Sara E Heisel
- The Odum School of Ecology, University of Georgia, Athens, GA
| | - Claire M Jardine
- The Department of Pathobiology, Canadian Wildlife Health Cooperative, University of Guelph, Guelph, Ontario, Canada
| | - Pauline L Kamath
- The School of Food and Agriculture, University of Maine, Orono, ME
| | | | | | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ
| | - Dagan A Loisel
- The Department of Biology, Saint Michael's College, Colchester, VT
| | - Cait McDonald
- The Department of Ecology & Evolutionary Biology, Cornell University, Ithaca, NY (McDonald)
| | - Steven Miller
- The Department of Biology, Drexel University, Philadelphia, PA
| | | | - Caitlin N Ott-Conn
- The Michigan Department of Natural Resources, Wildlife Disease Laboratory, Lansing, MI
| | - Mónica Páez-Vacas
- The Centro de Investigación de la Biodiversidad y Cambio Climático (BioCamb), Facultad de Ciencias de Medio Ambiente, Universidad Tecnológica Indoamérica, Machala y Sabanilla, Quito, Ecuador
| | - Alison J Peel
- The Environmental Futures Research Institute, Griffith University, Nathan, Queensland, Australia
| | - Wendy C Turner
- The Department of Biological Sciences, University at Albany, State University of New York, Albany, NY
| | - Meredith C VanAcker
- The Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY
| | - Sue VandeWoude
- The College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO
| | - Jill Pecon-Slattery
- The Center for Species Survival, Smithsonian Conservation Biology Institute-National Zoological Park, Front Royal, VA
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136
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Armbrecht L, Herrando-Pérez S, Eisenhofer R, Hallegraeff GM, Bolch CJS, Cooper A. An optimized method for the extraction of ancient eukaryote DNA from marine sediments. Mol Ecol Resour 2020; 20:906-919. [PMID: 32277584 DOI: 10.1111/1755-0998.13162] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 03/17/2020] [Accepted: 03/26/2020] [Indexed: 12/19/2022]
Abstract
Marine sedimentary ancient DNA (sedaDNA) provides a powerful means to reconstruct marine palaeo-communities across the food web. However, currently there are few optimized sedaDNA extraction protocols available to maximize the yield of small DNA fragments typical of ancient DNA (aDNA) across a broad diversity of eukaryotes. We compared seven combinations of sedaDNA extraction treatments and sequencing library preparations using marine sediments collected at a water depth of 104 m off Maria Island, Tasmania, in 2018. These seven methods contrasted frozen versus refrigerated sediment, bead-beating induced cell lysis versus ethylenediaminetetraacetic acid (EDTA) incubation, DNA binding in silica spin columns versus in silica-solution, diluted versus undiluted DNA in shotgun library preparations to test potential inhibition issues during amplification steps, and size-selection of low molecular-weight (LMW) DNA to increase the extraction efficiency of sedaDNA. Maximum efficiency was obtained from frozen sediments subjected to a combination of EDTA incubation and bead-beating, DNA binding in silica-solution, and undiluted DNA in shotgun libraries, across 45 marine eukaryotic taxa. We present an optimized extraction protocol integrating these steps, with an optional post-library LMW size-selection step to retain DNA fragments of ≤500 base pairs. We also describe a stringent bioinformatic filtering approach for metagenomic data and provide a comprehensive list of contaminants as a reference for future sedaDNA studies. The new extraction and data-processing protocol should improve quantitative paleo-monitoring of eukaryotes from marine sediments, as well as other studies relying on the detection of highly fragmented and degraded eukaryote DNA in sediments.
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Affiliation(s)
- Linda Armbrecht
- School of Biological Sciences, Faculty of Sciences, Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, SA, Australia
| | - Salvador Herrando-Pérez
- School of Biological Sciences, Faculty of Sciences, Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, SA, Australia
| | - Raphael Eisenhofer
- School of Biological Sciences, Faculty of Sciences, Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, SA, Australia
| | - Gustaaf M Hallegraeff
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tas., Australia
| | - Christopher J S Bolch
- Institute for Marine and Antarctic Studies, University of Tasmania, Launceston, Tas., Australia
| | - Alan Cooper
- South Australian Museum, Adelaide, SA, Australia
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137
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Abstract
The cultivation of yeasts from up to 5000‐year‐old beer vessels in Israel allows insights into early domestication of microbes for food production, but also raises questions about long‐term survival of microbes under dormancy or slow growth.
