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Dahlquist-Axe G, Standeven FJ, Speller CF, Tedder A, Meehan CJ. Inferring diet, disease and antibiotic resistance from ancient human oral microbiomes. Microb Genom 2024; 10:001251. [PMID: 38739117 PMCID: PMC11165619 DOI: 10.1099/mgen.0.001251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 04/24/2024] [Indexed: 05/14/2024] Open
Abstract
The interaction between a host and its microbiome is an area of intense study. For the human host, it is known that the various body-site-associated microbiomes impact heavily on health and disease states. For instance, the oral microbiome is a source of various pathogens and potential antibiotic resistance gene pools. The effect of historical changes to the human host and environment to the associated microbiome, however, has been less well explored. In this review, we characterize several historical and prehistoric events which are considered to have impacted the oral environment and therefore the bacterial communities residing within it. The link between evolutionary changes to the oral microbiota and the significant societal and behavioural changes occurring during the pre-Neolithic, Agricultural Revolution, Industrial Revolution and Antibiotic Era is outlined. While previous studies suggest the functional profile of these communities may have shifted over the centuries, there is currently a gap in knowledge that needs to be filled. Biomolecular archaeological evidence of innate antimicrobial resistance within the oral microbiome shows an increase in the abundance of antimicrobial resistance genes since the advent and widespread use of antibiotics in the modern era. Nevertheless, a lack of research into the prevalence and evolution of antimicrobial resistance within the oral microbiome throughout history hinders our ability to combat antimicrobial resistance in the modern era.
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Affiliation(s)
- Gwyn Dahlquist-Axe
- School of Chemistry and Biosciences, University of Bradford, Bradford, UK
| | | | - Camilla F. Speller
- Department of Anthropology, University of British Columbia, Vancouver, Canada
| | - Andrew Tedder
- School of Chemistry and Biosciences, University of Bradford, Bradford, UK
| | - Conor J. Meehan
- Department of Biosciences, Nottingham Trent University, Nottingham, UK
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Eisenhofer R, Wright S, Weyrich L. Benchmarking a targeted 16S ribosomal RNA gene enrichment approach to reconstruct ancient microbial communities. PeerJ 2024; 12:e16770. [PMID: 38440408 PMCID: PMC10911074 DOI: 10.7717/peerj.16770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/16/2023] [Indexed: 03/06/2024] Open
Abstract
The taxonomic characterization of ancient microbiomes is a key step in the rapidly growing field of paleomicrobiology. While PCR amplification of the 16S ribosomal RNA (rRNA) gene is a widely used technique in modern microbiota studies, this method has systematic biases when applied to ancient microbial DNA. Shotgun metagenomic sequencing has proven to be the most effective method in reconstructing taxonomic profiles of ancient dental calculus samples. Nevertheless, shotgun sequencing approaches come with inherent limitations that could be addressed through hybridization enrichment capture. When employed together, shotgun sequencing and hybridization capture have the potential to enhance the characterization of ancient microbial communities. Here, we develop, test, and apply a hybridization enrichment capture technique to selectively target 16S rRNA gene fragments from the libraries of ancient dental calculus samples generated with shotgun techniques. We simulated data sets generated from hybridization enrichment capture, indicating that taxonomic identification of fragmented and damaged 16S rRNA gene sequences was feasible. Applying this enrichment approach to 15 previously published ancient calculus samples, we observed a 334-fold increase of ancient 16S rRNA gene fragments in the enriched samples when compared to unenriched libraries. Our results suggest that 16S hybridization capture is less prone to the effects of background contamination than 16S rRNA amplification, yielding a higher percentage of on-target recovery. While our enrichment technique detected low abundant and rare taxa within a given sample, these assignments may not achieve the same level of specificity as those achieved by unenriched methods.
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Affiliation(s)
| | - Sterling Wright
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania, United States
| | - Laura Weyrich
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania, United States
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, United States
- School of Biological Sciences, University of Adelaide, Adelaide, Australia
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Duitama González C, Vicedomini R, Lemane T, Rascovan N, Richard H, Chikhi R. decOM: similarity-based microbial source tracking of ancient oral samples using k-mer-based methods. MICROBIOME 2023; 11:243. [PMID: 37926832 PMCID: PMC10626679 DOI: 10.1186/s40168-023-01670-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 09/13/2023] [Indexed: 11/07/2023]
Abstract
BACKGROUND The analysis of ancient oral metagenomes from archaeological human and animal samples is largely confounded by contaminant DNA sequences from modern and environmental sources. Existing methods for Microbial Source Tracking (MST) estimate the proportions of environmental sources, but do not perform well on ancient metagenomes. We developed a novel method called decOM for Microbial Source Tracking and classification of ancient and modern metagenomic samples using k-mer matrices. RESULTS We analysed a collection of 360 ancient oral, modern oral, sediment/soil and skin metagenomes, using stratified five-fold cross-validation. decOM estimates the contributions of these source environments in ancient oral metagenomic samples with high accuracy, outperforming two state-of-the-art methods for source tracking, FEAST and mSourceTracker. CONCLUSIONS decOM is a high-accuracy microbial source tracking method, suitable for ancient oral metagenomic data sets. The decOM method is generic and could also be adapted for MST of other ancient and modern types of metagenomes. We anticipate that decOM will be a valuable tool for MST of ancient metagenomic studies. Video Abstract.
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Affiliation(s)
- Camila Duitama González
- Sequence Bioinformatics, Department of Computational Biology, Institut Pasteur, Université Paris Cité, Sorbonne Université, Paris, F-75015, France.
| | - Riccardo Vicedomini
- Sequence Bioinformatics, Department of Computational Biology, Institut Pasteur, Université Paris Cité, Sorbonne Université, Paris, F-75015, France
- Université de Rennes, Inria, CNRS, IRISA, Rennes, France
| | - Téo Lemane
- Université de Rennes, Inria, CNRS, IRISA, Rennes, France
| | - Nicolas Rascovan
- Institut Pasteur, Université de Paris Cité, CNRS UMR 2000, Microbial Paleogenomics Unit, Paris, F-75015, France
| | - Hugues Richard
- Bioinformatics unit (MF1), Robert Koch Institute, Nordufer, 20, 13353, Berlin, Germany
| | - Rayan Chikhi
- Sequence Bioinformatics, Department of Computational Biology, Institut Pasteur, Université Paris Cité, Sorbonne Université, Paris, F-75015, France
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Reynoso-García J, Santiago-Rodriguez TM, Narganes-Storde Y, Cano RJ, Toranzos GA. Edible flora in pre-Columbian Caribbean coprolites: Expected and unexpected data. PLoS One 2023; 18:e0292077. [PMID: 37819893 PMCID: PMC10566737 DOI: 10.1371/journal.pone.0292077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 09/12/2023] [Indexed: 10/13/2023] Open
Abstract
Coprolites, or mummified feces, are valuable sources of information on ancient cultures as they contain ancient DNA (aDNA). In this study, we analyzed ancient plant DNA isolated from coprolites belonging to two pre-Columbian cultures (Huecoid and Saladoid) from Vieques, Puerto Rico, using shotgun metagenomic sequencing to reconstruct diet and lifestyles. We also analyzed DNA sequences of putative phytopathogenic fungi, likely ingested during food consumption, to further support dietary habits. Our findings show that pre-Columbian Caribbean cultures had a diverse diet consisting of maize (Zea mays), sweet potato (Ipomoea batatas), chili peppers (Capsicum annuum), peanuts (Arachis spp.), papaya (Carica papaya), tomato (Solanum lycopersicum) and, very surprisingly cotton (Gossypium barbadense) and tobacco (Nicotiana sylvestris). Modelling of putative phytopathogenic fungi and plant interactions confirmed the potential consumption of these plants as well as edible fungi, particularly Ustilago spp., which suggest the consumption of maize and huitlacoche. These findings suggest that a variety of dietary, medicinal, and hallucinogenic plants likely played an important role in ancient human subsistence and societal customs. We compared our results with coprolites found in Mexico and the United States, as well as present-day faeces from Mexico, Peru, and the United States. The results suggest that the diet of pre-Columbian cultures resembled that of present-day hunter-gatherers, while agriculturalists exhibited a transitional state in dietary lifestyles between the pre-Columbian cultures and larger scale farmers and United States individuals. Our study highlights differences in dietary patterns related to human lifestyles and provides insight into the flora present in the pre-Columbian Caribbean area. Importantly, data from ancient fecal specimens demonstrate the importance of ancient DNA studies to better understand pre-Columbian populations.
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Affiliation(s)
- Jelissa Reynoso-García
- Environmental Microbiology Laboratory, Biology Department, University of Puerto Rico, San Juan, Puerto Rico
| | | | | | - Raul J. Cano
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo, California, United States of America
| | - Gary A. Toranzos
- Environmental Microbiology Laboratory, Biology Department, University of Puerto Rico, San Juan, Puerto Rico
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5
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Chocholova E, Roudnicky P, Potesil D, Fialova D, Krystofova K, Drozdova E, Zdrahal Z. Extraction Protocol for Parallel Analysis of Proteins and DNA from Ancient Teeth and Dental Calculus. J Proteome Res 2023; 22:3311-3319. [PMID: 37699853 PMCID: PMC10563166 DOI: 10.1021/acs.jproteome.3c00370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
Dental calculus is becoming a crucial material in the study of past populations with increasing interest in its proteomic and genomic content. Here, we suggest further development of a protocol for analysis of ancient proteins and a combined approach for subsequent ancient DNA extraction. We tested the protocol on recent teeth, and the optimized protocol was applied to ancient tooth to limit the destruction of calculus as it is a precious and irreplaceable source of dietary, microbiological, and ecological information in the archeological context. Finally, the applicability of the protocol was demonstrated on samples of the ancient calculus.
