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Garg D, Patel N, Rawat A, Rosado AS. Cutting edge tools in the field of soil microbiology. CURRENT RESEARCH IN MICROBIAL SCIENCES 2024; 6:100226. [PMID: 38425506 PMCID: PMC10904168 DOI: 10.1016/j.crmicr.2024.100226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024] Open
Abstract
The study of the whole of the genetic material contained within the microbial populations found in a certain environment is made possible by metagenomics. This technique enables a thorough knowledge of the variety, function, and interactions of microbial communities that are notoriously difficult to research. Due to the limitations of conventional techniques such as culturing and PCR-based methodologies, soil microbiology is a particularly challenging field. Metagenomics has emerged as an effective technique for overcoming these obstacles and shedding light on the dynamic nature of the microbial communities in soil. This review focuses on the principle of metagenomics techniques, their potential applications and limitations in soil microbial diversity analysis. The effectiveness of target-based metagenomics in determining the function of individual genes and microorganisms in soil ecosystems is also highlighted. Targeted metagenomics, including high-throughput sequencing and stable-isotope probing, is essential for studying microbial taxa and genes in complex ecosystems. Shotgun metagenomics may reveal the diversity of soil bacteria, composition, and function impacted by land use and soil management. Sanger, Next Generation Sequencing, Illumina, and Ion Torrent sequencing revolutionise soil microbiome research. Oxford Nanopore Technology (ONT) and Pacific Biosciences (PacBio)'s third and fourth generation sequencing systems revolutionise long-read technology. GeoChip, clone libraries, metagenomics, and metabarcoding help comprehend soil microbial communities. The article indicates that metagenomics may improve environmental management and agriculture despite existing limitations.Metagenomics has revolutionised soil microbiology research by revealing the complete diversity, function, and interactions of microorganisms in soil. Metagenomics is anticipated to continue defining the future of soil microbiology research despite some limitations, such as the difficulty of locating the appropriate sequencing method for specific genes.
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Affiliation(s)
- Diksha Garg
- Department of Microbiology, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Niketan Patel
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Makkah, 23955, Saudi Arabia
- Computational Bioscience Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Makkah, 23955, Saudi Arabia
| | - Anamika Rawat
- Center of Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Makkah, 23955, Saudi Arabia
| | - Alexandre Soares Rosado
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Makkah, 23955, Saudi Arabia
- Computational Bioscience Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Makkah, 23955, Saudi Arabia
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2
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Sanjurjo-Sánchez J, Alves C, Freire-Lista DM. Biomineral deposits and coatings on stone monuments as biodeterioration fingerprints. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168846. [PMID: 38036142 DOI: 10.1016/j.scitotenv.2023.168846] [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: 07/27/2023] [Revised: 11/16/2023] [Accepted: 11/22/2023] [Indexed: 12/02/2023]
Abstract
Biominerals deposition processes, also called biomineralisation, are intimately related to biodeterioration on stone surfaces. They include complex processes not always completely well understood. The study of biominerals implies the identification of organisms, their molecular mechanisms, and organism/rock/atmosphere interactions. Sampling restrictions of monument stones difficult the biominerals study and the in situ demonstrating of biodeterioration processes. Multidisciplinary works are required to understand the whole process. Thus, studies in heritage buildings have taken advantage of previous knowledge acquired thanks to laboratory experiments, investigations carried out on rock outcrops and within caves from some years ago. With the extrapolation of such knowledge to heritage buildings and the advances in laboratory techniques, there has been a huge increase of knowledge regarding biomineralisation and biodeterioration processes in stone monuments during the last 20 years. These advances have opened new debates about the implications on conservation interventions, and the organism's role in stone conservation and decay. This is a review of the existing studies of biominerals formation, biodeterioration on laboratory experiments, rocks, caves, and their application to building stones of monuments.
