1
|
Alfonso P, Butković A, Fernández R, Riesgo A, Elena SF. Unveiling the hidden viromes across the animal tree of life: insights from a taxonomic classification pipeline applied to invertebrates of 31 metazoan phyla. mSystems 2024; 9:e0012424. [PMID: 38651902 PMCID: PMC11097642 DOI: 10.1128/msystems.00124-24] [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: 01/26/2024] [Accepted: 03/26/2024] [Indexed: 04/25/2024] Open
Abstract
Invertebrates constitute the majority of animal species on Earth, including most disease-causing agents or vectors, with more diverse viromes when compared to vertebrates. Recent advancements in high-throughput sequencing have significantly expanded our understanding of invertebrate viruses, yet this knowledge remains biased toward a few well-studied animal lineages. In this study, we analyze invertebrate DNA and RNA viromes for 31 phyla using 417 publicly available RNA-Seq data sets from diverse environments in the marine-terrestrial and marine-freshwater gradients. This study aims to (i) estimate virome compositions at the family level for the first time across the animal tree of life, including the first exploration of the virome in several phyla, (ii) quantify the diversity of invertebrate viromes and characterize the structure of invertebrate-virus infection networks, and (iii) investigate host phylum and habitat influence on virome differences. Results showed that a set of few viral families of eukaryotes, comprising Retroviridae, Flaviviridae, and several families of giant DNA viruses, were ubiquitous and highly abundant. Nevertheless, some differences emerged between phyla, revealing for instance a less diverse virome in Ctenophora compared to the other animal phyla. Compositional analysis of the viromes showed that the host phylum explained over five times more variance in composition than its habitat. Moreover, significant similarities were observed between the viromes of some phylogenetically related phyla, which could highlight the influence of co-evolution in shaping invertebrate viromes.IMPORTANCEThis study significantly enhances our understanding of the global animal virome by characterizing the viromes of previously unexamined invertebrate lineages from a large number of animal phyla. It showcases the great diversity of viromes within each phylum and investigates the role of habitat shaping animal viral communities. Furthermore, our research identifies dominant virus families in invertebrates and distinguishes phyla with analogous viromes. This study sets the road toward a deeper understanding of the virome across the animal tree of life.
Collapse
Affiliation(s)
- Pau Alfonso
- Instituto de Biología Integrativa de Sistemas (CSIC-Universitat de València), Paterna, València, Spain
| | - Anamarija Butković
- Institut Pasteur, Université Paris Cité, CNRS UMR6047 Archaeal Virology Unit, Paris, France
| | - Rosa Fernández
- Instituto de Biología Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Ana Riesgo
- Museo Nacional de Ciencias Naturales (CSIC), Madrid, Spain
- Department of Life Sciences, Natural History Museum of London, London, United Kingdom
| | - Santiago F. Elena
- Instituto de Biología Integrativa de Sistemas (CSIC-Universitat de València), Paterna, València, Spain
- The Santa Fe Institute, Santa Fe, New Mexico, USA
| |
Collapse
|
2
|
Hauptfeld E, Pappas N, van Iwaarden S, Snoek BL, Aldas-Vargas A, Dutilh BE, von Meijenfeldt FAB. Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes. Nat Commun 2024; 15:3373. [PMID: 38643272 PMCID: PMC11032395 DOI: 10.1038/s41467-024-47155-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 03/20/2024] [Indexed: 04/22/2024] Open
Abstract
Metagenomic analysis typically includes read-based taxonomic profiling, assembly, and binning of metagenome-assembled genomes (MAGs). Here we integrate these steps in Read Annotation Tool (RAT), which uses robust taxonomic signals from MAGs and contigs to enhance read annotation. RAT reconstructs taxonomic profiles with high precision and sensitivity, outperforming other state-of-the-art tools. In high-diversity groundwater samples, RAT annotates a large fraction of the metagenomic reads, calling novel taxa at the appropriate, sometimes high taxonomic ranks. Thus, RAT integrative profiling provides an accurate and comprehensive view of the microbiome from shotgun metagenomics data. The package of Contig Annotation Tool (CAT), Bin Annotation Tool (BAT), and RAT is available at https://github.com/MGXlab/CAT_pack (from CAT pack v6.0). The CAT pack now also supports Genome Taxonomy Database (GTDB) annotations.