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138
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Wadley L, Backwell L, d'Errico F, Sievers C. Cooked starchy rhizomes in Africa 170 thousand years ago. Science 2020; 367:87-91. [PMID: 31896717 DOI: 10.1126/science.aaz5926] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 11/05/2019] [Indexed: 01/20/2023]
Abstract
Plant carbohydrates were undoubtedly consumed in antiquity, yet starchy geophytes were seldom preserved archaeologically. We report evidence for geophyte exploitation by early humans from at least 170,000 years ago. Charred rhizomes from Border Cave, South Africa, were identified to the genus Hypoxis L. by comparing the morphology and anatomy of ancient and modern rhizomes. Hypoxis angustifolia Lam., the likely taxon, proliferates in relatively well-watered areas of sub-Saharan Africa and in Yemen, Arabia. In those areas and possibly farther north during moist periods, Hypoxis rhizomes would have provided reliable and familiar carbohydrate sources for mobile groups.
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Affiliation(s)
- Lyn Wadley
- Evolutionary Studies Institute, University of the Witwatersrand, Johannesburg, South Africa.
| | - Lucinda Backwell
- Evolutionary Studies Institute, University of the Witwatersrand, Johannesburg, South Africa.,Instituto Superior de Estudios Sociales, ISES-CONICET, Tucumán, Argentina
| | - Francesco d'Errico
- Centre National de la Recherche Scientifique, UMR 5199-PACEA, Université de Bordeaux, Bâtiment B2, Allée Geoffroy Saint Hilaire, CS 50023, 33615 Pessac, France.,SFF Centre for Early Sapiens Behaviour (SapienCE), University of Bergen, Øysteinsgate 3, Postboks 7805, 5020 Bergen, Norway
| | - Christine Sievers
- School of Geography, Archaeology and Environmental Studies, University of the Witwatersrand, Johannesburg, South Africa
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139
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Cribdon B, Ware R, Smith O, Gaffney V, Allaby RG. PIA: More Accurate Taxonomic Assignment of Metagenomic Data Demonstrated on sedaDNA From the North Sea. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00084] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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140
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Molecular Mechanism of Functional Ingredients in Barley to Combat Human Chronic Diseases. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:3836172. [PMID: 32318238 PMCID: PMC7149453 DOI: 10.1155/2020/3836172] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 03/10/2020] [Indexed: 12/18/2022]
Abstract
Barley plays an important role in health and civilization of human migration from Africa to Asia, later to Eurasia. We demonstrated the systematic mechanism of functional ingredients in barley to combat chronic diseases, based on PubMed, CNKI, and ISI Web of Science databases from 2004 to 2020. Barley and its extracts are rich in 30 ingredients to combat more than 20 chronic diseases, which include the 14 similar and 9 different chronic diseases between grains and grass, due to the major molecular mechanism of six functional ingredients of barley grass (GABA, flavonoids, SOD, K-Ca, vitamins, and tryptophan) and grains (β-glucans, polyphenols, arabinoxylan, phytosterols, tocols, and resistant starch). The antioxidant activity of barley grass and grain has the same and different functional components. These results support findings that barley grain and its grass are the best functional food, promoting ancient Babylonian and Egyptian civilizations, and further show the depending functional ingredients for diet from Pliocene hominids in Africa and Neanderthals in Europe to modern humans in the world. This review paper not only reveals the formation and action mechanism of barley diet overcoming human chronic diseases, but also provides scientific basis for the development of health products and drugs for the prevention and treatment of human chronic diseases.