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Affiliation(s)
| | - Carlos Alves
- LandS/Lab2PT-Landscapes, Heritage and Territory Laboratory (FCT-UIDB/04509/2020) and Earth Sciences Department/School of Sciences, University of Minho, 4710-057 Braga, Portugal
| | - David M Freire-Lista
- Universidade de Trás-os-Montes e Alto Douro, UTAD, Escola de Ciências da Vida e do Ambiente, Quinta dos Prados, 5000-801 Vila Real, Portugal; Centro de Geociências, Universidade de Coimbra, Portugal
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Chouaia B, Dittmer J. A 2000-Year-Old Bacillus stercoris Strain Sheds Light on the Evolution of Cyclic Antimicrobial Lipopeptide Synthesis. Microorganisms 2024; 12:338. [PMID: 38399742 PMCID: PMC10893106 DOI: 10.3390/microorganisms12020338] [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: 11/18/2023] [Revised: 01/25/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
Some bacteria (notably the genera Bacillus and Clostridium) have the capacity to form endospores that can survive for millions of years in isolated habitats. The genomes of such ancient bacteria provide unique opportunities to understand bacterial evolution and metabolic capabilities over longer time scales. Herein, we sequenced the genome of a 2000-year-old bacterial strain (Mal05) isolated from intact apple seeds recovered during archaeological excavations of a Roman villa in Italy. Phylogenomic analyses revealed that this strain belongs to the species Bacillus stercoris and that it is placed in an early-branching position compared to most other strains of this species. Similar to other Bacillus species, B. stercoris Mal05 had been previously shown to possess antifungal activity. Its genome encodes all the genes necessary for the biosynthesis of fengycin and surfactin, two cyclic lipopeptides known to play a role in the competition of Bacilli with other microorganisms due to their antimicrobial activity. Comparative genomics and analyses of selective pressure demonstrate that these genes are present in all sequenced B. stercoris strains, despite the fact that they are not under strong purifying selection. Hence, these genes may not be essential for the fitness of these bacteria, but they can still provide a competitive advantage against other microorganisms present in the same environment.
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Affiliation(s)
- Bessem Chouaia
- Department of Environmental Sciences, Informatics and Statistics, Ca’ Foscari University of Venice, 30172 Venice, Italy
| | - Jessica Dittmer
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen-Bolzano, 39100 Bolzano, Italy;
- UMR 1345, Institut Agro, INRAE, IRHS, SFR Quasav, Université d’Angers, 49070 Beaucouzé, France
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4
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Prescott RD, Chan YL, Tong EJ, Bunn F, Onouye CT, Handel C, Lo CC, Davenport K, Johnson S, Flynn M, Saito JA, Lee H, Wong K, Lawson BN, Hiura K, Sager K, Sadones M, Hill EC, Esibill D, Cockell CS, Santomartino R, Chain PS, Decho AW, Donachie SP. Bridging Place-Based Astrobiology Education with Genomics, Including Descriptions of Three Novel Bacterial Species Isolated from Mars Analog Sites of Cultural Relevance. ASTROBIOLOGY 2023; 23:1348-1367. [PMID: 38079228 PMCID: PMC10750312 DOI: 10.1089/ast.2023.0072] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 10/27/2023] [Indexed: 12/22/2023]
Abstract
Democratizing genomic data science, including bioinformatics, can diversify the STEM workforce and may, in turn, bring new perspectives into the space sciences. In this respect, the development of education and research programs that bridge genome science with "place" and world-views specific to a given region are valuable for Indigenous students and educators. Through a multi-institutional collaboration, we developed an ongoing education program and model that includes Illumina and Oxford Nanopore sequencing, free bioinformatic platforms, and teacher training workshops to address our research and education goals through a place-based science education lens. High school students and researchers cultivated, sequenced, assembled, and annotated the genomes of 13 bacteria from Mars analog sites with cultural relevance, 10 of which were novel species. Students, teachers, and community members assisted with the discovery of new, potentially chemolithotrophic bacteria relevant to astrobiology. This joint education-research program also led to the discovery of species from Mars analog sites capable of producing N-acyl homoserine lactones, which are quorum-sensing molecules used in bacterial communication. Whole genome sequencing was completed in high school classrooms, and connected students to funded space research, increased research output, and provided culturally relevant, place-based science education, with participants naming three novel species described here. Students at St. Andrew's School (Honolulu, Hawai'i) proposed the name Bradyrhizobium prioritasuperba for the type strain, BL16AT, of the new species (DSM 112479T = NCTC 14602T). The nonprofit organization Kauluakalana proposed the name Brenneria ulupoensis for the type strain, K61T, of the new species (DSM 116657T = LMG = 33184T), and Hawai'i Baptist Academy students proposed the name Paraflavitalea speifideiaquila for the type strain, BL16ET, of the new species (DSM 112478T = NCTC 14603T).