Collapse
Affiliation(s)
- Ernestina Hauptfeld
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Nikolaos Pappas
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Sandra van Iwaarden
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Basten L Snoek
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Andrea Aldas-Vargas
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700, EV Wageningen, The Netherlands
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Rosalind Franklin Strasse 1, 07743, Jena, Germany.
| | - F A Bastiaan von Meijenfeldt
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
- Department of Marine Microbiology and Biogeochemistry (MMB), NIOZ Royal Netherlands Institute for Sea Research, PO Box 59, 1790AB, Den Burg, The Netherlands.
| |
Collapse
|
3
|
Edwin NR, Fitzpatrick AH, Brennan F, Abram F, O'Sullivan O. An in-depth evaluation of metagenomic classifiers for soil microbiomes. ENVIRONMENTAL MICROBIOME 2024; 19:19. [PMID: 38549112 PMCID: PMC10979606 DOI: 10.1186/s40793-024-00561-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 03/11/2024] [Indexed: 04/01/2024]
Abstract
BACKGROUND Recent endeavours in metagenomics, exemplified by projects such as the human microbiome project and TARA Oceans, have illuminated the complexities of microbial biomes. A robust bioinformatic pipeline and meticulous evaluation of their methodology have contributed to the success of these projects. The soil environment, however, with its unique challenges, requires a specialized methodological exploration to maximize microbial insights. A notable limitation in soil microbiome studies is the dearth of soil-specific reference databases available to classifiers that emulate the complexity of soil communities. There is also a lack of in-vitro mock communities derived from soil strains that can be assessed for taxonomic classification accuracy. RESULTS In this study, we generated a custom in-silico mock community containing microbial genomes commonly observed in the soil microbiome. Using this mock community, we simulated shotgun sequencing data to evaluate the performance of three leading metagenomic classifiers: Kraken2 (supplemented with Bracken, using a custom database derived from GTDB-TK genomes along with its own default database), Kaiju, and MetaPhlAn, utilizing their respective default databases for a robust analysis. Our results highlight the importance of optimizing taxonomic classification parameters, database selection, as well as analysing trimmed reads and contigs. Our study showed that classifiers tailored to the specific taxa present in our samples led to fewer errors compared to broader databases including microbial eukaryotes, protozoa, or human genomes, highlighting the effectiveness of targeted taxonomic classification. Notably, an optimal classifier performance was achieved when applying a relative abundance threshold of 0.001% or 0.005%. The Kraken2 supplemented with bracken, with a custom database demonstrated superior precision, sensitivity, F1 score, and overall sequence classification. Using a custom database, this classifier classified 99% of in-silico reads and 58% of real-world soil shotgun reads, with the latter identifying previously overlooked phyla using a custom database. CONCLUSION This study underscores the potential advantages of in-silico methodological optimization in metagenomic analyses, especially when deciphering the complexities of soil microbiomes. We demonstrate that the choice of classifier and database significantly impacts microbial taxonomic profiling. Our findings suggest that employing Kraken2 with Bracken, coupled with a custom database of GTDB-TK genomes and fungal genomes at a relative abundance threshold of 0.001% provides optimal accuracy in soil shotgun metagenome analysis.
Collapse
Affiliation(s)
- Niranjana Rose Edwin
- Teagasc, Moorepark Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- Functional Environmental Microbiology, School of Biological and Chemical Sciences, Ryan Institute, University of Galway, Galway, Ireland
- VistaMilk SFI Research Centre, Cork, Ireland
| | | | - Fiona Brennan
- Teagasc, Soils, Environment and Landuse Department, Johnstown Castle, Wexford, Ireland
- VistaMilk SFI Research Centre, Cork, Ireland
| | - Florence Abram
- Functional Environmental Microbiology, School of Biological and Chemical Sciences, Ryan Institute, University of Galway, Galway, Ireland
| | - Orla O'Sullivan
- Teagasc, Moorepark Food Research Centre, Moorepark, Fermoy, Cork, Ireland.