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141
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Abstract
The Archaea domain was recognized as a separate phylogenetic lineage in the tree of life nearly 3 decades ago. It is now known as part of the human microbiome; however, given that its roles in oral sites are still poorly understood, this review aimed to establish the current level of evidence regarding archaea in the oral cavity to guide future research, providing insights on the present knowledge about the human oral archaeome. A scoping review was conducted with the PRISMA Extension for Scoping Reviews checklist. Five electronic databases were searched, as well as gray literature. Two independent reviewers performed the selection and characterization of the studies. Clinical studies were included when the target population consisted of humans of any age who were donors of samples from the oral cavity. A qualitative analysis was performed, based on the type of oral site and by considering the methods employed for archaeal identification and taxonomy, including the DNA extraction protocols, primers, and probes used. Fifty articles were included in the final scoping review, published from 1987 to 2019. Most studies sampled periodontal sites. Methanogens were the most abundant archaea in those sites, and their presence could be associated with other periodontal pathogens. No consistent relationship with different disease conditions was observed in studies that evaluated the microbiota surviving in endodontic sites. Few articles analyzed the presence of archaea in dental caries, saliva, or tongue microbiota, as well as in archaeologic samples, also showing a relationship with healthy microbiota. Archaea have been detected in different oral niches of individuals from diverse geographic locations and clinical conditions, suggesting potential roles in oral diseases. Methodological limitations may hamper our current knowledge about archaeal diversity and prevalence in oral samples, and future research with diversified methodological approaches may lead to a better comprehension of the human oral archaeome.
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Affiliation(s)
- A Belmok
- Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, Brazil
| | - J A de Cena
- Department of Dentistry, Faculty of Heath Sciences, University of Brasília, Brasília, Brazil
| | - C M Kyaw
- Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, Brazil
| | - N Damé-Teixeira
- Department of Dentistry, Faculty of Heath Sciences, University of Brasília, Brasília, Brazil
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142
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Ancient DNA analysis of food remains in human dental calculus from the Edo period, Japan. PLoS One 2020; 15:e0226654. [PMID: 32130218 PMCID: PMC7055813 DOI: 10.1371/journal.pone.0226654] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 12/01/2019] [Indexed: 11/21/2022] Open
Abstract
Although there are many methods for reconstructing diets of the past, detailed taxon identification is still challenging, and most plants hardly remain at a site. In this study, we applied DNA metabarcoding to dental calculus of premodern Japan for the taxonomic identification of food items. DNA was extracted from 13 human dental calculi from the Unko-in site (18th–19th century) of the Edo period, Japan. Polymerase chain reaction (PCR) and sequencing were performed using a primer set specific to the genus Oryza because rice (Oryza sativa) was a staple food and this was the only member of this genus present in Japan at that time. DNA metabarcoding targeting plants, animals (meat and fish), and fungi were also carried out to investigate dietary diversity. We detected amplified products of the genus Oryza from more than half of the samples using PCR and Sanger sequencing. DNA metabarcoding enabled us to identify taxa of plants and fungi, although taxa of animals were not detected, except human. Most of the plant taxonomic groups (family/genus level) are present in Japan and include candidate species consumed as food at that time, as confirmed by historical literature. The other groups featured in the lifestyle of Edo people, such as for medicinal purposes and tobacco. The results indicate that plant DNA analysis from calculus provides information about food diversity and lifestyle habits from the past and can complement other analytical methods such as microparticle analysis and stable isotope analysis.
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143
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Emery MV, Bolhofner K, Winingear S, Oldt R, Montes M, Kanthaswamy S, Buikstra JE, Fulginiti LC, Stone AC. Reconstructing full and partial STR profiles from severely burned human remains using comparative ancient and forensic DNA extraction techniques. Forensic Sci Int Genet 2020; 46:102272. [PMID: 32172220 DOI: 10.1016/j.fsigen.2020.102272] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 02/28/2020] [Accepted: 02/29/2020] [Indexed: 12/19/2022]
Abstract
Thermal degeneration of the DNA molecule presents a special challenge to medico-legal investigations since low DNA yields, fragmented DNA molecules, and damaged nucleotide bases hinder accurate STR genotyping. As a consequence, fragments of severely burned human remains are often not amenable to standard DNA recovery. However, current ancient DNA (aDNA) extraction methods have proven highly effective at obtaining ultrashort DNA fragments (∼50 bp) from degraded palaeontological and archaeological specimens. In this study, we compare DNA yields and STR results obtained from two established aDNA and forensic DNA extraction protocols by sampling multiple skeletal elements recovered from victims (n = 23) involved in fire-related incidents. DNA yields and STR results suggest an inverse correlation between DNA yield and STR quality and increasing temperature. Despite the rapid thermal destruction of DNA at high temperatures, we generated higher quality full and partial STR profiles using the aDNA extraction protocol across all burn categories than the forensic total bone demineralization extraction method. Our analysis suggests adopting aDNA extraction methods as an alternative to current forensic practices to improve DNA yields from challenging human remains.