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Affiliation(s)
- Rebecca D. Prescott
- Department of Biology, University of Mississippi, University, Mississippi, USA
- School of Life Sciences, University of Hawai‘i at Mānoa, Honolulu, Hawai‘i, USA
- National Aeronautics and Space Administration, Johnson Space Center, Houston, Texas, USA
| | - Yvonne L. Chan
- Office of Community Science, ‘Iolani School, Honolulu, Hawai‘i, USA
| | - Eric J. Tong
- Office of Community Science, ‘Iolani School, Honolulu, Hawai‘i, USA
| | - Fiona Bunn
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, United Kingdom
| | - Chiyoko T. Onouye
- School of Life Sciences, University of Hawai‘i at Mānoa, Honolulu, Hawai‘i, USA
| | - Christy Handel
- School of Life Sciences, University of Hawai‘i at Mānoa, Honolulu, Hawai‘i, USA
| | - Chien-Chi Lo
- Los Alamos National Laboratory, Biosciences Division, Los Alamos, New Mexico, USA
| | - Karen Davenport
- Los Alamos National Laboratory, Biosciences Division, Los Alamos, New Mexico, USA
| | - Shannon Johnson
- Los Alamos National Laboratory, Biosciences Division, Los Alamos, New Mexico, USA
| | - Mark Flynn
- Los Alamos National Laboratory, Biosciences Division, Los Alamos, New Mexico, USA
| | - Jennifer A. Saito
- School of Life Sciences, University of Hawai‘i at Mānoa, Honolulu, Hawai‘i, USA
| | - Herb Lee
- Pacific American Foundation, Kailua, Hawai‘i, USA
| | | | - Brittany N. Lawson
- School of Life Sciences, University of Hawai‘i at Mānoa, Honolulu, Hawai‘i, USA
| | - Kayla Hiura
- School of Life Sciences, University of Hawai‘i at Mānoa, Honolulu, Hawai‘i, USA
| | - Kailey Sager
- School of Life Sciences, University of Hawai‘i at Mānoa, Honolulu, Hawai‘i, USA
| | - Mia Sadones
- School of Life Sciences, University of Hawai‘i at Mānoa, Honolulu, Hawai‘i, USA
| | - Ethan C. Hill
- Office of Community Science, ‘Iolani School, Honolulu, Hawai‘i, USA
| | | | - Charles S. Cockell
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, United Kingdom
| | - Rosa Santomartino
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, United Kingdom
| | - Patrick S.G. Chain
- Los Alamos National Laboratory, Biosciences Division, Los Alamos, New Mexico, USA
| | - Alan W. Decho
- Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina, Columbia, South Carolina, USA
| | - Stuart P. Donachie
- School of Life Sciences, University of Hawai‘i at Mānoa, Honolulu, Hawai‘i, USA
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5
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Roche K, Dalle F, Capelli N, Borne R, Jouffroy-Bapicot I, Valot B, Grenouillet F, Le Bailly M. From modern-day parasitology to paleoparasitology: the elusive past record and evolution of Cryptosporidium. Front Microbiol 2023; 14:1249884. [PMID: 37928683 PMCID: PMC10622768 DOI: 10.3389/fmicb.2023.1249884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/05/2023] [Indexed: 11/07/2023] Open
Abstract
Recent efforts have been made to review the state of the art on a variety of questions and targets in paleoparasitology, including protozoan taxa. Meanwhile, these efforts seemed to let aside Cryptosporidium, and we then intended to review its paleoparasitological record to assess its past distribution and favored detection methods, and eventually highlight needed research trajectories. This review shows that contrary to other parasites, most of the positive results came from South-American sites and coprolites rather than sediment samples, highlighting the need to test this kind of material, notably in Europe where many negative results were reported in the published literature from sediment samples. Moreover, aDNA-based detections are nearly absent from the paleoparasitological record of this parasite, though punctually shown successful. With their potential to address the evolutionary history of Cryptosporidium species, notably through their 18S rRNA tree, aDNA-based approaches should be encouraged in the future. In sum, and though the limits of currently used methods and materials remain unclear, this review highlights the potential role of coprolites and aDNA for the study of Cryptosporidium species in the past and how this history shaped their current diversity and distribution, notably among human populations but also farm animals.