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Affiliation(s)
- Eva Chocholova
- Laboratory of Biological and Molecular Anthropology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Pavel Roudnicky
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - David Potesil
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Dana Fialova
- Laboratory of Biological and Molecular Anthropology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Karolina Krystofova
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Eva Drozdova
- Laboratory of Biological and Molecular Anthropology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Zbynek Zdrahal
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
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Jiang LX, Guo L, Shapleigh JP, Liu Y, Huang Y, Lian JS, Xie L, Deng LW, Wang WG, Wang L. The long-term effect of glutaraldehyde on the bacterial community in anaerobic ammonium oxidation reactor. BIORESOURCE TECHNOLOGY 2023; 385:129448. [PMID: 37399960 DOI: 10.1016/j.biortech.2023.129448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/28/2023] [Accepted: 06/30/2023] [Indexed: 07/05/2023]
Abstract
A 160-day incubation was performed with two anammox reactors (GA and CK) to investigate the effect of glutaraldehyde. The results indicated that anammox bacteria were very sensitive when glutaraldehyde in GA reactor increased to 40 mg/L, the nitrogen removal efficiency sharply decreased to 11%, only one-quarter of CK. Glutaraldehyde changed spatial distribution of exopolysaccharides, caused anammox bacteria (Brocadia CK_gra75) to disassociate from granules (24.70% of the reads in CK but only 14.09% in GA granules). Metagenome analysis indicated glutaraldehyde led to the denitrifier community succession from strains without nir (nitrite reductase) and nor (nitric oxide reductases) genes to those with them, and the rapid growth of denitrifiers with NodT (an outer membrane factor)-related efflux pumps replacing those with another TolC -related ones. Meanwhile, Brocadia CK_gra75 lacks the NodT proteins. This study provides important insight into community adaptation and potential resistance mechanism in an active anammox community after exposure to disinfectant.
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Affiliation(s)
- Long-Xing Jiang
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China; Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China
| | - Lu Guo
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | | | - Yi Liu
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China
| | - Yan Huang
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China; Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China
| | - Jin-Shi Lian
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China; Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China
| | - Ling Xie
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China; Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China
| | - Liang-Wei Deng
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China; Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China
| | - Wen-Guo Wang
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China; Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China
| | - Lan Wang
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China; Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China.
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Regueira-Iglesias A, Vázquez-González L, Balsa-Castro C, Vila-Blanco N, Blanco-Pintos T, Tamames J, Carreira MJ, Tomás I. In silico evaluation and selection of the best 16S rRNA gene primers for use in next-generation sequencing to detect oral bacteria and archaea. MICROBIOME 2023; 11:58. [PMID: 36949474 PMCID: PMC10035280 DOI: 10.1186/s40168-023-01481-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Sequencing has been widely used to study the composition of the oral microbiome present in various health conditions. The extent of the coverage of the 16S rRNA gene primers employed for this purpose has not, however, been evaluated in silico using oral-specific databases. This paper analyses these primers using two databases containing 16S rRNA sequences from bacteria and archaea found in the human mouth and describes some of the best primers for each domain. RESULTS A total of 369 distinct individual primers were identified from sequencing studies of the oral microbiome and other ecosystems. These were evaluated against a database reported in the literature of 16S rRNA sequences obtained from oral bacteria, which was modified by our group, and a self-created oral archaea database. Both databases contained the genomic variants detected for each included species. Primers were evaluated at the variant and species levels, and those with a species coverage (SC) ≥75.00% were selected for the pair analyses. All possible combinations of the forward and reverse primers were identified, with the resulting 4638 primer pairs also evaluated using the two databases. The best bacteria-specific pairs targeted the 3-4, 4-7, and 3-7 16S rRNA gene regions, with SC levels of 98.83-97.14%; meanwhile, the optimum archaea-specific primer pairs amplified regions 5-6, 3-6, and 3-6, with SC estimates of 95.88%. Finally, the best pairs for detecting both domains targeted regions 4-5, 3-5, and 5-9, and produced SC values of 95.71-94.54% and 99.48-96.91% for bacteria and archaea, respectively. CONCLUSIONS Given the three amplicon length categories (100-300, 301-600, and >600 base pairs), the primer pairs with the best coverage values for detecting oral bacteria were as follows: KP_F048-OP_R043 (region 3-4; primer pair position for Escherichia coli J01859.1: 342-529), KP_F051-OP_R030 (4-7; 514-1079), and KP_F048-OP_R030 (3-7; 342-1079). For detecting oral archaea, these were as follows: OP_F066-KP_R013 (5-6; 784-undefined), KP_F020-KP_R013 (3-6; 518-undefined), and OP_F114-KP_R013 (3-6; 340-undefined). Lastly, for detecting both domains jointly they were KP_F020-KP_R032 (4-5; 518-801), OP_F114-KP_R031 (3-5; 340-801), and OP_F066-OP_R121 (5-9; 784-1405). The primer pairs with the best coverage identified herein are not among those described most widely in the oral microbiome literature. Video Abstract.
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Affiliation(s)
- Alba Regueira-Iglesias
- Oral Sciences Research Group, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute Foundation of Santiago (FIDIS), C/ Entrerrios s/n, 15872 Santiago de Compostela, Spain
| | - Lara Vázquez-González
- Centro Singular de Investigación en Tecnoloxías Intelixentes and Departamento de Electrónica e Computación, Universidade de Santiago de Compostela, Health Research Institute Foundation of Santiago (FIDIS), Rúa de Jenaro de la Fuente, s/n, 15705 Santiago de Compostela, Spain
| | - Carlos Balsa-Castro
- Oral Sciences Research Group, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute Foundation of Santiago (FIDIS), C/ Entrerrios s/n, 15872 Santiago de Compostela, Spain
| | - Nicolás Vila-Blanco
- Centro Singular de Investigación en Tecnoloxías Intelixentes and Departamento de Electrónica e Computación, Universidade de Santiago de Compostela, Health Research Institute Foundation of Santiago (FIDIS), Rúa de Jenaro de la Fuente, s/n, 15705 Santiago de Compostela, Spain
| | - Triana Blanco-Pintos
- Oral Sciences Research Group, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute Foundation of Santiago (FIDIS), C/ Entrerrios s/n, 15872 Santiago de Compostela, Spain
| | - Javier Tamames
- Microbiome Analysis Laboratory, Systems Biology Department, Centro Nacional de Biotecnología (CNB)-CSIC, Madrid, Spain
| | - Maria José Carreira
- Centro Singular de Investigación en Tecnoloxías Intelixentes and Departamento de Electrónica e Computación, Universidade de Santiago de Compostela, Health Research Institute Foundation of Santiago (FIDIS), Rúa de Jenaro de la Fuente, s/n, 15705 Santiago de Compostela, Spain
| | - Inmaculada Tomás
- Oral Sciences Research Group, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute Foundation of Santiago (FIDIS), C/ Entrerrios s/n, 15872 Santiago de Compostela, Spain
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The Role of Gut Dysbiosis in the Pathophysiology of Neuropsychiatric Disorders. Cells 2022; 12:cells12010054. [PMID: 36611848 PMCID: PMC9818777 DOI: 10.3390/cells12010054] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/09/2022] [Accepted: 12/14/2022] [Indexed: 12/25/2022] Open
Abstract
Mounting evidence shows that the complex gut microbial ecosystem in the human gastrointestinal (GI) tract regulates the physiology of the central nervous system (CNS) via microbiota and the gut-brain (MGB) axis. The GI microbial ecosystem communicates with the brain through the neuroendocrine, immune, and autonomic nervous systems. Recent studies have bolstered the involvement of dysfunctional MGB axis signaling in the pathophysiology of several neurodegenerative, neurodevelopmental, and neuropsychiatric disorders (NPDs). Several investigations on the dynamic microbial system and genetic-environmental interactions with the gut microbiota (GM) have shown that changes in the composition, diversity and/or functions of gut microbes (termed "gut dysbiosis" (GD)) affect neuropsychiatric health by inducing alterations in the signaling pathways of the MGB axis. Interestingly, both preclinical and clinical evidence shows a positive correlation between GD and the pathogenesis and progression of NPDs. Long-term GD leads to overstimulation of hypothalamic-pituitary-adrenal (HPA) axis and the neuroimmune system, along with altered neurotransmitter levels, resulting in dysfunctional signal transduction, inflammation, increased oxidative stress (OS), mitochondrial dysfunction, and neuronal death. Further studies on the MGB axis have highlighted the significance of GM in the development of brain regions specific to stress-related behaviors, including depression and anxiety, and the immune system in the early life. GD-mediated deregulation of the MGB axis imbalances host homeostasis significantly by disrupting the integrity of the intestinal and blood-brain barrier (BBB), mucus secretion, and gut immune and brain immune functions. This review collates evidence on the potential interaction between GD and NPDs from preclinical and clinical data. Additionally, we summarize the use of non-therapeutic modulators such as pro-, pre-, syn- and post-biotics, and specific diets or fecal microbiota transplantation (FMT), which are promising targets for the management of NPDs.
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Warinner C. An Archaeology of Microbes. JOURNAL OF ANTHROPOLOGICAL RESEARCH 2022. [DOI: 10.1086/721976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Christina Warinner
- Department of Anthropology, Harvard University, Cambridge MA, USA 02138, and Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany 04103
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10
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Girija AS, Ganesh PS. Functional biomes beyond the bacteriome in the oral ecosystem. JAPANESE DENTAL SCIENCE REVIEW 2022; 58:217-226. [PMID: 35814739 PMCID: PMC9260289 DOI: 10.1016/j.jdsr.2022.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/28/2022] [Accepted: 05/12/2022] [Indexed: 11/16/2022] Open
Abstract
Selective constraint and pressures upon the host tissues often signifies a beneficial microbiome in any species. In the context of oral microbiome this displays a healthy microbial cosmos resisting the colonization and helps in rendering protection. This review highlights the endeavors of the oral microbiome beyond the bacteriome encompassing virome, mycobiome, protozoa and archaeomes in maintaining the oral homeostasis in health and disease. Scientific data based on the peer-reviewed publications on the microbial communities of the oral microbiome were selected and collated from the scientific database collection sites of web of science (WOS), pubmed central, Inspec etc., from 2010 to 2021 using the search key words like oral microbiome, oral microbiota, oral virome, oral bacteriome, oral mycobiome and oral archaeome. Data excluded were from conference proceedings, abstracts and book chapters. The oral homeostasis in both the health and disease conditions, mostly is balanced by the unrevealed virome, mycobiome, oral protozoa and archaeome. The review documents the need to comprehend the diversity that prevails among the kingdoms in order to determine the specific role played by each domain. Oral microbiome is also a novel research arena to develop drug and targeted therapies to treat various oro-dental infections.