- VistaMilk SFI Research Centre, Cork, Ireland.
| |
Collapse
|
4
|
Muter O, Gudrā D, Daumova G, Idrisheva Z, Rakhymberdina M, Tabors G, Dirnēna B, Dobkeviča L, Petrova O, Apshikur B, Luņģe M, Fridmanis D, Denissov I, Bekishev Y, Kasparinskis R, Mukulysova Z, Polezhayev S. Impact of Anthropogenic Activities on Microbial Community Structure in Riverbed Sediments of East Kazakhstan. Microorganisms 2024; 12:246. [PMID: 38399650 PMCID: PMC10893015 DOI: 10.3390/microorganisms12020246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
Heavy metal (HMe) pollution in regions with mining and metallurgy activities is known to be a serious environmental problem worldwide. Hydrological processes contribute to the dissemination of HMes (drainage, precipitation, flow rate). The aim of the present study is to investigate the microbial community structure in ten river sediments sampled in different regions of East Kazakhstan, which are contaminated with HMes. The overall degree of sediment contamination with HMes (Cr, Cu, Zn, Pb, and Cd) was assessed using the pollution index Zc, which ranged from 0.43 to 21.6, with the highest in Ridder City (Zc = 21.6) and Ust-Kamenogorsk City, 0.8 km below the dam of the hydroelectric power station (Zc = 19.6). The tested samples considerably differed in organic matter, total carbon, nitrogen, and phosphorus content, as well as in the abundance of HMe-related functional gene families and antibiotic resistance genes. Metagenomic analysis of benthic microorganisms showed the prevalence of Proteobacteria (88.84-97.61%) and Actinobacteria (1.21-5.98%) at the phylum level in all samples. At the class level, Actinobacteria (21.68-57.48%), Betaproteobacteria (19.38-41.17%), and Alphaproteobacteria (10.0-39.78%) were the most common among the classified reads. To the best of our knowledge, this is the first study on the metagenomic characteristics of benthic microbial communities exposed to chronic HMe pressure in different regions of East Kazakhstan.
Collapse
Affiliation(s)
- Olga Muter
- Faculty of Biology, University of Latvia, 1 Jelgavas Str., LV-1004 Riga, Latvia;
| | - Dita Gudrā
- Latvian Biomedical Research and Study Centre, 1 Ratsupites Str., LV-1067 Riga, Latvia; (D.G.); (M.L.); (D.F.)
| | - Gulzhan Daumova
- School of Geosciences, D. Serikbayev East Kazakhstan Technical University, 19, Serikbayev Str., Ust-Kamenogorsk 070000, Kazakhstan; (G.D.); (Z.I.); (M.R.); (O.P.); (B.A.); (I.D.); (Y.B.); (Z.M.)
| | - Zhanat Idrisheva
- School of Geosciences, D. Serikbayev East Kazakhstan Technical University, 19, Serikbayev Str., Ust-Kamenogorsk 070000, Kazakhstan; (G.D.); (Z.I.); (M.R.); (O.P.); (B.A.); (I.D.); (Y.B.); (Z.M.)
| | - Marzhan Rakhymberdina
- School of Geosciences, D. Serikbayev East Kazakhstan Technical University, 19, Serikbayev Str., Ust-Kamenogorsk 070000, Kazakhstan; (G.D.); (Z.I.); (M.R.); (O.P.); (B.A.); (I.D.); (Y.B.); (Z.M.)