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Affiliation(s)
- Kévin Roche
- UMR CNRS-UFC 6249 Chrono-environnement, University of Franche-Comté, Besançon, France
| | - Frédéric Dalle
- CNR LE Cryptosporidiosis Collaborating Laboratory, Santé Publique France, Dijon, France
- Department of Parasitology/Mycology, University Hospital of Dijon, Dijon, France
| | - Nicolas Capelli
- UMR CNRS-UFC 6249 Chrono-environnement, University of Franche-Comté, Besançon, France
| | - Romain Borne
- UMR CNRS-UFC 6249 Chrono-environnement, University of Franche-Comté, Besançon, France
| | | | - Benoit Valot
- UMR CNRS-UFC 6249 Chrono-environnement, University of Franche-Comté, Besançon, France
| | - Frédéric Grenouillet
- UMR CNRS-UFC 6249 Chrono-environnement, University of Franche-Comté, Besançon, France
| | - Matthieu Le Bailly
- UMR CNRS-UFC 6249 Chrono-environnement, University of Franche-Comté, Besançon, France
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Bauer IL. The oral repellent - science fiction or common sense? Insects, vector-borne diseases, failing strategies, and a bold proposition. Trop Dis Travel Med Vaccines 2023; 9:7. [PMID: 37381000 DOI: 10.1186/s40794-023-00195-9] [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: 12/21/2022] [Accepted: 06/09/2023] [Indexed: 06/30/2023] Open
Abstract
Over the last decades, unimaginable amounts of money have gone into research and development of vector control measures, repellents, treatment, and vaccines for vector borne diseases. Technological progress and scientific breakthroughs allowed for ever more sophisticated and futuristic strategies. Yet, each year, millions of people still die or suffer from potentially serious consequences of malaria or dengue to more recent infections, such as zika or chikungunya, or of debilitating consequences of neglected tropical diseases. This does not seem value for money. In addition, all current vector control strategies and personal protection methods have shortcomings, some serious, that are either destructive to non-target species or unsatisfactory in their effectiveness. On the other hand, the rapid decline in insect populations and their predators reflects decades-long aggressive and indiscriminate vector control. This major disruption of biodiversity has an impact on human life not anticipated by the well-meaning killing of invertebrates. The objective of this paper is to re-examine current control methods, their effectiveness, their impact on biodiversity, human and animal health, and to call for scientific courage in the pursuit of fresh ideas. This paper brings together topics that are usually presented in isolation, thereby missing important links that offer potential solutions to long-standing problems in global health. First, it serves as a reminder of the importance of insects to human life and discusses the few that play a role in transmitting disease. Next, it examines critically the many currently employed vector control strategies and personal protection methods. Finally, based on new insights into insect chemo-sensation and attractants, this perspective makes a case for revisiting a previously abandoned idea, the oral repellent, and its use via currently successful methods of mass-application. The call is out for focused research to provide a powerful tool for public health, tropical medicine, and travel medicine.
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Affiliation(s)
- Irmgard L Bauer
- College of Healthcare Sciences, Academy - Tropical Health and Medicine, James Cook University, Townsville, QLD, 4811, Australia.