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11
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Remembering St. Louis individual-structural violence and acute bacterial infections in a historical anatomical collection. Commun Biol 2022; 5:1050. [PMID: 36192528 PMCID: PMC9527723 DOI: 10.1038/s42003-022-03890-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 08/25/2022] [Indexed: 11/26/2022] Open
Abstract
Incomplete documentary evidence, variable biomolecular preservation, and limited skeletal responses have hindered assessment of acute infections in the past. This study was initially developed to explore the diagnostic potential of dental calculus to identify infectious diseases, however, the breadth and depth of information gained from a particular individual, St. Louis Individual (St.LI), enabled an individualized assessment and demanded broader disciplinary introspection of ethical research conduct. Here, we document the embodiment of structural violence in a 23-year-old Black and/or African American male, who died of lobar pneumonia in 1930s St. Louis, Missouri. St.LI exhibits evidence of systemic poor health, including chronic oral infections and a probable tuberculosis infection. Metagenomic sequencing of dental calculus recovered three pre-antibiotic era pathogen genomes, which likely contributed to the lobar pneumonia cause of death (CoD): Klebsiella pneumoniae (13.8X); Acinetobacter nosocomialis (28.4X); and Acinetobacter junii (30.1X). Ante- and perimortem evidence of St.LI’s lived experiences chronicle the poverty, systemic racism, and race-based structural violence experienced by marginalized communities in St. Louis, which contributed to St.LI’s poor health, CoD, anatomization, and inclusion in the Robert J. Terry Anatomical Collection. These same embodied inequalities continue to manifest as health disparities affecting many contemporary communities in the United States. An investigation into the cause of death of St. Louis Individual, a 23-year old Black or African American male who died in the 1930s, reveals evidence of structural violence and the impact of systemic racism in historically marginalized communities.
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12
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Pérez V, Liu Y, Hengst MB, Weyrich LS. A Case Study for the Recovery of Authentic Microbial Ancient DNA from Soil Samples. Microorganisms 2022; 10:microorganisms10081623. [PMID: 36014039 PMCID: PMC9414430 DOI: 10.3390/microorganisms10081623] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/01/2022] [Accepted: 08/02/2022] [Indexed: 11/16/2022] Open
Abstract
High Throughput DNA Sequencing (HTS) revolutionized the field of paleomicrobiology, leading to an explosive growth of microbial ancient DNA (aDNA) studies, especially from environmental samples. However, aDNA studies that examine environmental microbes routinely fail to authenticate aDNA, examine laboratory and environmental contamination, and control for biases introduced during sample processing. Here, we surveyed the available literature for environmental aDNA projects—from sample collection to data analysis—and assessed previous methodologies and approaches used in the published microbial aDNA studies. We then integrated these concepts into a case study, using shotgun metagenomics to examine methodological, technical, and analytical biases during an environmental aDNA study of soil microbes. Specifically, we compared the impact of five DNA extraction methods and eight bioinformatic pipelines on the recovery of microbial aDNA information in soil cores from extreme environments. Our results show that silica-based methods optimized for aDNA research recovered significantly more damaged and shorter reads (<100 bp) than a commercial kit or a phenol−chloroform method. Additionally, we described a stringent pipeline for data preprocessing, efficiently decreasing the representation of low-complexity and duplicated reads in our datasets and downstream analyses, reducing analytical biases in taxonomic classification.
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Affiliation(s)
- Vilma Pérez
- Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Correspondence:
| | - Yichen Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Martha B. Hengst
- Laboratorio de Ecología Molecular y Microbiología Aplicada, Departamento de Ciencias Farmacéuticas, Facultad de Ciencias, Universidad Católica del Norte, Antofagasta 1270300, Chile
| | - Laura S. Weyrich
- ARC Centre of Excellence for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Department of Anthropology and Huck Institutes of the Life Sciences, The Pennsylvania State University, State College, PA 16802, USA
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13
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Yarlagadda K, Zachwieja AJ, de Flamingh A, Phungviwatnikul T, Rivera-Colón AG, Roseman C, Shackelford L, Swanson KS, Malhi RS. Geographically diverse canid sampling provides novel insights into pre-industrial microbiomes. Proc Biol Sci 2022; 289:20220052. [PMID: 35506233 PMCID: PMC9065982 DOI: 10.1098/rspb.2022.0052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Canine microbiome studies are often limited in the geographic and temporal scope of samples studied. This results in a paucity of data on the canine microbiome around the world, especially in contexts where dogs may not be pets or human associated. Here, we present the shotgun sequences of fecal microbiomes of pet dogs from South Africa, shelter and stray dogs from India, and stray village dogs in Laos. We additionally performed a dietary experiment with dogs housed in a veterinary medical school, attempting to replicate the diet of the sampled dogs from Laos. We analyse the taxonomic diversity in these populations and identify the underlying functional redundancy of these microbiomes. Our results show that diet alone is not sufficient to recapitulate the higher diversity seen in the microbiome of dogs from Laos. Comparisons to previous studies and ancient dog fecal microbiomes highlight the need for greater population diversity in studies of canine microbiomes, as modern analogues can provide better comparisons to ancient microbiomes. We identify trends in microbial diversity and industrialization in dogs that mirror results of human studies, suggesting future research can make use of these companion animals as substitutes for humans in studying the effects of industrialization on the microbiome.
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Affiliation(s)
- K Yarlagadda
- Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - A J Zachwieja
- Department of Biomedical Sciences, University of Minnesota Medical School Duluth, Duluth, Minnesota, USA
| | - A de Flamingh
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - T Phungviwatnikul
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - A G Rivera-Colón
- Department of Evolution, Ecology, and Behavior, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - C Roseman
- School of Integrative Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - L Shackelford
- Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - K S Swanson
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - R S Malhi
- Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, IL, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.,Department of Evolution, Ecology, and Behavior, University of Illinois Urbana-Champaign, Urbana, IL, USA.,School of Integrative Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
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14
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Fagernäs Z, Salazar-García DC, Haber Uriarte M, Avilés Fernández A, Henry AG, Lomba Maurandi J, Ozga AT, Velsko IM, Warinner C. Understanding the microbial biogeography of ancient human dentitions to guide study design and interpretation. FEMS MICROBES 2022; 3:xtac006. [PMID: 37332506 PMCID: PMC10117714 DOI: 10.1093/femsmc/xtac006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 01/04/2022] [Accepted: 02/28/2022] [Indexed: 10/22/2023] Open
Abstract
The oral cavity is a heterogeneous environment, varying in factors such as pH, oxygen levels, and salivary flow. These factors affect the microbial community composition and distribution of species in dental plaque, but it is not known how well these patterns are reflected in archaeological dental calculus. In most archaeological studies, a single sample of dental calculus is studied per individual and is assumed to represent the entire oral cavity. However, it is not known if this sampling strategy introduces biases into studies of the ancient oral microbiome. Here, we present the results of a shotgun metagenomic study of a dense sampling of dental calculus from four Chalcolithic individuals from the southeast Iberian peninsula (ca. 4500-5000 BP). Interindividual differences in microbial composition are found to be much larger than intraindividual differences, indicating that a single sample can indeed represent an individual in most cases. However, there are minor spatial patterns in species distribution within the oral cavity that should be taken into account when designing a study or interpreting results. Finally, we show that plant DNA identified in the samples is likely of postmortem origin, demonstrating the importance of including environmental controls or additional lines of biomolecular evidence in dietary interpretations.
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Affiliation(s)
- Zandra Fagernäs
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Domingo C Salazar-García
- Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, València, 46010, Spain
- Grupo de Investigación en Prehistoria IT-1223-19 (UPV-EHU)/IKERBASQUE-Basque Foundation for Science, Vitoria, 01006, Spain
- Department of Geological Sciences, University of Cape Town, Cape Town, 7701, South Africa
| | - María Haber Uriarte
- Departamento de Prehistoria, Arqueología, Historia Antigua, Historia Medieval y Ciencias y Técnicas Historiográficas, Universidad de Murcia, Murcia, 30001, Spain
| | - Azucena Avilés Fernández
- Departamento de Prehistoria, Arqueología, Historia Antigua, Historia Medieval y Ciencias y Técnicas Historiográficas, Universidad de Murcia, Murcia, 30001, Spain
| | - Amanda G Henry
- Faculty of Archaeology, Leiden University, Leiden, 2332 CC, The Netherlands
| | - Joaquín Lomba Maurandi
- Departamento de Prehistoria, Arqueología, Historia Antigua, Historia Medieval y Ciencias y Técnicas Historiográficas, Universidad de Murcia, Murcia, 30001, Spain
| | - Andrew T Ozga
- Halmos College of Arts and Sciences, Nova Southeastern University, Fort Lauderdale, FL, 33314, USA
| | - Irina M Velsko
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Faculty of Biological Sciences, Friedrich Schiller University, 07743 Jena, Germany
- Department of Anthropology, Harvard University, Cambridge, MA, 02138, USA
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15
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Malyarchuk AB, Andreeva TV, Kuznetsova IL, Kunizheva SS, Protasova MS, Uralsky LI, Tyazhelova TV, Gusev FE, Manakhov AD, Rogaev EI. Genomics of Ancient Pathogens: First Advances and Prospects. BIOCHEMISTRY (MOSCOW) 2022; 87:242-258. [PMID: 35526849 PMCID: PMC8916790 DOI: 10.1134/s0006297922030051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Paleogenomics is one of the urgent and promising areas of interdisciplinary research in the today’s world science. New genomic methods of ancient DNA (aDNA) analysis, such as next generation sequencing (NGS) technologies, make it possible not only to obtain detailed genetic information about historical and prehistoric human populations, but also to study individual microbial and viral pathogens and microbiomes from different ancient and historical objects. Studies of aDNA of pathogens by reconstructing their genomes have so far yielded complete sequences of the ancient pathogens that played significant role in the history of the world: Yersiniapestis (plague), Variola virus (smallpox), Vibriocholerae (cholera), HBV (hepatitis B virus), as well as the equally important endemic human infectious agents: Mycobacteriumtuberculosis (tuberculosis), Mycobacteriumleprae (leprosy), and Treponemapallidum (syphilis). Genomic data from these pathogens complemented the information previously obtained by paleopathologists and allowed not only to identify pathogens from the past pandemics, but also to recognize the pathogen lineages that are now extinct, to refine chronology of the pathogen appearance in human populations, and to reconstruct evolutionary history of the pathogens that are still relevant to public health today. In this review, we describe state-of-the-art genomic research of the origins and evolution of many ancient pathogens and viruses and examine mechanisms of the emergence and spread of the ancient infections in the mankind history.
