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Microbial Paleogenomics: The Role of Microbes on Evolutionary Trends and...
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Microbial Paleogenomics: The Role of Microbes on Evolutionary Trends and Future Discoveries

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Microbial Genetics and Genomics".

Deadline for manuscript submissions: closed (30 April 2018) | Viewed by 22850

Special Issue Editors

Dr. Raul J. Cano

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Guest Editor
Director of Research, ATCC Programs, ATCC Center for Translational Microbiology, 1075 Morris Avenue – STEM Building 5-19, Union, NJ 07083, USA
Dr. Gary A. Toranzos

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Guest Editor
Environmental Microbiology Laboratory, Biology Department, University of Puerto Rico, San Juan, PR 00932, USA
Interests: environmental microbiology; microbial ecology; indicators of fecal contamination; ancient microbiomes and viromes; virology
Special Issues, Collections and Topics in MDPI journals
Dr. Tasha M. Santiago-Rodriguez

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Guest Editor
Diversigen Inc., Houston, TX 77046, USA
Interests: microbiome; virome; phage biology; phage ecology; antibiotic-resistance
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The fields of paleogenomics is experiencing a new technological revolution as a result of a much greater armamentarium of techniques, such as next generation sequencing and corresponding bioinformatics analysis to reconstruct ancestral genomes. Molecular and “omics” approaches are increasingly allowing the investigation of ancient cultures and environments farther than previously imagined. Until recently, studies of ancient cultures have been limited by the quality and analysis methods of DNA in artifacts and remains found during excavations other explorations of ancient life on Earth. The application of the most recent technological advances in DNA sequencing and analysis, however, ancient materials of human, animal and microbial origin have provided important insights of the microbiome, resistome, dietary habits, and health and disease states of ancient times and civilizations. Such studies offer the possibility of providing a point of reference or milestone for the study of microbial genome evolution. Of particular interest is the study of the ancient resistome evolution and predictive trends in antimicrobial resistant determinants that the resistome can provide. The same armamentarium of tools can be applied to the study of ancient environments in an attempt to better understand environmental issues, such as global warming and species extinctions. This Special Issue of Genes will explore the genomics and metagenomics of ancient microbial life and their impact on the environment and human and animal populations and putative antibiotic-resistance genes compositions of such environments prior the antibiotic therapy era.

Dr. Raul J. Cano
Dr. Gary A. Toranzos
Dr. Tasha M. Santiago-Rodriguez
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

 

Keywords

  • DNA sequencing
  • Metagenomics
  • Microbiome
  • Epigenomics
  • Evolution
  • Genome evolution
  • Next Generation Sequencing
  • Resistome
  • Ancient DNA
  • Archaeology
  • Viromes
  • Paleoviromes
  • Phageomes

Published Papers (3 papers)