| | - Guntis Tabors
- Faculty of Biology, University of Latvia, 1 Jelgavas Str., LV-1004 Riga, Latvia;
| | - Baiba Dirnēna
- Faculty of Geography and Earth Sciences, University of Latvia, 1 Jelgavas Str., LV-1004 Riga, Latvia; (B.D.); (L.D.); (R.K.)
| | - Linda Dobkeviča
- Faculty of Geography and Earth Sciences, University of Latvia, 1 Jelgavas Str., LV-1004 Riga, Latvia; (B.D.); (L.D.); (R.K.)
| | - Olga Petrova
- School of Geosciences, D. Serikbayev East Kazakhstan Technical University, 19, Serikbayev Str., Ust-Kamenogorsk 070000, Kazakhstan; (G.D.); (Z.I.); (M.R.); (O.P.); (B.A.); (I.D.); (Y.B.); (Z.M.)
| | - Baitak Apshikur
- School of Geosciences, D. Serikbayev East Kazakhstan Technical University, 19, Serikbayev Str., Ust-Kamenogorsk 070000, Kazakhstan; (G.D.); (Z.I.); (M.R.); (O.P.); (B.A.); (I.D.); (Y.B.); (Z.M.)
| | - Megija Luņģe
- Latvian Biomedical Research and Study Centre, 1 Ratsupites Str., LV-1067 Riga, Latvia; (D.G.); (M.L.); (D.F.)
| | - Dāvids Fridmanis
- Latvian Biomedical Research and Study Centre, 1 Ratsupites Str., LV-1067 Riga, Latvia; (D.G.); (M.L.); (D.F.)
| | - Igor Denissov
- School of Geosciences, D. Serikbayev East Kazakhstan Technical University, 19, Serikbayev Str., Ust-Kamenogorsk 070000, Kazakhstan; (G.D.); (Z.I.); (M.R.); (O.P.); (B.A.); (I.D.); (Y.B.); (Z.M.)
| | - Yerkebulan Bekishev
- School of Geosciences, D. Serikbayev East Kazakhstan Technical University, 19, Serikbayev Str., Ust-Kamenogorsk 070000, Kazakhstan; (G.D.); (Z.I.); (M.R.); (O.P.); (B.A.); (I.D.); (Y.B.); (Z.M.)
| | - Raimonds Kasparinskis
- Faculty of Geography and Earth Sciences, University of Latvia, 1 Jelgavas Str., LV-1004 Riga, Latvia; (B.D.); (L.D.); (R.K.)
| | - Zarina Mukulysova
- School of Geosciences, D. Serikbayev East Kazakhstan Technical University, 19, Serikbayev Str., Ust-Kamenogorsk 070000, Kazakhstan; (G.D.); (Z.I.); (M.R.); (O.P.); (B.A.); (I.D.); (Y.B.); (Z.M.)
| | - Stanislav Polezhayev
- Center of Excellence “Veritas”, D. Serikbayev East Kazakhstan Technical University, 19, Serikbayev Str., Ust-Kamenogorsk 070000, Kazakhstan;
| |
Collapse
|
5
|
Valencia EM, Maki KA, Dootz JN, Barb JJ. Mock community taxonomic classification performance of publicly available shotgun metagenomics pipelines. Sci Data 2024; 11:81. [PMID: 38233447 PMCID: PMC10794705 DOI: 10.1038/s41597-023-02877-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 12/22/2023] [Indexed: 01/19/2024] Open
Abstract
Shotgun metagenomic sequencing comprehensively samples the DNA of a microbial sample. Choosing the best bioinformatics processing package can be daunting due to the wide variety of tools available. Here, we assessed publicly available shotgun metagenomics processing packages/pipelines including bioBakery, Just a Microbiology System (JAMS), Whole metaGenome Sequence Assembly V2 (WGSA2), and Woltka using 19 publicly available mock community samples and a set of five constructed pathogenic gut microbiome samples. Also included is a workflow for labelling bacterial scientific names with NCBI taxonomy identifiers for better resolution in assessing results. The Aitchison distance, a sensitivity metric, and total False Positive Relative Abundance were used for accuracy assessments for all pipelines and mock samples. Overall, bioBakery4 performed the best with most of the accuracy metrics, while JAMS and WGSA2, had the highest sensitivities. Furthermore, bioBakery is commonly used and only requires a basic knowledge of command line usage. This work provides an unbiased assessment of shotgun metagenomics packages and presents results assessing the performance of the packages using mock community sequence data.