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Affiliation(s)
- Alexandra B Malyarchuk
- Center for Genetics and Genetic Technologies, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
| | - Tatiana V Andreeva
- Center for Genetics and Genetic Technologies, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia
| | - Irina L Kuznetsova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, 354340, Russia
| | - Svetlana S Kunizheva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, 354340, Russia
| | - Maria S Protasova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia
| | - Lev I Uralsky
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, 354340, Russia
| | - Tatiana V Tyazhelova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia
| | - Fedor E Gusev
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia
| | - Andrey D Manakhov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, 354340, Russia
| | - Evgeny I Rogaev
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia.
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, 354340, Russia
- Department of Psychiatry, UMass Chan Medical School, Shrewsbury, MA 01545, USA
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16
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Armbrecht L, Eisenhofer R, Utge J, Sibert EC, Rocha F, Ward R, Pierella Karlusich JJ, Tirichine L, Norris R, Summers M, Bowler C. Paleo-diatom composition from Santa Barbara Basin deep-sea sediments: a comparison of 18S-V9 and diat-rbcL metabarcoding vs shotgun metagenomics. ISME COMMUNICATIONS 2021; 1:66. [PMID: 36755065 PMCID: PMC9723766 DOI: 10.1038/s43705-021-00070-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 10/08/2021] [Accepted: 10/18/2021] [Indexed: 11/08/2022]
Abstract
Sedimentary ancient DNA (sedaDNA) analyses are increasingly used to reconstruct marine ecosystems. The majority of marine sedaDNA studies use a metabarcoding approach (extraction and analysis of specific DNA fragments of a defined length), targeting short taxonomic marker genes. Promising examples are 18S-V9 rRNA (~121-130 base pairs, bp) and diat-rbcL (76 bp), targeting eukaryotes and diatoms, respectively. However, it remains unknown how 18S-V9 and diat-rbcL derived compositional profiles compare to metagenomic shotgun data, the preferred method for ancient DNA analyses as amplification biases are minimised. We extracted DNA from five Santa Barbara Basin sediment samples (up to ~11 000 years old) and applied both a metabarcoding (18S-V9 rRNA, diat-rbcL) and a metagenomic shotgun approach to (i) compare eukaryote, especially diatom, composition, and (ii) assess sequence length and database related biases. Eukaryote composition differed considerably between shotgun and metabarcoding data, which was related to differences in read lengths (~112 and ~161 bp, respectively), and overamplification of short reads in metabarcoding data. Diatom composition was influenced by reference bias that was exacerbated in metabarcoding data and characterised by increased representation of Chaetoceros, Thalassiosira and Pseudo-nitzschia. Our results are relevant to sedaDNA studies aiming to accurately characterise paleo-ecosystems from either metabarcoding or metagenomic data.
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Affiliation(s)
- Linda Armbrecht
- Institute for Marine and Antarctic Studies (IMAS), Ecology & Biodiversity Centre, University of Tasmania, Battery Point, TAS, 7004, Australia.
- Australian Centre for Ancient DNA, School of Biological Sciences, Faculty of Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia.
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France.
| | - Raphael Eisenhofer
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - José Utge
- UMR 7206, Muséum National d'Histoire Naturelle, CNRS, Université Paris Diderot, 75016, Paris, France
| | - Elizabeth C Sibert
- Department of Earth and Planetary Sciences, Yale University, New Haven, CT, 06511, USA
- Yale Institute for Biospheric Studies, Yale University, New Haven, CT, 06511, USA
| | - Fabio Rocha
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Ryan Ward
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Juan José Pierella Karlusich
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Leila Tirichine
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
- Université de Nantes, CNRS, UFIP, UMR 6286, F-44000, Nantes, France
| | - Richard Norris
- GRD, Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, 92093-0244, USA
| | - Mindi Summers
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France.
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17
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Janßen R, Beck AJ, Werner J, Dellwig O, Alneberg J, Kreikemeyer B, Maser E, Böttcher C, Achterberg EP, Andersson AF, Labrenz M. Machine Learning Predicts the Presence of 2,4,6-Trinitrotoluene in Sediments of a Baltic Sea Munitions Dumpsite Using Microbial Community Compositions. Front Microbiol 2021; 12:626048. [PMID: 34659134 PMCID: PMC8513674 DOI: 10.3389/fmicb.2021.626048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 08/24/2021] [Indexed: 01/04/2023] Open
Abstract
Bacteria are ubiquitous and live in complex microbial communities. Due to differences in physiological properties and niche preferences among community members, microbial communities respond in specific ways to environmental drivers, potentially resulting in distinct microbial fingerprints for a given environmental state. As proof of the principle, our goal was to assess the opportunities and limitations of machine learning to detect microbial fingerprints indicating the presence of the munition compound 2,4,6-trinitrotoluene (TNT) in southwestern Baltic Sea sediments. Over 40 environmental variables including grain size distribution, elemental composition, and concentration of munition compounds (mostly at pmol⋅g–1 levels) from 150 sediments collected at the near-to-shore munition dumpsite Kolberger Heide by the German city of Kiel were combined with 16S rRNA gene amplicon sequencing libraries. Prediction was achieved using Random Forests (RFs); the robustness of predictions was validated using Artificial Neural Networks (ANN). To facilitate machine learning with microbiome data we developed the R package phyloseq2ML. Using the most classification-relevant 25 bacterial genera exclusively, potentially representing a TNT-indicative fingerprint, TNT was predicted correctly with up to 81.5% balanced accuracy. False positive classifications indicated that this approach also has the potential to identify samples where the original TNT contamination was no longer detectable. The fact that TNT presence was not among the main drivers of the microbial community composition demonstrates the sensitivity of the approach. Moreover, environmental variables resulted in poorer prediction rates than using microbial fingerprints. Our results suggest that microbial communities can predict even minor influencing factors in complex environments, demonstrating the potential of this approach for the discovery of contamination events over an integrated period of time. Proven for a distinct environment future studies should assess the ability of this approach for environmental monitoring in general.
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Affiliation(s)
- René Janßen
- Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
| | - Aaron J Beck
- Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Johannes Werner
- Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
| | - Olaf Dellwig
- Marine Geology, Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
| | - Johannes Alneberg
- Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Bernd Kreikemeyer
- Institute of Medical Microbiology, Virology and Hygiene, University of Rostock, Rostock, Germany
| | - Edmund Maser
- Institute of Toxicology and Pharmacology for Natural Scientists, University Medical School Schleswig-Holstein, Kiel, Germany
| | - Claus Böttcher
- State Ministry of Energy, Agriculture, The Environment, Nature and Digitization, Kiel, Germany
| | - Eric P Achterberg
- Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Anders F Andersson
- Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Matthias Labrenz
- Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
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18
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Shiba T, Komatsu K, Sudo T, Sawafuji R, Saso A, Ueda S, Watanabe T, Nemoto T, Kano C, Nagai T, Ohsugi Y, Katagiri S, Takeuchi Y, Kobayashi H, Iwata T. Comparison of Periodontal Bacteria of Edo and Modern Periods Using Novel Diagnostic Approach for Periodontitis With Micro-CT. Front Cell Infect Microbiol 2021; 11:723821. [PMID: 34616690 PMCID: PMC8488429 DOI: 10.3389/fcimb.2021.723821] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/17/2021] [Indexed: 11/07/2022] Open
Abstract
Ancient dental calculus, formed from dental plaque, is a rich source of ancient DNA and can provide information regarding the food and oral microbiology at that time. Genomic analysis of dental calculus from Neanderthals has revealed the difference in bacterial composition of oral microbiome between Neanderthals and modern humans. There are few reports investigating whether the pathogenic bacteria of periodontitis, a polymicrobial disease induced in response to the accumulation of dental plaque, were different between ancient and modern humans. This study aimed to compare the bacterial composition of the oral microbiome in ancient and modern human samples and to investigate whether lifestyle differences depending on the era have altered the bacterial composition of the oral microbiome and the causative bacteria of periodontitis. Additionally, we introduce a novel diagnostic approach for periodontitis in ancient skeletons using micro-computed tomography. Ancient 16S rDNA sequences were obtained from 12 samples at the Unko-in site (18th-19th century) of the Edo era (1603–1867), a characteristic period in Japan when immigrants were not accepted. Furthermore, modern 16S rDNA data from 53 samples were obtained from a database to compare the modern and ancient microbiome. The microbial co-occurrence network was analyzed based on 16S rDNA read abundance. Eubacterium species, Mollicutes species, and Treponema socranskii were the core species in the Edo co-occurrence network. The co-occurrence relationship between Actinomyces oricola and Eggerthella lenta appeared to have played a key role in causing periodontitis in the Edo era. However, Porphyromonas gingivalis, Fusobacterium nucleatum subsp. vincentii, and Prevotella pleuritidis were the core and highly abundant species in the co-occurrence network of modern samples. These results suggest the possibility of differences in the pathogens causing periodontitis during different eras in history.