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7
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Vassallo A, Modi A, Quagliariello A, Bacci G, Faddetta T, Gallo M, Provenzano A, La Barbera A, Lombardo G, Maggini V, Firenzuoli F, Zaccaroni M, Gallo G, Caramelli D, Aleo Nero C, Baldi F, Fani R, Palumbo Piccionello A, Pucciarelli S, Puglia AM, Sineo L. Novel Sources of Biodiversity and Biomolecules from Bacteria Isolated from a High Middle Ages Soil Sample in Palermo (Sicily, Italy). Microbiol Spectr 2023; 11:e0437422. [PMID: 37071008 PMCID: PMC10269861 DOI: 10.1128/spectrum.04374-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 03/26/2023] [Indexed: 04/19/2023] Open
Abstract
The urban plan of Palermo (Sicily, Italy) has evolved throughout Punic, Roman, Byzantine, Arab, and Norman ages until it stabilized within the borders that correspond to the current historic center. During the 2012 to 2013 excavation campaign, new remains of the Arab settlement, directly implanted above the structures of the Roman age, were found. The materials investigated in this study derived from the so-called Survey No 3, which consists of a rock cavity of subcylindrical shape covered with calcarenite blocks: it was probably used to dispose of garbage during the Arabic age and its content, derived from daily activities, included grape seeds, scales and bones of fish, small animal bones, and charcoals. Radiocarbon dating confirmed the medieval origin of this site. The composition of the bacterial community was characterized through a culture-dependent and a culture-independent approach. Culturable bacteria were isolated under aerobic and anaerobic conditions and the total bacterial community was characterized through metagenomic sequencing. Bacterial isolates were tested for the production of compounds with antibiotic activity: a Streptomyces strain, whose genome was sequenced, was of particular interest because of its inhibitory activity, which was due to the Type I polyketide aureothin. Moreover, all strains were tested for the production of secreted proteases, with those belonging to the genus Nocardioides having the most active enzymes. Finally, protocols commonly used for ancient DNA studies were applied to evaluate the antiquity of isolated bacterial strains. Altogether these results show how paleomicrobiology might represent an innovative and unexplored source of novel biodiversity and new biotechnological tools. IMPORTANCE One of the goals of paleomicrobiology is the characterization of the microbial community present in archaeological sites. These analyses can usually provide valuable information about past events, such as occurrence of human and animal infectious diseases, ancient human activities, and environmental changes. However, in this work, investigations about the composition of the bacterial community of an ancient soil sample (harvested in Palermo, Italy) were carried out aiming to screen ancient culturable strains with biotechnological potential, such as the ability to produce bioactive molecules and secreted hydrolytic enzymes. Besides showing the biotechnological relevance of paleomicrobiology, this work reports a case of germination of putatively ancient bacterial spores recovered from soil rather than extreme environments. Moreover, in the case of spore-forming species, these results raise questions about the accuracy of techniques usually applied to estimate antiquity of DNA, as they could lead to its underestimation.
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Affiliation(s)
- Alberto Vassallo
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino (MC), Italy
| | - Alessandra Modi
- Department of Biology, University of Florence, Florence (FI), Italy
| | - Andrea Quagliariello
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro (PD), Italy
| | - Giovanni Bacci
- Department of Biology, University of Florence, Florence (FI), Italy
| | - Teresa Faddetta
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo (PA), Italy
| | - Michele Gallo
- Department of Molecular Sciences and Nanosystems, Ca’ Foscari University of Venice, Venezia Mestre (VE), Italy
| | - Aldesia Provenzano
- Department of Clinical and Experimental Biomedical Sciences “Mario Serio,” University of Florence, Florence (FI), Italy
| | - Andrea La Barbera
- Unit of Medical Genetics, IRCCS Ospedale Policlinico San Martino, Genoa (GE), Italy
| | - Giovanna Lombardo
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo (PA), Italy
| | - Valentina Maggini
- Research and Innovation Center in Phytotherapy and Integrated Medicine, Tuscany Region, Careggi University Hospital, Florence (FI), Italy
| | - Fabio Firenzuoli