Collapse
Affiliation(s)
- E Michael Valencia
- Translational Biobehavioral and Health Disparities Branch, National Institutes of Health Clinical Center, Bethesda, MD, 20814, USA
| | - Katherine A Maki
- Translational Biobehavioral and Health Disparities Branch, National Institutes of Health Clinical Center, Bethesda, MD, 20814, USA
| | - Jennifer N Dootz
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Jennifer J Barb
- Translational Biobehavioral and Health Disparities Branch, National Institutes of Health Clinical Center, Bethesda, MD, 20814, USA.
| |
Collapse
|
6
|
Hartmann M, Herzog C, Brunner I, Stierli B, Meyer F, Buchmann N, Frey B. Long-term mitigation of drought changes the functional potential and life-strategies of the forest soil microbiome involved in organic matter decomposition. Front Microbiol 2023; 14:1267270. [PMID: 37840720 PMCID: PMC10570739 DOI: 10.3389/fmicb.2023.1267270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/14/2023] [Indexed: 10/17/2023] Open
Abstract
Climate change can alter the flow of nutrients and energy through terrestrial ecosystems. Using an inverse climate change field experiment in the central European Alps, we explored how long-term irrigation of a naturally drought-stressed pine forest altered the metabolic potential of the soil microbiome and its ability to decompose lignocellulolytic compounds as a critical ecosystem function. Drought mitigation by a decade of irrigation stimulated profound changes in the functional capacity encoded in the soil microbiome, revealing alterations in carbon and nitrogen metabolism as well as regulatory processes protecting microorganisms from starvation and desiccation. Despite the structural and functional shifts from oligotrophic to copiotrophic microbial lifestyles under irrigation and the observation that different microbial taxa were involved in the degradation of cellulose and lignin as determined by a time-series stable-isotope probing incubation experiment with 13C-labeled substrates, degradation rates of these compounds were not affected by different water availabilities. These findings provide new insights into the impact of precipitation changes on the soil microbiome and associated ecosystem functioning in a drought-prone pine forest and will help to improve our understanding of alterations in biogeochemical cycling under a changing climate.
Collapse
Affiliation(s)
- Martin Hartmann
- Department of Environmental Systems Science, Sustainable Agroecosystems, Institute of Agricultural Sciences, ETH Zürich, Zürich, Switzerland
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Claude Herzog
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
- Department of Environmental Systems Science, Grassland Sciences, Institute of Agricultural Sciences, ETH Zürich, Zürich, Switzerland
| | - Ivano Brunner
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Beat Stierli
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Folker Meyer
- Data Science, Institute for AI in Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Argonne National Laboratory, Argonne, IL, United States
- Computation Institute, University of Chicago, Chicago, IL, United States
- Department of Medicine, University of Chicago, Chicago, IL, United States
| | - Nina Buchmann
- Department of Environmental Systems Science, Grassland Sciences, Institute of Agricultural Sciences, ETH Zürich, Zürich, Switzerland
| | - Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| |
Collapse
|
7
|
Medina-Chávez NO, Viladomat-Jasso M, Zarza E, Islas-Robles A, Valdivia-Anistro J, Thalasso-Siret F, Eguiarte LE, Olmedo-Álvarez G, Souza V, De la Torre-Zavala S. A Transiently Hypersaline Microbial Mat Harbors a Diverse and Stable Archaeal Community in the Cuatro Cienegas Basin, Mexico. ASTROBIOLOGY 2023; 23:796-811. [PMID: 37279013 DOI: 10.1089/ast.2021.0047] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Microbial mats are biologically diverse communities that are analogs to some of the earliest ecosystems on Earth. In this study, we describe a unique transiently hypersaline microbial mat uncovered in a shallow pond within the Cuatro Cienegas Basin (CCB) in northern México. The CCB is an endemism-rich site that harbors living stromatolites that have been studied to understand the conditions of the Precambrian Earth. These microbial mats form elastic domes filled