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Affiliation(s)
- M V Emery
- School of Human Evolution and Social Change, Arizona State University, United States; Center for Evolution and Medicine, Arizona State University, United States.
| | - K Bolhofner
- Center for Bioarchaeological Research, Arizona State University, United States; Maricopa County Office of the Medical Examiner, Phoenix, AZ, United States; School of Mathematical and Natural Sciences, Arizona State University, United States
| | - S Winingear
- School of Human Evolution and Social Change, Arizona State University, United States; Center for Evolution and Medicine, Arizona State University, United States
| | - R Oldt
- School of Life Sciences, Arizona State University, United States
| | - M Montes
- School of Mathematical and Natural Sciences, Arizona State University, United States
| | - S Kanthaswamy
- School of Life Sciences, Arizona State University, United States; School of Mathematical and Natural Sciences, Arizona State University, United States
| | - J E Buikstra
- School of Human Evolution and Social Change, Arizona State University, United States; Center for Evolution and Medicine, Arizona State University, United States; Center for Bioarchaeological Research, Arizona State University, United States
| | - L C Fulginiti
- School of Human Evolution and Social Change, Arizona State University, United States; Maricopa County Office of the Medical Examiner, Phoenix, AZ, United States
| | - A C Stone
- School of Human Evolution and Social Change, Arizona State University, United States; Center for Evolution and Medicine, Arizona State University, United States; Center for Bioarchaeological Research, Arizona State University, United States.
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144
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Albuquerque UP, do Nascimento ALB, Silva Chaves L, Feitosa IS, de Moura JMB, Gonçalves PHS, da Silva RH, da Silva TC, Ferreira Júnior WS. The chemical ecology approach to modern and early human use of medicinal plants. CHEMOECOLOGY 2020. [DOI: 10.1007/s00049-020-00302-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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145
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Kim SW, Goossens A, Libert C, Van Immerseel F, Staal J, Beyaert R. Phytohormones: Multifunctional nutraceuticals against metabolic syndrome and comorbid diseases. Biochem Pharmacol 2020; 175:113866. [PMID: 32088261 DOI: 10.1016/j.bcp.2020.113866] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 02/18/2020] [Indexed: 12/12/2022]
Abstract
Metabolic syndrome is characterized by the co-occurrence of diverse symptoms initiating the development of type 2 diabetes, cardiovascular diseases, and a variety of comorbid diseases. The complex constellation of numerous comorbidities makes it difficult to develop common therapeutic approaches that ameliorate these pathological features simultaneously. The plant hormones abscisic acid, salicylic acid, auxin, and cytokinins, have shown promising anti-inflammatory and pro-metabolic effects that could mitigate several disorders relevant to metabolic syndrome. Intriguingly, besides plants, human cells and gut microbes also endogenously produce these molecules, indicating a role in the complex interplay between inflammatory responses associated with metabolic syndrome, the gut microbiome, and nutrition. Here, we introduce how bioactive phytohormones can be generated endogenously and through the gut microbiome. These molecules subsequently influence immune responses and metabolism. We also elaborate on how phytohormones can beneficially modulate metabolic syndrome comorbidities, and propose them as nutraceuticals.