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Research

17 pages, 2463 KiB  
Article
Assessing Metagenomic Signals Recovered from Lyuba, a 42,000-Year-Old Permafrost-Preserved Woolly Mammoth Calf
by Giada Ferrari, Heidi E. L. Lischer, Judith Neukamm, Enrique Rayo, Nicole Borel, Andreas Pospischil, Frank Rühli, Abigail S. Bouwman and Michael G. Campana
Genes 2018, 9(9), 436; https://doi.org/10.3390/genes9090436 - 31 Aug 2018
Cited by 2 | Viewed by 9856
Abstract
The reconstruction of ancient metagenomes from archaeological material, and their implication in human health and evolution, is one of the most recent advances in paleomicrobiological studies. However, as for all ancient DNA (aDNA) studies, environmental and laboratory contamination need to be specifically addressed. [...] Read more.
The reconstruction of ancient metagenomes from archaeological material, and their implication in human health and evolution, is one of the most recent advances in paleomicrobiological studies. However, as for all ancient DNA (aDNA) studies, environmental and laboratory contamination need to be specifically addressed. Here we attempted to reconstruct the tissue-specific metagenomes of a 42,000-year-old, permafrost-preserved woolly mammoth calf through shotgun high-throughput sequencing. We analyzed the taxonomic composition of all tissue samples together with environmental and non-template experimental controls and compared them to metagenomes obtained from permafrost and elephant fecal samples. Preliminary results suggested the presence of tissue-specific metagenomic signals. We identified bacterial species that were present in only one experimental sample, absent from controls, and consistent with the nature of the samples. However, we failed to further authenticate any of these signals and conclude that, even when experimental samples are distinct from environmental and laboratory controls, this does not necessarily indicate endogenous presence of ancient host-associated microbiomic signals. Full article
(This article belongs to the Special Issue Microbial Paleogenomics: The Role of Microbes on Evolutionary Trends and Future Discoveries)
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12 pages, 2979 KiB  
Article
Pathogen Species Identification from Metagenomes in Ancient Remains: The Challenge of Identifying Human Pathogenic Species of Trypanosomatidae via Bioinformatic Tools
by Denis Sereno, Franck Dorkeld, Mohammad Akhoundi and Pascale Perrin
Genes 2018, 9(8), 418; https://doi.org/10.3390/genes9080418 - 20 Aug 2018
Cited by 5 | Viewed by 4696
Abstract
Accurate species identification from ancient DNA samples is a difficult task that would shed light on the evolutionary history of pathogenic microorganisms. The field of palaeomicrobiology has undoubtedly benefited from the advent of untargeted metagenomic approaches that use next-generation sequencing methodologies. Nevertheless, assigning [...] Read more.
Accurate species identification from ancient DNA samples is a difficult task that would shed light on the evolutionary history of pathogenic microorganisms. The field of palaeomicrobiology has undoubtedly benefited from the advent of untargeted metagenomic approaches that use next-generation sequencing methodologies. Nevertheless, assigning ancient DNA at the species level is a challenging process. Recently, the gut microbiome analysis of three pre-Columbian Andean mummies (Santiago-Rodriguez et al., 2016) has called into question the identification of Leishmania in South America. The accurate assignment would be important because it will provide some key elements that are linked to the evolutionary scenario for visceral leishmaniasis agents in South America. Here, we recovered the metagenomic data filed in the metagenomics RAST server (MG-RAST) to identify the different members of the Trypanosomatidae family that have infected these ancient remains. For this purpose, we used the ultrafast metagenomic sequence classifier, based on an exact alignment of k-mers (Kraken) and Bowtie2, an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. The analyses, which have been conducted on the most exhaustive genomic database possible on Trypanosomatidae, show that species assignments could be biased by a lack of some genomic sequences of Trypanosomatidae species (strains). Nevertheless, our work raises the issue of possible co-infections by multiple members of the Trypanosomatidae family in these three pre-Columbian mummies. In the three mummies, we show the presence of DNA that is reminiscent of a probable co-infection with Leptomonas seymouri, a parasite of insect’s gut, and Lotmaria. Full article
(This article belongs to the Special Issue Microbial Paleogenomics: The Role of Microbes on Evolutionary Trends and Future Discoveries)
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2623 KiB  
Article
Gut Microbiome and Putative Resistome of Inca and Italian Nobility Mummies
by Tasha M. Santiago-Rodriguez, Gino Fornaciari, Stefania Luciani, Gary A. Toranzos, Isolina Marota, Valentina Giuffra and Raul J. Cano
Genes 2017, 8(11), 310; https://doi.org/10.3390/genes8110310 - 07 Nov 2017
Cited by 18 | Viewed by 7552
Abstract
Little is still known about the microbiome resulting from the process of mummification of the human gut. In the present study, the gut microbiota, genes associated with metabolism, and putative resistome of Inca and Italian nobility mummies were characterized by using high-throughput sequencing. [...] Read more.
Little is still known about the microbiome resulting from the process of mummification of the human gut. In the present study, the gut microbiota, genes associated with metabolism, and putative resistome of Inca and Italian nobility mummies were characterized by using high-throughput sequencing. The Italian nobility mummies exhibited a higher bacterial diversity as compared to the Inca mummies when using 16S ribosomal (rRNA) gene amplicon sequencing, but both groups showed bacterial and fungal taxa when using shotgun metagenomic sequencing that may resemble both the thanatomicrobiome and extant human gut microbiomes. Identification of sequences associated with plants, animals, and carbohydrate-active enzymes (CAZymes) may provide further insights into the dietary habits of Inca and Italian nobility mummies. Putative antibiotic-resistance genes in the Inca and Italian nobility mummies support a human gut resistome prior to the antibiotic therapy era. The higher proportion of putative antibiotic-resistance genes in the Inca compared to Italian nobility mummies may support the hypotheses that a greater exposure to the environment may result in a greater acquisition of antibiotic-resistance genes. The present study adds knowledge of the microbiome resulting from the process of mummification of the human gut, insights of ancient dietary habits, and the preserved putative human gut resistome prior the antibiotic therapy era. Full article
(This article belongs to the Special Issue Microbial Paleogenomics: The Role of Microbes on Evolutionary Trends and Future Discoveries)
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