with biogenic gas, and the mats have a relatively large and stable subpopulation of archaea. For this reason, this site has been termed archaean domes (AD). The AD microbial community was analyzed by metagenomics over three seasons. The mat exhibited a highly diverse prokaryotic community dominated by bacteria. Bacterial sequences are represented in 37 phyla, mainly Proteobacteria, Firmicutes, and Actinobacteria, that together comprised >50% of the sequences from the mat. Archaea represented up to 5% of the retrieved sequences, with up to 230 different archaeal species that belong to 5 phyla (Euryarchaeota, Crenarchaeota, Thaumarchaeota, Korarchaeota, and Nanoarchaeota). The archaeal taxa showed low variation despite fluctuations in water and nutrient availability. In addition, predicted functions highlight stress responses to extreme conditions present in the AD, including salinity, pH, and water/drought fluctuation. The observed complexity of the AD mat thriving in high pH and fluctuating water and salt conditions within the CCB provides an extant model of great value for evolutionary studies, as well as a suitable analog to the early Earth and Mars.
Collapse
Affiliation(s)
- Nahui-Olin Medina-Chávez
- Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, USA
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, Instituto de Biotecnología, San Nicolás de los Garza, México
| | | | - Eugenia Zarza
- Departamento de Ciencias de la Sustentabilidad, El Colegio de la Frontera Sur, Tapachula, Mexico
- Consejo Nacional de Ciencia y Tecnología, Ciudad de México, México
| | - Africa Islas-Robles
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del I.P.N. Campus Irapuato, Irapuato, México
| | - Jorge Valdivia-Anistro
- Unidad Multidisciplinaria de Investigación Experimental Zaragoza, Facultad de Estudios Superiores Zaragoza, UNAM, Ciudad de México, México
| | - Frédéric Thalasso-Siret
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Luis E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, UNAM, Ciudad de México, México
- Centro de Estudios del Cuaternario de Fuego-Patagonia y Antártica (CEQUA), Punta Arenas, Chile
| | - Gabriela Olmedo-Álvarez
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del I.P.N. Campus Irapuato, Irapuato, México
| | - Valeria Souza
- Departamento de Ecología Evolutiva, Instituto de Ecología, UNAM, Ciudad de México, México
- Centro de Estudios del Cuaternario de Fuego-Patagonia y Antártica (CEQUA), Punta Arenas, Chile
| | - Susana De la Torre-Zavala
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, Instituto de Biotecnología, San Nicolás de los Garza, México
| |
Collapse
|
8
|
Santiago BCF, de Souza ID, Cavalcante JVF, Morais DAA, da Silva MB, Pasquali MADB, Dalmolin RJS. Metagenomic Analyses Reveal the Influence of Depth Layers on Marine Biodiversity on Tropical and Subtropical Regions. Microorganisms 2023; 11:1668. [PMID: 37512841 PMCID: PMC10386303 DOI: 10.3390/microorganisms11071668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/07/2023] [Accepted: 06/10/2023] [Indexed: 07/30/2023] Open
Abstract
The emergence of open ocean global-scale studies provided important information about the genomics of oceanic microbial communities. Metagenomic analyses shed light on the structure of marine habitats, unraveling the biodiversity of different water masses. Many biological and environmental factors can contribute to marine organism composition, such as depth. However, much remains unknown about microbial communities' taxonomic and functional features in different water layer depths. Here, we performed a metagenomic analysis of 76 publicly available samples from the Tara Ocean Project, distributed in 8 collection stations located in tropical or subtropical regions, and sampled from three layers of depth (surface water layer-SRF, deep chlorophyll maximum layer-DCM, and mesopelagic zone-MES). The SRF and DCM depth layers are similar in abundance and diversity, while the MES layer presents greater diversity than the other layers. Diversity clustering analysis shows differences regarding the taxonomic content of samples. At the domain level, bacteria prevail in most samples, and the MES layer presents the highest proportion of archaea among all samples. Taken together, our results indicate that the depth layer influences microbial sample composition and diversity.