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Affiliation(s)
- Seo Woo Kim
- VIB-UGent Center for Inflammation Research, VIB, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; VIB-UGent Center for Plant Systems Biology, VIB, Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Alain Goossens
- VIB-UGent Center for Plant Systems Biology, VIB, Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Claude Libert
- VIB-UGent Center for Inflammation Research, VIB, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Filip Van Immerseel
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Jens Staal
- VIB-UGent Center for Inflammation Research, VIB, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
| | - Rudi Beyaert
- VIB-UGent Center for Inflammation Research, VIB, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
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146
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Dunn RR, Amato KR, Archie EA, Arandjelovic M, Crittenden AN, Nichols LM. The Internal, External and Extended Microbiomes of Hominins. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00025] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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147
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Liu Y, Weyrich LS, Llamas B. More Arrows in the Ancient DNA Quiver: Use of Paleoepigenomes and Paleomicrobiomes to Investigate Animal Adaptation to Environment. Mol Biol Evol 2020; 37:307-319. [PMID: 31638147 DOI: 10.1093/molbev/msz231] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Whether and how epigenetic mechanisms and the microbiome play a role in mammalian adaptation raised considerable attention and controversy, mainly because they have the potential to add new insights into the Modern Synthesis. Recent attempts to reconcile neo-Darwinism and neo-Lamarckism in a unified theory of molecular evolution give epigenetic mechanisms and microbiome a prominent role. However, supporting empirical data are still largely missing. Because experimental studies using extant animals can hardly be done over evolutionary timescales, we propose that advances in ancient DNA techniques provide a valid alternative. In this piece, we evaluate 1) the possible roles of epigenomes and microbiomes in animal adaptation, 2) advances in the retrieval of paleoepigenome and paleomicrobiome data using ancient DNA techniques, and 3) the plasticity of either and interactions between the epigenome and the microbiome, while emphasizing that it is essential to take both into account, as well as the underlying genetic factors that may confound the findings. We propose that advanced ancient DNA techniques should be applied to a wide range of past animals, so novel dynamics in animal evolution and adaption can be revealed.
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Affiliation(s)
- Yichen Liu
- Australian Centre for Ancient DNA, School of Biological Sciences, Environment Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Laura S Weyrich
- Australian Centre for Ancient DNA, School of Biological Sciences, Environment Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences, Environment Institute, University of Adelaide, Adelaide, South Australia, Australia
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Host-adapted lactobacilli in food fermentations: impact of metabolic traits of host adapted lactobacilli on food quality and human health. Curr Opin Food Sci 2020. [DOI: 10.1016/j.cofs.2020.02.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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149
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Gismondi A, Baldoni M, Gnes M, Scorrano G, D’Agostino A, Di Marco G, Calabria G, Petrucci M, Müldner G, Von Tersch M, Nardi A, Enei F, Canini A, Rickards O, Alexander M, Martínez-Labarga C. A multidisciplinary approach for investigating dietary and medicinal habits of the Medieval population of Santa Severa (7th-15th centuries, Rome, Italy). PLoS One 2020; 15:e0227433. [PMID: 31990948 PMCID: PMC6986732 DOI: 10.1371/journal.pone.0227433] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 12/18/2019] [Indexed: 12/31/2022] Open
Abstract
A multidisciplinary approach, combining stable isotope analysis from bone proteins and investigations on dental calculus using DNA analysis, light microscopy, and gas chromatography coupled with mass spectrometry, was applied to reconstruct dietary and medicinal habits of the individuals recovered in the cemetery of the Castle of Santa Severa (7th-15th centuries CE; Rome, Italy). Stable isotope analysis was performed on 120 humans, 41 faunal specimens and 8 charred seeds. Dental calculus analyses were carried out on 94 samples. Overall, isotope data indicated an omnivorous diet based on C3-terrestrial protein, although some individuals possessed carbon values indicative of C4 plant consumption. In terms of animal protein, the diet was probably based on cattle, sheep, pig and chicken products, as witnessed by the archaeozoological findings. Evidence from calculus suggested the consumption of C3 cereals, Fabaceae, Fagaceae, milk and dairy products. Secondary metabolites of herbs and wine were also detected. The detection of marine fish ancient DNA, as well as of ω3 fatty acids in calculus, hypothesized the consumption of marine foodstuffs for this coastal population, despite the lack of a clear marine isotopic signal and the presence of polyunsaturated fatty acids in plant tissues. Moreover, the knowledge of ethnopharmacological tradition and the application of medicinal plants (e.g. Punica granatum L., Ephedra sp. L.) were also identified. The detection of artemisinin, known to have antimalarial properties, led to hypothesize the presence of malaria in the area. Altogether, the combined application of microscopy and biomolecular techniques provided an innovative reconstruction of Medieval lifeways in Central Italy.