- Research and Innovation Center in Phytotherapy and Integrated Medicine, Tuscany Region, Careggi University Hospital, Florence (FI), Italy
| | - Marco Zaccaroni
- Department of Biology, University of Florence, Florence (FI), Italy
| | - Giuseppe Gallo
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo (PA), Italy
| | - David Caramelli
- Department of Biology, University of Florence, Florence (FI), Italy
| | - Carla Aleo Nero
- Soprintendenza ai Beni culturali e ambientali di Palermo, Palermo (PA), Italy
| | - Franco Baldi
- Department of Molecular Sciences and Nanosystems, Ca’ Foscari University of Venice, Venezia Mestre (VE), Italy
| | - Renato Fani
- Department of Biology, University of Florence, Florence (FI), Italy
| | - Antonio Palumbo Piccionello
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo (PA), Italy
| | - Sandra Pucciarelli
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino (MC), Italy
| | - Anna Maria Puglia
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo (PA), Italy
| | - Luca Sineo
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo (PA), Italy
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8
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Tessler M, Cunningham SW, Ingala MR, Warring SD, Brugler MR. An Environmental DNA Primer for Microbial and Restoration Ecology. MICROBIAL ECOLOGY 2023; 85:796-808. [PMID: 36735064 DOI: 10.1007/s00248-022-02168-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 12/28/2022] [Indexed: 05/04/2023]
Abstract
Environmental DNA (eDNA) sequencing-DNA collected from the environment from living cells or shed DNA-was first developed for working with microbes and has greatly benefitted microbial ecologists for decades since. These tools have only become increasingly powerful with the advent of metabarcoding and metagenomics. Most new studies that examine diverse assemblages of bacteria, archaea, protists, fungi, and viruses lean heavily into eDNA using these newer technologies, as the necessary sequencing technology and bioinformatic tools have become increasingly affordable and user friendly. However, eDNA methods are rapidly evolving, and sometimes it can feel overwhelming to simply keep up with the basics. In this review, we provide a starting point for microbial ecologists who are new to DNA-based methods by detailing the eDNA methods that are most pertinent, including study design, sample collection and storage, selecting the right sequencing technology, lab protocols, equipment, and a few bioinformatic tools. Furthermore, we focus on how eDNA work can benefit restoration and what modifications are needed when working in this subfield.
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Affiliation(s)
- Michael Tessler
- Department of Biology, St. Francis College, Brooklyn, NY, USA.
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA.
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA.
| | - Seth W Cunningham
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA
- Department of Biological Sciences, Fordham University, Bronx, NY, 10458, USA
| | - Melissa R Ingala
- Department of Biological Sciences, Fairleigh Dickinson University, Madison, NJ, 07940, USA
| | | | - Mercer R Brugler
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA
- Department of Natural Sciences, University of South Carolina Beaufort, 801 Carteret Street, Beaufort, SC, 29902, USA
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9
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Alkatheri AH, Yap PSX, Abushelaibi A, Lai KS, Cheng WH, Erin Lim SH. Microbial Genomics: Innovative Targets and Mechanisms. Antibiotics (Basel) 2023; 12:190. [PMID: 36830101 PMCID: PMC9951906 DOI: 10.3390/antibiotics12020190] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
Multidrug resistance (MDR) has become an increasing threat to global health because bacteria can develop resistance to antibiotics over time. Scientists worldwide are searching for new approaches that go beyond traditional antibiotic discovery and development pipelines. Advances in genomics, however, opened up an unexplored therapeutic opportunity for the discovery of new antibacterial agents. Genomic approaches have been used to discover several novel antibiotics that target critical processes for bacterial growth and survival, including histidine kinases (HKs), LpxC, FabI, peptide deformylase (PDF), and aminoacyl-tRNA synthetases (AaRS). In this review, we will discuss the use of microbial genomics in the search for innovative and promising drug targets as well as the mechanisms of action for novel antimicrobial agents. We will also discuss future directions on how the utilization of the microbial genomics approach could improve the odds of antibiotic development having a more successful outcome.