Collapse
Affiliation(s)
- Bianca C F Santiago
- Bioinformatics Multidisciplinary Environment-IMD, Federal University of Rio Grande do Norte, Natal 59078-400, Brazil
| | - Iara D de Souza
- Bioinformatics Multidisciplinary Environment-IMD, Federal University of Rio Grande do Norte, Natal 59078-400, Brazil
| | - João Vitor F Cavalcante
- Bioinformatics Multidisciplinary Environment-IMD, Federal University of Rio Grande do Norte, Natal 59078-400, Brazil
| | - Diego A A Morais
- Bioinformatics Multidisciplinary Environment-IMD, Federal University of Rio Grande do Norte, Natal 59078-400, Brazil
| | - Mikaelly B da Silva
- Food Engineering Department, Federal University of Campina Grande, Campina Grande 58401-490, Brazil
| | | | - Rodrigo J S Dalmolin
- Bioinformatics Multidisciplinary Environment-IMD, Federal University of Rio Grande do Norte, Natal 59078-400, Brazil
- Department of Biochemistry-CB, Federal University of Rio Grande do Norte, Natal 59078-970, Brazil
| |
Collapse
|
9
|
Wright RJ, Comeau AM, Langille MGI. From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools. Microb Genom 2023; 9. [PMID: 36867161 PMCID: PMC10132073 DOI: 10.1099/mgen.0.000949] [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: 03/04/2023] Open
Abstract
In metagenomic analyses of microbiomes, one of the first steps is usually the taxonomic classification of reads by comparison to a database of previously taxonomically classified genomes. While different studies comparing metagenomic taxonomic classification methods have determined that different tools are 'best', there are two tools that have been used the most to-date: Kraken (k-mer-based classification against a user-constructed database) and MetaPhlAn (classification by alignment to clade-specific marker genes), the latest versions of which are Kraken2 and MetaPhlAn 3, respectively. We found large discrepancies in both the proportion of reads that were classified as well as the number of species that were identified when we used both Kraken2 and MetaPhlAn 3 to classify reads within metagenomes from human-associated or environmental datasets. We then investigated which of these tools would give classifications closest to the real composition of metagenomic samples using a range of simulated and mock samples and examined the combined impact of tool-parameter-database choice on the taxonomic classifications given. This revealed that there may not be a one-size-fits-all 'best' choice. While Kraken2 can achieve better overall performance, with higher precision, recall and F1 scores, as well as alpha- and beta-diversity measures closer to the known composition than MetaPhlAn 3, the computational resources required for this may be prohibitive for many researchers, and the default database and parameters should not be used. We therefore conclude that the best tool-parameter-database choice for a particular application depends on the scientific question of interest, which performance metric is most important for this question and the limit of available computational resources.