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Affiliation(s)
- Angelo Gismondi
- Laboratory of Botany, Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Marica Baldoni
- Centro di Antropologia Molecolare per lo Studio del DNA Antico, Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Micaela Gnes
- Centro di Antropologia Molecolare per lo Studio del DNA Antico, Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Gabriele Scorrano
- Centro di Antropologia Molecolare per lo Studio del DNA Antico, Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Alessia D’Agostino
- Laboratory of Botany, Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Gabriele Di Marco
- Laboratory of Botany, Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Giulietta Calabria
- Centro di Antropologia Molecolare per lo Studio del DNA Antico, Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Michela Petrucci
- Centro di Antropologia Molecolare per lo Studio del DNA Antico, Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Gundula Müldner
- Department of Archaeology, University of Reading, Reading, England, United Kingdom
| | - Matthew Von Tersch
- Department of Archaeology, BioArCh, University of York, York, England, United Kingdom
| | - Alessandra Nardi
- Department of Mathematics, University of Rome “Tor Vergata”, Rome, Italy
| | - Flavio Enei
- Museo Civico di Santa Marinella “Museo del Mare e della Navigazione Antica”, Castello di Santa Severa (Roma–Italia)
| | - Antonella Canini
- Laboratory of Botany, Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Olga Rickards
- Centro di Antropologia Molecolare per lo Studio del DNA Antico, Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Michelle Alexander
- Department of Archaeology, BioArCh, University of York, York, England, United Kingdom
| | - Cristina Martínez-Labarga
- Centro di Antropologia Molecolare per lo Studio del DNA Antico, Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
- * E-mail:
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150
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Ottoni C, Guellil M, Ozga AT, Stone AC, Kersten O, Bramanti B, Porcier S, Van Neer W. Metagenomic analysis of dental calculus in ancient Egyptian baboons. Sci Rep 2019; 9:19637. [PMID: 31873124 PMCID: PMC6927955 DOI: 10.1038/s41598-019-56074-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 12/06/2019] [Indexed: 02/07/2023] Open
Abstract
Dental calculus, or mineralized plaque, represents a record of ancient biomolecules and food residues. Recently, ancient metagenomics made it possible to unlock the wealth of microbial and dietary information of dental calculus to reconstruct oral microbiomes and lifestyle of humans from the past. Although most studies have so far focused on ancient humans, dental calculus is known to form in a wide range of animals, potentially informing on how human-animal interactions changed the animals' oral ecology. Here, we characterise the oral microbiome of six ancient Egyptian baboons held in captivity during the late Pharaonic era (9th-6th centuries BC) and of two historical baboons from a zoo via shotgun metagenomics. We demonstrate that these captive baboons possessed a distinctive oral microbiome when compared to ancient and modern humans, Neanderthals and a wild chimpanzee. These results may reflect the omnivorous dietary behaviour of baboons, even though health, food provisioning and other factors associated with human management, may have changed the baboons' oral microbiome. We anticipate our study to be a starting point for more extensive studies on ancient animal oral microbiomes to examine the extent to which domestication and human management in the past affected the diet, health and lifestyle of target animals.
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Affiliation(s)
- Claudio Ottoni
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, N-0316, Oslo, Norway.
- Department of Oral and Maxillofacial Sciences, Diet and Ancient Technology Laboratory (DANTE), Sapienza University, Rome, Italy.
| | - Meriam Guellil
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, N-0316, Oslo, Norway
- University of Tartu, Institute of Genomics, Estonian Biocentre, 51010, Tartu, Estonia
| | - Andrew T Ozga
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, FL, USA
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
- Institute of Human Origins, Arizona State University, Tempe, AZ, USA
| | - Oliver Kersten
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, N-0316, Oslo, Norway
| | - Barbara Bramanti
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, N-0316, Oslo, Norway
- Department of Biomedical and Specialty Surgical Sciences, Faculty of Medicine, Pharmacy, and Prevention, University of Ferrara, 35-441221, Ferrara, Italy
| | - Stéphanie Porcier
- Laboratoire CNRS ASM ≪ Archéologie des Sociétés Méditerranéennes (UMR 5140), Université Paul-Valéry, LabEx Archimede, F-34199, Montpellier, France
| | - Wim Van Neer
- Royal Belgian Institute of Natural Sciences, B-1000, Brussels, Belgium.
- KU Leuven-University of Leuven, Department of Biology, Laboratory of Biodiversity and Evolutionary Genomics, Center of Archaeological Sciences, B-3000, Leuven, Belgium.
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