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Affiliation(s)
- Takahiko Shiba
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Keiji Komatsu
- Department of Lifetime Oral Health Care Sciences, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takeaki Sudo
- Institute of Education, Tokyo Medical and Dental University, Tokyo, Japan
| | - Rikai Sawafuji
- Department of Evolutionary Studies of Biosystems, The Graduate University for Advanced Studies (SOKENDAI), Kanagawa, Japan
| | - Aiko Saso
- Department of Physical Therapy, Faculty of Rehabilitation, Niigata University of Health and Welfare, Niigata, Japan
| | - Shintaroh Ueda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan
| | - Takayasu Watanabe
- Department of Chemistry, Nihon University School of Dentistry, Tokyo, Japan
| | - Takashi Nemoto
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Chihiro Kano
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takahiko Nagai
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yujin Ohsugi
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Sayaka Katagiri
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yasuo Takeuchi
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroaki Kobayashi
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takanori Iwata
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
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19
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Granehäll L, Huang KD, Tett A, Manghi P, Paladin A, O’Sullivan N, Rota-Stabelli O, Segata N, Zink A, Maixner F. Metagenomic analysis of ancient dental calculus reveals unexplored diversity of oral archaeal Methanobrevibacter. MICROBIOME 2021; 9:197. [PMID: 34593021 PMCID: PMC8485483 DOI: 10.1186/s40168-021-01132-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 07/01/2021] [Indexed: 05/22/2023]
Abstract
BACKGROUND Dental calculus (mineralised dental plaque) preserves many types of microfossils and biomolecules, including microbial and host DNA, and ancient calculus are thus an important source of information regarding our ancestral human oral microbiome. In this study, we taxonomically characterised the dental calculus microbiome from 20 ancient human skeletal remains originating from Trentino-South Tyrol, Italy, dating from the Neolithic (6000-3500 BCE) to the Early Middle Ages (400-1000 CE). RESULTS We found a high abundance of the archaeal genus Methanobrevibacter in the calculus. However, only a fraction of the sequences showed high similarity to Methanobrevibacter oralis, the only described Methanobrevibacter species in the human oral microbiome so far. To further investigate the diversity of this genus, we used de novo metagenome assembly to reconstruct 11 Methanobrevibacter genomes from the ancient calculus samples. Besides the presence of M. oralis in one of the samples, our phylogenetic analysis revealed two hitherto uncharacterised and unnamed oral Methanobrevibacter species that are prevalent in ancient calculus samples sampled from a broad range of geographical locations and time periods. CONCLUSIONS We have shown the potential of using de novo metagenomic assembly on ancient samples to explore microbial diversity and evolution. Our study suggests that there has been a possible shift in the human oral microbiome member Methanobrevibacter over the last millennia. Video abstract.
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Affiliation(s)
- Lena Granehäll
- Institute for Mummy Studies, Eurac Research, 39100 Bolzano, Italy
- Faculty of Biology, Department of Biology II, Anthropology and Human Genomics, Ludwig-Maximilians-University of Munich, 82152 Planegg-Martinsried, Germany
| | - Kun D. Huang
- CIBIO Department, University of Trento, 38123 Trento, Italy
- Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy
| | - Adrian Tett
- CIBIO Department, University of Trento, 38123 Trento, Italy
- CUBE - Division of Computational Systems Biology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Paolo Manghi
- CIBIO Department, University of Trento, 38123 Trento, Italy
| | - Alice Paladin
- Institute for Mummy Studies, Eurac Research, 39100 Bolzano, Italy
| | - Niall O’Sullivan
- Institute for Mummy Studies, Eurac Research, 39100 Bolzano, Italy
| | - Omar Rota-Stabelli
- Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy
- Center Agriculture Food Environment, University of Trento, 38123 Trento, Italy
| | - Nicola Segata
- CIBIO Department, University of Trento, 38123 Trento, Italy
| | - Albert Zink
- Institute for Mummy Studies, Eurac Research, 39100 Bolzano, Italy
| | - Frank Maixner
- Institute for Mummy Studies, Eurac Research, 39100 Bolzano, Italy
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20
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A Standardized Approach for Shotgun Metagenomic Analysis of Ancient Dental Calculus. Methods Mol Biol 2021. [PMID: 34410642 DOI: 10.1007/978-1-0716-1518-8_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
Ancient dental calculus provides a challenging, yet unparalleled, opportunity to reconstruct ancient oral microbial communities and trace the origins of modern microbiota-associated diseases. Metagenomic analysis of ancient dental calculus using high-throughput DNA sequencing has proven itself as an effective method to accurately reconstruct microorganisms that once lived in the mouths of ancient humans. Here, we provide the strategy, methodologies, and approaches used to establish an ancient dental calculus project, from project conception, community engagement, sampling, extracting DNA, and preparing shotgun metagenomic DNA libraries for sequencing on an Illumina platform. We also discuss techniques to minimize background or contaminant DNA by monitoring and reducing contamination in calculus data sets, utilizing appropriate protective gear, and employing the use of sample decontamination strategies. In this methodology chapter, we hope to promote transparency in the ancient dental calculus research field and encourage collaboration across the ancient DNA research community.
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21
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Kim JA, Jang BR, Kim YR, Jung YC, Kim KS, Lee KH. Vibrio vulnificus induces the death of a major bacterial species in the mouse gut via cyclo-Phe-Pro. MICROBIOME 2021; 9:161. [PMID: 34284824 PMCID: PMC8293591 DOI: 10.1186/s40168-021-01095-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 05/12/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND A foodborne pathogen, Vibrio vulnificus, encounters normal microflora inhabiting the gut environments prior to causing fatal septicemia or gastroenteritis and should overcome the barriers derived from the gut commensals for successful infection. Its interactions with gut commensals during the infection process, however, have not yet been understood. In the present study, the effect of V. vulnificus on the community structures of gut microbiota in mice was examined. RESULTS Analyses of microbiota in the fecal samples of mice that died due to V. vulnificus infection revealed the decreased abundance of bacteria belonged to Bacteroidetes, notably, the species Bacteroides vulgatus. In vitro coculturing of the two bacterial species resulted in the decreased survival of B. vulgatus. The antagonistic effect of V. vulnificus against B. vulgatus was found to be mediated by cyclo-Phe-Pro (cFP), one of the major compounds secreted by V. vulnificus. cFP-treated B. vulgatus showed collapsed cellular morphology with an undulated cell surface, enlarged periplasmic space, and lysed membranes, suggesting the occurrence of membrane disruption. The degree of membrane disruption caused by cFP was dependent upon the cellular levels of ObgE in B. vulgatus. Recombinant ObgE exhibited a high affinity to cFP at a 1:1 ratio. When mice were orally injected with cFP, their feces contained significantly reduced B. vulgatus levels, and their susceptibility to V. vulnificus infection was considerably increased. CONCLUSIONS This study demonstrates that V. vulnificus-derived cFP modulates the abundance of the predominant species among gut commensals, which made V. vulnificus increase its pathogenicity in the hosts. Video abstract.
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Affiliation(s)
- Jeong-A Kim
- Department of Life Science, Sogang University, 35 Baekbeom-Ro, Mapo-Gu, Seoul, South Korea
| | - Bo-Ram Jang
- Department of Life Science, Sogang University, 35 Baekbeom-Ro, Mapo-Gu, Seoul, South Korea
| | - Yu-Ra Kim
- Department of Life Science, Sogang University, 35 Baekbeom-Ro, Mapo-Gu, Seoul, South Korea
| | - You-Chul Jung
- Department of Life Science, Sogang University, 35 Baekbeom-Ro, Mapo-Gu, Seoul, South Korea
| | - Kun-Soo Kim
- Department of Life Science, Sogang University, 35 Baekbeom-Ro, Mapo-Gu, Seoul, South Korea
| | - Kyu-Ho Lee
- Department of Life Science, Sogang University, 35 Baekbeom-Ro, Mapo-Gu, Seoul, South Korea.
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22
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Rampelli S, Turroni S, Debandi F, Alberdi A, Schnorr SL, Hofman CA, Taddia A, Helg R, Biagi E, Brigidi P, D'Amico F, Cattani M, Candela M. The gut microbiome buffers dietary adaptation in Bronze Age domesticated dogs. iScience 2021; 24:102816. [PMID: 34377966 PMCID: PMC8327155 DOI: 10.1016/j.isci.2021.102816] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/14/2021] [Accepted: 07/01/2021] [Indexed: 02/07/2023] Open
Abstract
In an attempt to explore the role of the gut microbiome during recent canine evolutionary history, we sequenced the metagenome of 13 canine coprolites dated ca. 3,600–3,450 years ago from the Bronze Age archaeological site of Solarolo (Italy), which housed a complex farming community. The microbiome structure of Solarolo dogs revealed continuity with that of modern dogs, but it also shared some features with the wild wolf microbiome, as a kind of transitional state between them. The dietary niche, as also inferred from the microbiome composition, was omnivorous, with evidence of consumption of starchy agricultural foods. Of interest, the Solarolo dog microbiome was particularly enriched in sequences encoding alpha-amylases and complemented a low copy number of the host amylase gene. These findings suggest that Neolithic dogs could have responded to the transition to a starch-rich diet by expanding microbial functionalities devoted to starch catabolism, thus compensating for delayed host response. Ancient DNA of Bronze Age canine coprolites from Solarolo was sequenced Solarolo dogs share gut microbiome features with modern wolves and dogs The gut microbiome of Solarolo dogs shows high number of reads for alpha-amylase Neolithic canine gut microbiome complemented delay in host genome adaptation
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Affiliation(s)
- Simone Rampelli
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Florencia Debandi
- Department of History and Cultures, University of Bologna, Bologna, Italy
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Stephanie L Schnorr
- Konrad Lorenz Institute for Evolution and Cognition Research, Klosterneuburg, Austria.,Department of Anthropology, University of Nevada, Las Vegas, NV, USA
| | - Courtney A Hofman
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK, USA.,Department of Anthropology, University of Oklahoma, Norman, OK, USA
| | - Alberto Taddia
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Riccardo Helg
- Department of History and Cultures, University of Bologna, Bologna, Italy
| | - Elena Biagi
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Patrizia Brigidi
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Federica D'Amico
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.,Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Maurizio Cattani
- Department of History and Cultures, University of Bologna, Bologna, Italy
| | - Marco Candela
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
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23
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Are Bacterio- and Phytoplankton Community Compositions Related in Lakes Differing in Their Cyanobacteria Contribution and Physico-Chemical Properties? Genes (Basel) 2021; 12:genes12060855. [PMID: 34199405 PMCID: PMC8227929 DOI: 10.3390/genes12060855] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 05/24/2021] [Accepted: 05/28/2021] [Indexed: 12/05/2022] Open
Abstract
Bacterioplankton community composition has become the center of research attention in recent years. Bacteria associated with toxic cyanobacteria blooms have attracted considerable interest. However, little is known about the environmental factors driving the bacteria community, including the impact of invasive cyanobacteria. Therefore, our aim has been to determine the relationships between heterotrophic bacteria and phytoplankton community composition across 24 Polish lakes with different contributions of cyanobacteria including the invasive species Raphidiopsis raciborskii. This analysis revealed that cyanobacteria were present in 16 lakes, while R. raciborskii occurred in 14 lakes. Our results show that bacteria communities differed between lakes dominated by cyanobacteria and lakes with minor contributions of cyanobacteria but did not differ between lakes with R. raciborskii and other lakes. Physical factors, including water and Secchi depth, were the major drivers of bacteria and phytoplankton community composition. However, in lakes dominated by cyanobacteria, bacterial community composition was also influenced by biotic factors such as the amount of R. raciborskii, chlorophyll-a and total phytoplankton biomass. Thus, our study provides novel evidence on the influence of environmental factors and R. raciborskii on lake bacteria communities.