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Affiliation(s)
- Asma Hussain Alkatheri
- Health Sciences Division, Abu Dhabi Women’s College, Higher Colleges of Technology, Abu Dhabi 41012, United Arab Emirates
| | - Polly Soo-Xi Yap
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor 47500, Malaysia
| | - Aisha Abushelaibi
- Office of Campus Director, Abu Dhabi Colleges, Higher Colleges of Technology, Abu Dhabi 41012, United Arab Emirates
| | - Kok-Song Lai
- Health Sciences Division, Abu Dhabi Women’s College, Higher Colleges of Technology, Abu Dhabi 41012, United Arab Emirates
| | - Wan-Hee Cheng
- Faculty of Health and Life Sciences, INTI International University, Persiaran Perdana BBN, Nilai 71800, Malaysia
| | - Swee-Hua Erin Lim
- Health Sciences Division, Abu Dhabi Women’s College, Higher Colleges of Technology, Abu Dhabi 41012, United Arab Emirates
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10
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Gancz AS, Weyrich LS. Studying ancient human oral microbiomes could yield insights into the evolutionary history of noncommunicable diseases. F1000Res 2023; 12:109. [PMID: 37065506 PMCID: PMC10090864 DOI: 10.12688/f1000research.129036.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/05/2023] [Indexed: 04/19/2023] Open
Abstract
Noncommunicable diseases (NCDs) have played a critical role in shaping human evolution and societies. Despite the exceptional impact of NCDs economically and socially, little is known about the prevalence or impact of these diseases in the past as most do not leave distinguishing features on the human skeleton and are not directly associated with unique pathogens. The inability to identify NCDs in antiquity precludes researchers from investigating how changes in diet, lifestyle, and environments modulate NCD risks in specific populations and from linking evolutionary processes to modern health patterns and disparities. In this review, we highlight how recent advances in ancient DNA (aDNA) sequencing and analytical methodologies may now make it possible to reconstruct NCD-related oral microbiome traits in past populations, thereby providing the first proxies for ancient NCD risk. First, we review the direct and indirect associations between modern oral microbiomes and NCDs, specifically cardiovascular disease, diabetes mellitus, rheumatoid arthritis, and Alzheimer's disease. We then discuss how oral microbiome features associated with NCDs in modern populations may be used to identify previously unstudied sources of morbidity and mortality differences in ancient groups. Finally, we conclude with an outline of the challenges and limitations of employing this approach, as well as how they might be circumvented. While significant experimental work is needed to verify that ancient oral microbiome markers are indeed associated with quantifiable health and survivorship outcomes, this new approach is a promising path forward for evolutionary health research.
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Affiliation(s)
- Abigail S Gancz
- Department of Anthropology, Pennsylvania State University, State College, PA, 16802, USA
| | - Laura S Weyrich
- Department of Anthropology, Pennsylvania State University, State College, PA, 16802, USA
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
- Huck Institutes of the Life Sciences, Pennsylvania State University, State College, PA, 16802, USA
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11
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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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12
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Spang A, Mahendrarajah TA, Offre P, Stairs CW. Evolving Perspective on the Origin and Diversification of Cellular Life and the Virosphere. Genome Biol Evol 2022; 14:evac034. [PMID: 35218347 PMCID: PMC9169541 DOI: 10.1093/gbe/evac034] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2022] [Indexed: 11/14/2022] Open
Abstract
The tree of life (TOL) is a powerful framework to depict the evolutionary history of cellular organisms through time, from our microbial origins to the diversification of multicellular eukaryotes that shape the visible biosphere today. During the past decades, our perception of the TOL has fundamentally changed, in part, due to profound methodological advances, which allowed a more objective approach to studying organismal and viral diversity and led to the discovery of major new branches in the TOL as well as viral lineages. Phylogenetic and comparative genomics analyses of these data have, among others, revolutionized our understanding of the deep roots and diversity of microbial life, the origin of the eukaryotic cell, eukaryotic diversity, as well as the origin, and diversification of viruses. In this review, we provide an overview of some of the recent discoveries on the evolutionary history of cellular organisms and their viruses and discuss a variety of complementary techniques that we consider crucial for making further progress in our understanding of the TOL and its interconnection with the virosphere.
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Affiliation(s)
- Anja Spang
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, The Netherlands
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Tara A Mahendrarajah
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, The Netherlands
| | - Pierre Offre
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Utrecht University, Den Burg, The Netherlands
| | - Courtney W Stairs
- Department of Biology, Microbiology research group, Lund University, Lund, Sweden
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13
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Belman S, Chaguza C, Kumar N, Lo S, Bentley SD. A new perspective on ancient Mitis group streptococcal genetics. Microb Genom 2022; 8. [PMID: 35225216 PMCID: PMC8942026 DOI: 10.1099/mgen.0.000753] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Mitis group Streptococcus are human obligate bacteria residing in the nasopharynx and oral cavity. They comprise both commensal and pathogenic species with the most well-known being Streptococcus pneumoniae – a leading cause of meningitis and pneumonia. A primary difference between the commensal and pathogenic species is the presence of the polysaccharide capsule – a major virulence factor in S. pneumoniae, also present in other commensal species. Our current understanding of the evolutionary divergence of the pathogenic and commensal species has been inferred from extant strains. Ancient genomes can further elucidate streptococcal evolutionary history. We extracted streptococcal genome reads from a 5700-year-old ancient metagenome and worked towards characterizing them. Due to excessive within- and between-species recombination common among streptococci we were unable to parse individual species. Further, the composite reads of the ancient metagenome do not fit within the diversity of any specific extant species. Using a capsular gene database and AT-content analysis we determined that this ancient metagenome is missing polysaccharide synthesis genes integral to streptococcal capsule formation. The presence of multiple zinc metalloproteases suggests that adaptation to host IgA1 had begun and the presence of other virulence factors further implies development of close host–microbe interactions, though the absence of a capsule suggests an inability to cause invasive disease. The presence of specific virulence factors such as pneumolysin implies stable maintenance of such genes through streptococcal evolution that may strengthen their value as anti-pneumococcal vaccine antigens, while maintaining awareness of their potential presence in commensal species. Following from Jensen et al.’s initial analysis we provide historical context for this long time human nasopharyngeal resident, the Mitis group Streptococcus.
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Affiliation(s)
- Sophie Belman
- Department of Genetics, University of Cambridge, Cambridge, UK
- Parasites & Microbes, Wellcome Sanger Institute, Hinxton, UK
| | - Chrispin Chaguza
- Yale School of Medicine, New Haven, CT, USA
- Parasites & Microbes, Wellcome Sanger Institute, Hinxton, UK
| | - Narender Kumar
- Parasites & Microbes, Wellcome Sanger Institute, Hinxton, UK
| | - Stephanie Lo
- Parasites & Microbes, Wellcome Sanger Institute, Hinxton, UK
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14
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Michail G, Karapetsi L, Madesis P, Reizopoulou A, Vagelas I. Metataxonomic Analysis of Bacteria Entrapped in a Stalactite's Core and Their Possible Environmental Origins. Microorganisms 2021; 9:microorganisms9122411. [PMID: 34946013 PMCID: PMC8705861 DOI: 10.3390/microorganisms9122411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 02/02/2023] Open
Abstract
Much is known about microbes originally identified in caves, but little is known about the entrapment of microbes (bacteria) in stalactites and their possible environmental origins. This study presents data regarding the significant environmental distribution of prokaryotic bacterial taxa of a Greek stalactite core. We investigated the involvement of those bacteria communities in stalactites using a metataxonomic analysis approach of partial 16S rRNA genes. The metataxonomic analysis of stalactite core material revealed an exceptionally broad ecological spectrum of bacteria classified as members of Proteobacteria, Actinobacteria, Firmicutes, Verrucomicrobia, and other unclassified bacteria. We concluded that (i) the bacterial transport process is possible through water movement from the upper ground cave environment, forming cave speleothems such as stalactites, (ii) bacterial genera such as Polaromonas, Thioprofundum, and phylum Verrucomicrobia trapped inside the stalactite support the paleoecology, paleomicrobiology, and paleoclimate variations, (iii) the entrapment of certain bacteria taxa associated with water, soil, animals, and plants such as Micrococcales, Propionibacteriales, Acidimicrobiales, Pseudonocardiales, and α-, β-, and γ-Proteobacteria.
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Affiliation(s)
- George Michail
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece
- Correspondence:
| | - Lefkothea Karapetsi
- Laboratory of Molecular Biology of Plants, Department of Agriculture Crop Production and Rural Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece; (L.K.); (P.M.)
- Centre for Research and Technology (CERTH), Institute of Applied Biosciences (INAB), 57001 Thessaloniki, Greece
| | - Panagiotis Madesis
- Laboratory of Molecular Biology of Plants, Department of Agriculture Crop Production and Rural Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece; (L.K.); (P.M.)
- Centre for Research and Technology (CERTH), Institute of Applied Biosciences (INAB), 57001 Thessaloniki, Greece
| | | | - Ioannis Vagelas
- Department of Agriculture Crop Production and Rural Environment, University of Thessaly, 38446 Volos, Greece;
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15
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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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