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24
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Nodari R, Drancourt M, Barbieri R. Paleomicrobiology of the human digestive tract: A review. Microb Pathog 2021; 157:104972. [PMID: 34029658 DOI: 10.1016/j.micpath.2021.104972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 04/23/2021] [Accepted: 05/14/2021] [Indexed: 10/21/2022]
Abstract
The microbiota is a hot topic of research in medical microbiology, boosted by culturomics and metagenomics, with unanticipated knowledge outputs in physiology and pathology. Knowledge of the microbiota in ancient populations may therefore be of prime interest in understanding factors shaping the coevolution of the microbiota and populations. Studies on ancient human microbiomes can help us understand how the community of microorganisms presents in the oral cavity and the gut was shaped during the evolution of our species and what environmental, social or cultural changes may have changed it. This review cumulates and summarizes the discoveries in the field of the ancient human microbiota, focusing on the remains used as samples and techniques used to handle and analyze them.
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Affiliation(s)
- Riccardo Nodari
- Department of Biosciences and Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", University of Milan, Milan, 20133, Italy
| | - Michel Drancourt
- Aix-Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Rémi Barbieri
- Aix-Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France; UMR 7268, Anthropologie Bioculturelle, Droit, Ethique et Santé, Aix Marseille Univ., 11 CNRS, EFS, ADES, Marseille, France.
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25
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Yang C, Bohmann K, Wang X, Cai W, Wales N, Ding Z, Gopalakrishnan S, Yu DW. Biodiversity Soup II: A bulk‐sample metabarcoding pipeline emphasizing error reduction. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13602] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Chunyan Yang
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences Kunming China
| | - Kristine Bohmann
- Section for Evolutionary Genomics Globe Institute Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
| | - Xiaoyang Wang
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences Kunming China
| | - Wang Cai
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences Kunming China
| | - Nathan Wales
- Section for Evolutionary Genomics Globe Institute Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
- Department of Archaeology University of York York UK
| | - Zhaoli Ding
- Biodiversity Genomics Center Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics Globe Institute Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
| | - Douglas W. Yu
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences Kunming China
- School of Biological Sciences University of East AngliaNorwich Research Park Norwich UK
- Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China
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26
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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: 8] [Impact Index Per Article: 2.7] [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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27
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Zhao L, Zhang X, Xu M, Mao Y, Huang Y. DNA metabarcoding of zooplankton communities: species diversity and seasonal variation revealed by 18S rRNA and COI. PeerJ 2021; 9:e11057. [PMID: 33777533 PMCID: PMC7983862 DOI: 10.7717/peerj.11057] [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: 06/25/2020] [Accepted: 02/12/2021] [Indexed: 01/05/2023] Open
Abstract
Background Zooplankton is an important component of aquatic organisms and has important biological and economical significance in freshwater ecosystems. However, traditional methods that rely on morphology to classify zooplankton require expert taxonomic skills. Moreover, traditional classification methods are time-consuming and labor-intensive, which is not practical for the design of conservation measures and ecological management tools based on zooplankton diversity assessment. Methods We used DNA metabarcoding technology with two different markers: the nuclear small subunit ribosomal RNA (18S rRNA) and mitochondrial cytochrome c oxidase (COI), to analyze 72 zooplankton samples collected in 4 seasons and 9 locations from the Sanmenxia Reservoir. We investigated seasonal changes in the zooplankton community and their relationship with water environmental factors. Results A total of 190 species of zooplankton were found, belonging to 12 phyla, 24 classes, 61 orders, 111 families, and 174 genera. Protozoa, especially ciliates, were the most diverse taxa. Richness and relative abundance of zooplankton showed significant seasonal changes. Both alpha and beta diversity showed seasonal trends: the diversity in summer and autumn was higher than that in winter and spring. The zooplankton diversity was most similar in winter and spring. By correlating metabarcoding data and water environmental factors, we proved that water temperature, chemical oxygen demand, total nitrogen and ammoniacal nitrogen were the main environmental factors driving the seasonal changes in zooplankton in the Sanmenxia Reservoir. Water temperature, followed by total nitrogen, were the most influential factors. This study highlights the advantages and some limitations of zooplankton molecular biodiversity assessment using two molecular markers.
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Affiliation(s)
- Lina Zhao
- College of Life Sciences, Shaanxi Normal University, Xian, Shaanxi, China
| | - Xue Zhang
- College of Life Sciences, Shaanxi Normal University, Xian, Shaanxi, China
| | - Mengyue Xu
- College of Life Sciences, Shaanxi Normal University, Xian, Shaanxi, China
| | - Ying Mao
- College of Life Sciences, Shaanxi Normal University, Xian, Shaanxi, China
| | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xian, Shaanxi, China
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28
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Kazarina A, Petersone-Gordina E, Kimsis J, Kuzmicka J, Zayakin P, Griškjans Ž, Gerhards G, Ranka R. The Postmedieval Latvian Oral Microbiome in the Context of Modern Dental Calculus and Modern Dental Plaque Microbial Profiles. Genes (Basel) 2021; 12:genes12020309. [PMID: 33671794 PMCID: PMC7927102 DOI: 10.3390/genes12020309] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 02/17/2021] [Accepted: 02/19/2021] [Indexed: 02/07/2023] Open
Abstract
Recent advantages in paleomicrobiology have provided an opportunity to investigate the composition of ancient microbial ecologies. Here, using metagenome analysis, we investigated the microbial profiles of historic dental calculus retrieved from archaeological human remains from postmedieval Latvia dated 16–17th century AD and examined the associations of oral taxa and microbial diversity with specific characteristics. We evaluated the preservation of human oral microbiome patterns in historic samples and compared the microbial composition of historic dental calculus, modern human dental plaque, modern human dental calculus samples and burial soil microbiota. Overall, the results showed that the majority of microbial DNA in historic dental calculus originated from the oral microbiome with little impact of the burial environment. Good preservation of ancient DNA in historical dental calculus samples has provided reliable insight into the composition of the oral microbiome of postmedieval Latvian individuals. The relative stability of the classifiable oral microbiome composition was observed. Significant differences between the microbiome profiles of dental calculus and dental plaque samples were identified, suggesting microbial adaptation to a specific human body environment.
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Affiliation(s)
- Alisa Kazarina
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, LV-1067 Riga, Latvia
| | - Elina Petersone-Gordina
- Institute of Latvian History, University of Latvia, Kalpaka Bulvaris 4, LV-1050 Riga, Latvia
| | - Janis Kimsis
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, LV-1067 Riga, Latvia
| | - Jevgenija Kuzmicka
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, LV-1067 Riga, Latvia
| | - Pawel Zayakin
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, LV-1067 Riga, Latvia
| | - Žans Griškjans
- Institute of Stomatology, Riga Stradins University, Dzirciema Str. 20, LV-1007 Riga, Latvia
| | - Guntis Gerhards
- Institute of Latvian History, University of Latvia, Kalpaka Bulvaris 4, LV-1050 Riga, Latvia
| | - Renate Ranka
- Latvian Biomedical Research and Study Centre, Ratsupites Str. 1, LV-1067 Riga, Latvia
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29
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Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations. QUATERNARY 2021. [DOI: 10.3390/quat4010006] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building on the most recent literature and seven original case studies, we synthesize the state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation of DNA inventories from sedimentary ancient DNA (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based on current knowledge and best practises.
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30
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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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31
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Thomas K, Ironside K, Clark L, Bingle L. Preliminary microbiological and chemical analysis of two historical stock ales from Victorian and Edwardian brewing. JOURNAL OF THE INSTITUTE OF BREWING 2021. [DOI: 10.1002/jib.641] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Keith Thomas
- Brewlab Unit One West Quay Court, Sunderland Enterprise Park Sunderland SR5 2TE UK
| | - Kayleigh Ironside
- Faculty of Health Sciences and Wellbeing University of Sunderland Chester Road Sunderland SR1 3SD UK
| | - Lisa Clark
- Brewlab Unit One West Quay Court, Sunderland Enterprise Park Sunderland SR5 2TE UK
| | - Lewis Bingle
- Faculty of Health Sciences and Wellbeing University of Sunderland Chester Road Sunderland SR1 3SD UK
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32
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Wang Q, Huang Q, Guo G, Qin J, Luo J, Zhu Z, Hong Y, Xu Y, Hu S, Hu W, Yang C, Wang J. Reducing bioavailability of heavy metals in contaminated soil and uptake by maize using organic-inorganic mixed fertilizer. CHEMOSPHERE 2020; 261:128122. [PMID: 33113643 DOI: 10.1016/j.chemosphere.2020.128122] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/23/2020] [Accepted: 08/25/2020] [Indexed: 06/11/2023]
Abstract
Heavy metals in soil are harmful to human health via the food chain, but little is known about the mechanism of reducing bioavailability of Cd or Pb to maize (Zea mays L.) by applying complex amendments to soil. A field experiment was conducted at a tropical site in Hainan Province, China, that had been subjected to soil pollution by Cd and Pb from past mining activities. There were ten treatment groups comprising a mixture of biochar, hydroxyapatite (HAP), manure, and plant ash in varying proportions and at three different rates. Compared with untreated soil, all treatments increased pH by 2-3 units in bulk soil or 1-2 units in rhizosphere soil. For all amendments, the concentration of Cd in all parts of maize plants was decreased compared with unamended soil, but this effect was much smaller for Pb. The greatest effect was found with a mixture containing the ratio of HAP:manure:biochar:plant ash as 6:4:2:1 when applied at 20.1 t ha-1. The dominant microbial group in contaminated soil was Proteobacteria. There is evidence that this group can immobilize Cd by mechanisms that include biosorption and bioprecipitation. It was concluded that the mixed amendments containing biochar, HAP, manure, and plant ash can be useful in decreasing Cd uptake by maize. The amendment in this study likely operates through a combination of soil chemical changes and by influencing the soil-microbe-plant interaction.
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Affiliation(s)
- Qingqing Wang
- College of Ecology & Environment, Hainan University, Haikou, Hainan, 570228, PR China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, PR China; Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Hainan University, Haikou, Hainan, 570228, PR China; Center for Eco-Environmental Restoration Engineering of Hainan Province, Hainan University, Haikou, Hainan, 570228, PR China; Key Laboratory for Environmental Toxicology of Haikou, Hainan University, Haikou, Hainan, 570228, PR China
| | - Qing Huang
- College of Ecology & Environment, Hainan University, Haikou, Hainan, 570228, PR China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, PR China; Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Hainan University, Haikou, Hainan, 570228, PR China; Center for Eco-Environmental Restoration Engineering of Hainan Province, Hainan University, Haikou, Hainan, 570228, PR China; Key Laboratory for Environmental Toxicology of Haikou, Hainan University, Haikou, Hainan, 570228, PR China.
| | - Genmao Guo
- College of Ecology & Environment, Hainan University, Haikou, Hainan, 570228, PR China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, PR China; Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Hainan University, Haikou, Hainan, 570228, PR China; Center for Eco-Environmental Restoration Engineering of Hainan Province, Hainan University, Haikou, Hainan, 570228, PR China; Key Laboratory for Environmental Toxicology of Haikou, Hainan University, Haikou, Hainan, 570228, PR China
| | - Jiemin Qin
- College of Ecology & Environment, Hainan University, Haikou, Hainan, 570228, PR China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, PR China; Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Hainan University, Haikou, Hainan, 570228, PR China; Center for Eco-Environmental Restoration Engineering of Hainan Province, Hainan University, Haikou, Hainan, 570228, PR China; Key Laboratory for Environmental Toxicology of Haikou, Hainan University, Haikou, Hainan, 570228, PR China
| | - Junyi Luo
- College of Ecology & Environment, Hainan University, Haikou, Hainan, 570228, PR China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, PR China; Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Hainan University, Haikou, Hainan, 570228, PR China; Center for Eco-Environmental Restoration Engineering of Hainan Province, Hainan University, Haikou, Hainan, 570228, PR China; Key Laboratory for Environmental Toxicology of Haikou, Hainan University, Haikou, Hainan, 570228, PR China
| | - Zhiqiang Zhu
- Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropic Crops, Hainan University, Haikou, Hainan, 570228, PR China
| | - Yi Hong
- Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropic Crops, Hainan University, Haikou, Hainan, 570228, PR China
| | - Yuxin Xu
- College of Ecology & Environment, Hainan University, Haikou, Hainan, 570228, PR China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, PR China; Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Hainan University, Haikou, Hainan, 570228, PR China; Center for Eco-Environmental Restoration Engineering of Hainan Province, Hainan University, Haikou, Hainan, 570228, PR China; Key Laboratory for Environmental Toxicology of Haikou, Hainan University, Haikou, Hainan, 570228, PR China
| | - Shan Hu
- College of Ecology & Environment, Hainan University, Haikou, Hainan, 570228, PR China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, PR China; Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Hainan University, Haikou, Hainan, 570228, PR China; Center for Eco-Environmental Restoration Engineering of Hainan Province, Hainan University, Haikou, Hainan, 570228, PR China; Key Laboratory for Environmental Toxicology of Haikou, Hainan University, Haikou, Hainan, 570228, PR China
| | - Wen Hu
- College of Ecology & Environment, Hainan University, Haikou, Hainan, 570228, PR China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, PR China; Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Hainan University, Haikou, Hainan, 570228, PR China; Center for Eco-Environmental Restoration Engineering of Hainan Province, Hainan University, Haikou, Hainan, 570228, PR China; Key Laboratory for Environmental Toxicology of Haikou, Hainan University, Haikou, Hainan, 570228, PR China
| | - Chen Yang
- College of Ecology & Environment, Hainan University, Haikou, Hainan, 570228, PR China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, PR China; Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Hainan University, Haikou, Hainan, 570228, PR China; Center for Eco-Environmental Restoration Engineering of Hainan Province, Hainan University, Haikou, Hainan, 570228, PR China; Key Laboratory for Environmental Toxicology of Haikou, Hainan University, Haikou, Hainan, 570228, PR China
| | - Junfeng Wang
- College of Ecology & Environment, Hainan University, Haikou, Hainan, 570228, PR China; State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, 570228, PR China; Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Hainan University, Haikou, Hainan, 570228, PR China; Center for Eco-Environmental Restoration Engineering of Hainan Province, Hainan University, Haikou, Hainan, 570228, PR China; Key Laboratory for Environmental Toxicology of Haikou, Hainan University, Haikou, Hainan, 570228, PR China.
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33
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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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34
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Garner RE, Gregory-Eaves I, Walsh DA. Sediment Metagenomes as Time Capsules of Lake Microbiomes. mSphere 2020; 5:e00512-20. [PMID: 33148818 PMCID: PMC7643826 DOI: 10.1128/msphere.00512-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 10/21/2020] [Indexed: 12/22/2022] Open
Abstract
The reconstruction of ecological time series from lake sediment archives can retrace the environmental impact of human activities. Molecular genetic approaches in paleolimnology have provided unprecedented access to DNA time series, which record evidence of the microbial ecologies that underlaid historical lake ecosystems. Such studies often rely on single-gene surveys, and consequently, the full diversity of preserved microorganisms remains unexplored. In this study, we probed the diversity archived in contemporary and preindustrial sediments by comparative shotgun metagenomic analysis of surface water and sediment samples from three eastern Canadian lakes. In a strategy that was aimed at disentangling historical DNA from the indigenous sediment background, microbial preservation signals were captured by mapping sequence similarities between sediment metagenome reads and reference surface water metagenome assemblies. We detected preserved Cyanobacteria, diverse bacterioplankton, microeukaryotes, and viruses in sediment metagenomes. Among the preserved microorganisms were important groups never before reported in paleolimnological reconstructions, including bacteriophages (Caudovirales) and ubiquitous freshwater Betaproteobacteria (Polynucleobacter and Limnohabitans). In contrast, ultramicroscopic Actinobacteria ("Candidatus Nanopelagicales") and Alphaproteobacteria (Pelagibacterales) were apparently not well preserved in sediment metagenomes even though they were numerically dominant in surface water metagenomes. Overall, our study explored a novel application of whole-metagenome shotgun sequencing for discovering the DNA remains of a broad diversity of microorganisms preserved in lake sediments. The recovery of diverse microbial time series supports the taxonomic expansion of microbiome reconstructions and the development of novel microbial paleoindicators.IMPORTANCE Lakes are critical freshwater resources under mounting pressure from climate change and other anthropogenic stressors. The reconstruction of ecological time series from sediment archives with paleolimnological techniques has been shown to be an effective means of understanding how humans are modifying lake ecosystems over extended timescales. In this study, we combined shotgun DNA sequencing with a novel comparative analysis of surface water and sediment metagenomes to expose the diversity of microorganisms preserved in lake sediments. The detection of DNA from a broad diversity of preserved microbes serves to more fully reconstruct historical microbiomes and describe preimpact lake conditions.
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Affiliation(s)
- Rebecca E Garner
- Department of Biology, Concordia University, Montreal, Quebec, Canada
- Groupe de Recherche Interuniversitaire en Limnologie, Montreal, Quebec, Canada
| | - Irene Gregory-Eaves
- Department of Biology, McGill University, Montreal, Quebec, Canada
- Groupe de Recherche Interuniversitaire en Limnologie, Montreal, Quebec, Canada
| | - David A Walsh
- Department of Biology, Concordia University, Montreal, Quebec, Canada
- Groupe de Recherche Interuniversitaire en Limnologie, Montreal, Quebec, Canada
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35
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Williams L, Cugini C, Duffy S. Two Nearly Complete Nosocomial Pathogen Genome Sequences Reconstructed from Early-Middle 20th-Century Dental Calculus. Microbiol Resour Announc 2020; 9:e00850-20. [PMID: 33093055 PMCID: PMC7585846 DOI: 10.1128/mra.00850-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 09/24/2020] [Indexed: 11/20/2022] Open
Abstract
Acinetobacter baumannii and Stenotrophomonas maltophilia genomes were reconstructed from early-middle 20th-century human skeletal remains, maintained in natural history museums, using a metagenomic binning approach.
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Affiliation(s)
- LaShanda Williams
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, New Jersey, USA
| | - Carla Cugini
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, New Jersey, USA
| | - Siobain Duffy
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, New Jersey, USA
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36
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Eriksen AMH, Nielsen TK, Matthiesen H, Carøe C, Hansen LH, Gregory DJ, Turner-Walker G, Collins MJ, Gilbert MTP. Bone biodeterioration-The effect of marine and terrestrial depositional environments on early diagenesis and bone bacterial community. PLoS One 2020; 15:e0240512. [PMID: 33057402 PMCID: PMC7561151 DOI: 10.1371/journal.pone.0240512] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/29/2020] [Indexed: 11/18/2022] Open
Abstract
Bacteria play an important role in the degradation of bone material. However, much remains to be learnt about the structure of their communities in degrading bone, and how the depositional environment influences their diversity throughout the exposure period. We genetically profiled the bacterial community in an experimental series of pig bone fragments (femur and humeri) deposited at different well-defined environments in Denmark. The bacterial community in the bone fragments and surrounding depositional environment were studied over one year, and correlated with the bioerosion damage patterns observed microscopically in the bones. We observed that the bacterial communities within the bones were heavily influenced by the local microbial community, and that the general bone microbial diversity increases with time after exposure. We found the presence of several known collagenase producing bacterial groups, and also observed increases in the relative abundance of several of these in bones with tunneling. We anticipate that future analyses using shotgun metagenomics on this and similar datasets will be able to provide insights into mechanisms of microbiome driven bone degradation.
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Affiliation(s)
- Anne Marie Høier Eriksen
- Environmental Archaeology & Materials Science, Conservation & Natural Sciences, National Museum of Denmark, København, Denmark
- The GLOBE Institute, University of Copenhagen, København, Denmark
| | - Tue Kjærgaard Nielsen
- Department of Plant and Environmental Science, University of Copenhagen, København, Denmark
| | - Henning Matthiesen
- Environmental Archaeology & Materials Science, Conservation & Natural Sciences, National Museum of Denmark, København, Denmark
| | - Christian Carøe
- The GLOBE Institute, University of Copenhagen, København, Denmark
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Science, University of Copenhagen, København, Denmark
| | - David John Gregory
- Environmental Archaeology & Materials Science, Conservation & Natural Sciences, National Museum of Denmark, København, Denmark
| | - Gordon Turner-Walker
- Department of Cultural Heritage Conservation, National Yunlin University of Science & Technology, Douliu, Yunlin County, Taiwan
| | - Matthew James Collins
- The GLOBE Institute, University of Copenhagen, København, Denmark
- McDonald Institute for Archaeological Research, Cambridge, United Kingdom
| | - M. Thomas P. Gilbert
- The GLOBE Institute, University of Copenhagen, København, Denmark
- Norwegian University of Science and Technology, University Museum, Trondheim, Norway
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, København, Denmark
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37
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Skelly E, Johnson NW, Kapellas K, Kroon J, Lalloo R, Weyrich L. Response of Salivary Microbiota to Caries Preventive Treatment in Aboriginal and Torres Strait Islander Children. J Oral Microbiol 2020; 12:1830623. [PMID: 33149844 PMCID: PMC7586720 DOI: 10.1080/20002297.2020.1830623] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
A once-annual caries preventive (Intervention) treatment was offered to Aboriginal and Torres Strait Islander schoolchildren—a population with disproportionately poorer oral health than non-Indigenous Australian children—in the Northern Peninsula Area (NPA) of Far North Queensland (FNQ), which significantly improved their oral health. Here, we examine the salivary microbiota of these children (mean age = 10 ± 2.96 years; n = 103), reconstructing the bacterial community composition with high-throughput sequencing of the V4 region of bacterial 16S rRNA gene. Microbial communities of children who received the Intervention had lower taxonomic diversity than those who did not receive treatment (Shannon, p < 0.05). Moreover, the Intervention resulted in further decreased microbial diversity in children with active carious lesions existing at the time of saliva collection. Microbial species associated with caries were detected; Lactobacillus salivarius, Lactobacillus reuteri, Lactobacillus gasseri, Prevotella multisaccharivorax, Parascardovia denticolens, and Mitsuokella HMT 131 were significantly increased (p < 0.05) in children with severe caries, especially in children who did not receive the Intervention. These insights into microbial associations and community differences prompt future considerations to the mechanisms behind caries-preventive therapy induced change; important for understanding the long-term implications of like treatment to improve oral health disparities within Australia. Trial registration: ANZCTR, ACTRN12615000693527. Registered 3 July 2015, https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=368750&isReview=true
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Affiliation(s)
- Emily Skelly
- Australian Centre for Ancient DNA, University of Adelaide, Adelaide, Australia
| | - Newell W Johnson
- School of Dentistry and Oral Health, Griffith University, Gold Coast, Australia.,Menzies Health Institute Queensland, Griffith University, Gold Coast, Australia.,Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London, UK
| | - Kostas Kapellas
- Australian Research Centre for Population Oral Health, School of Dentistry, University of Adelaide, Adelaide, Australia
| | - Jeroen Kroon
- School of Dentistry and Oral Health, Griffith University, Gold Coast, Australia
| | - Ratilal Lalloo
- School of Dentistry, The University of Queensland, Herston, Australia
| | - Laura Weyrich
- Australian Centre for Ancient DNA, University of Adelaide, Adelaide, Australia.,Department of Anthropology, The Pennsylvania State University, University Park, PA, USA
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38
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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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39
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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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40
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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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41
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Dommain R, Andama M, McDonough MM, Prado NA, Goldhammer T, Potts R, Maldonado JE, Nkurunungi JB, Campana MG. The Challenges of Reconstructing Tropical Biodiversity With Sedimentary Ancient DNA: A 2200-Year-Long Metagenomic Record From Bwindi Impenetrable Forest, Uganda. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00218] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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42
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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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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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44
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Dziga D, Kokociński M, Barylski J, Nowicki G, Maksylewicz A, Antosiak A, Banaś AK, Strzałka W. Correlation between specific groups of heterotrophic bacteria and microcystin biodegradation in freshwater bodies of central Europe. FEMS Microbiol Ecol 2020; 95:5586992. [PMID: 31609415 DOI: 10.1093/femsec/fiz162] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 10/11/2019] [Indexed: 01/20/2023] Open
Abstract
Microcystins produced by several toxic cyanobacterial strains constitute an important problem for public health. Bacterial degradation of these hepatotoxins may play an important role in natural ecosystems, however the nature of the process is very poorly understood. The aim of our study was to investigate the possible interactions between cyanotoxin producers and degraders. Samples collected from 24 water bodies in western Poland were analysed to determine the chemo-physical parameters, phytoplankton content, bacterial community structure and microcystin-biodegradation potency. A redundancy analysis identified a positive correlation between the capacity of a community to degrade microcystin LR (MC-LR) and temperature, pH, chlorophyll a concentration and the abundance of MC-producers. The relative abundance of classes F38, TM7-3 and the order WCHB1-81c (Actinobacteria) was significantly higher in the lakes with MC-biodegradation potency. Some specific bacterial genera belonging to Acidobacteria, Chloroflexi, Gemmatimonadetes, Firmicutes and TM7 were closely correlated with the occurrence of Microcystis spp. Furthermore, the MC biodegradation process was connected with the same bacterial groups. Thus, our approach allowed us to provide a broader picture of some specific relations between microcystin producers and potential microcystin degraders. A more comprehensive analysis of the existing correlations may be helpful in our understanding of natural mechanisms of MC elimination using bacteria such as MC-degraders.
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Affiliation(s)
- Dariusz Dziga
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30387 Krakow, Poland
| | - Mikołaj Kokociński
- Department of Hydrobiology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Jakub Barylski
- Department of Molecular Virology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Grzegorz Nowicki
- Department of Molecular Virology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Anna Maksylewicz
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30387 Krakow, Poland
| | - Adam Antosiak
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30387 Krakow, Poland
| | - Agnieszka Katarzyna Banaś
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30387 Krakow, Poland
| | - Wojciech Strzałka
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30387 Krakow, Poland
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45
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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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Kistler L, Bieker VC, Martin MD, Pedersen MW, Ramos Madrigal J, Wales N. Ancient Plant Genomics in Archaeology, Herbaria, and the Environment. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:605-629. [PMID: 32119793 DOI: 10.1146/annurev-arplant-081519-035837] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The ancient DNA revolution of the past 35 years has driven an explosion in the breadth, nuance, and diversity of questions that are approachable using ancient biomolecules, and plant research has been a constant, indispensable facet of these developments. Using archaeological, paleontological, and herbarium plant tissues, researchers have probed plant domestication and dispersal, plant evolution and ecology, paleoenvironmental composition and dynamics, and other topics across related disciplines. Here, we review the development of the ancient DNA discipline and the role of plant research in its progress and refinement. We summarize our understanding of long-term plant DNA preservation and the characteristics of degraded DNA. In addition, we discuss challenges in ancient DNA recovery and analysis and the laboratory and bioinformatic strategies used to mitigate them. Finally, we review recent applications of ancient plant genomic research.
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Affiliation(s)
- Logan Kistler
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA;
| | - Vanessa C Bieker
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway; ,
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway; ,
| | - Mikkel Winther Pedersen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark;
| | - Jazmín Ramos Madrigal
- Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark;
| | - Nathan Wales
- Department of Archaeology, University of York, York YO1 7EP, United Kingdom;
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47
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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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48
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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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49
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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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50
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Hagan RW, Hofman CA, Hübner A, Reinhard K, Schnorr S, Lewis CM, Sankaranarayanan K, Warinner CG. Comparison of extraction methods for recovering ancient microbial DNA from paleofeces. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2019; 171:275-284. [PMID: 31785113 DOI: 10.1002/ajpa.23978] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/31/2019] [Accepted: 11/09/2019] [Indexed: 12/13/2022]
Abstract
OBJECTIVES Paleofeces are valuable to archeologists and evolutionary biologists for their potential to yield health, dietary, and host information. As a rich source of preserved biomolecules from host-associated microorganisms, they can also provide insights into the recent evolution and changing ecology of the gut microbiome. However, there is currently no standard method for DNA extraction from paleofeces, which combine the dual challenges of complex biological composition and degraded DNA. Due to the scarcity and relatively poor preservation of paleofeces when compared with other archeological remains, it is important to use efficient methods that maximize ancient DNA (aDNA) recovery while also minimizing downstream taxonomic biases. METHODS In this study, we use shotgun metagenomics to systematically compare the performance of five DNA extraction methods on a set of well-preserved human and dog paleofeces from Mexico (~1,300 BP). RESULTS Our results show that all tested DNA extraction methods yield a consistent microbial taxonomic profile, but that methods optimized for ancient samples recover significantly more DNA. CONCLUSIONS These results show promise for future studies that seek to explore the evolution of the human gut microbiome by comparing aDNA data with those generated in modern studies.
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Affiliation(s)
- Richard W Hagan
- Max Planck Institute for the Science of Human History, Jena, Germany.,Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, Oklahoma.,Department of Anthropology, University of Oklahoma, Norman, Oklahoma
| | - Courtney A Hofman
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, Oklahoma.,Department of Anthropology, University of Oklahoma, Norman, Oklahoma
| | - Alexander Hübner
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Karl Reinhard
- School of Natural Resources, University of Nebraska-Lincoln, Lincoln, Nebraska
| | - Stephanie Schnorr
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, Oklahoma.,Department of Anthropology, University of Oklahoma, Norman, Oklahoma.,Department of Anthropology, University of Nevada, Las Vegas, Nevada.,Konrad Lorenz Institute for Evolutionary and Cognition Research, Klosterneuburg, Austria
| | - Cecil M Lewis
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, Oklahoma.,Department of Anthropology, University of Oklahoma, Norman, Oklahoma
| | - Krithivasan Sankaranarayanan
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, Oklahoma.,Department of Molecular Biology and Plant Biology, University of Oklahoma, Norman, Oklahoma
| | - Christina G Warinner
- Max Planck Institute for the Science of Human History, Jena, Germany.,Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, Oklahoma.,Department of Anthropology, University of Oklahoma, Norman, Oklahoma.,Faculty of Biological Sciences, Friedrich-Schiller University, Jena, Germany.,Department of Anthropology, Harvard University, Cambridge, Massachusetts
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