Collapse
Affiliation(s)
- Robyn J Wright
- Department of Pharmacology, Faculty of Medicine, Dalhousie University, Halifax, Canada
| | - Andrè M Comeau
- Integrated Microbiome Resource (IMR), Dalhousie University, Halifax, Canada
| | - Morgan G I Langille
- Department of Pharmacology, Faculty of Medicine, Dalhousie University, Halifax, Canada.,Integrated Microbiome Resource (IMR), Dalhousie University, Halifax, Canada
| |
Collapse
|
10
|
Zafeiropoulos H, Beracochea M, Ninidakis S, Exter K, Potirakis A, De Moro G, Richardson L, Corre E, Machado J, Pafilis E, Kotoulas G, Santi I, Finn RD, Cox CJ, Pavloudi C. metaGOflow: a workflow for the analysis of marine Genomic Observatories shotgun metagenomics data. Gigascience 2022; 12:giad078. [PMID: 37850871 PMCID: PMC10583283 DOI: 10.1093/gigascience/giad078] [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: 05/10/2023] [Revised: 06/30/2023] [Accepted: 09/11/2023] [Indexed: 10/19/2023] Open
Abstract
BACKGROUND Genomic Observatories (GOs) are sites of long-term scientific study that undertake regular assessments of the genomic biodiversity. The European Marine Omics Biodiversity Observation Network (EMO BON) is a network of GOs that conduct regular biological community samplings to generate environmental and metagenomic data of microbial communities from designated marine stations around Europe. The development of an effective workflow is essential for the analysis of the EMO BON metagenomic data in a timely and reproducible manner. FINDINGS Based on the established MGnify resource, we developed metaGOflow. metaGOflow supports the fast inference of taxonomic profiles from GO-derived data based on ribosomal RNA genes and their functional annotation using the raw reads. Thanks to the Research Object Crate packaging, relevant metadata about the sample under study, and the details of the bioinformatics analysis it has been subjected to, are inherited to the data product while its modular implementation allows running the workflow partially. The analysis of 2 EMO BON samples and 1 Tara Oceans sample was performed as a use case. CONCLUSIONS metaGOflow is an efficient and robust workflow that scales to the needs of projects producing big metagenomic data such as EMO BON. It highlights how containerization technologies along with modern workflow languages and metadata package approaches can support the needs of researchers when dealing with ever-increasing volumes of biological data. Despite being initially oriented to address the needs of EMO BON, metaGOflow is a flexible and easy-to-use workflow that can be broadly used for one-sample-at-a-time analysis of shotgun metagenomics data.
Collapse
Affiliation(s)
- Haris Zafeiropoulos
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Former U.S. Base of Gournes, 71003 Heraklion, Crete, Greece
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, 3000 Leuven, Belgium
| | - Martin Beracochea
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stelios Ninidakis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Former U.S. Base of Gournes, 71003 Heraklion, Crete, Greece
| | - Katrina Exter
- Flanders Marine Institute (VLIZ), 8400 Oostende, Belgium
| | - Antonis Potirakis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Former U.S. Base of Gournes, 71003 Heraklion, Crete, Greece
| | - Gianluca De Moro
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Lorna Richardson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Erwan Corre
- CNRS, FR 2424, ABiMS Platform, Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - João Machado
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Evangelos Pafilis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Former U.S. Base of Gournes, 71003 Heraklion, Crete, Greece
| | - Georgios Kotoulas
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Former U.S. Base of Gournes, 71003 Heraklion, Crete, Greece
| | - Ioulia Santi
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Former U.S. Base of Gournes, 71003 Heraklion, Crete, Greece
- European Marine Biological Resource Centre (EMBRC-ERIC), 75005 Paris, France
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Cymon J Cox
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Christina Pavloudi
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Former U.S. Base of Gournes, 71003 Heraklion, Crete, Greece
- Department of Biological Sciences, The George Washington University, 20052 Washington, DC, USA
| |
Collapse
|
11
|
Portik DM, Brown CT, Pierce-Ward NT. Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets. BMC Bioinformatics 2022; 23:541. [PMID: 36513983 PMCID: PMC9749362 DOI: 10.1186/s12859-022-05103-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Long-read shotgun metagenomic sequencing is gaining in popularity and offers many advantages over short-read sequencing. The higher information content in long reads is useful for a variety of metagenomics analyses, including taxonomic classification and profiling. The development of long-read specific tools for taxonomic classification is accelerating, yet there is a lack of information regarding their relative performance. Here, we perform a critical benchmarking study using 11 methods, including five methods designed specifically for long reads. We applied these tools to several mock community datasets generated using Pacific Biosciences (PacBio) HiFi or Oxford Nanopore Technology sequencing, and evaluated their performance based on read utilization, detection metrics, and relative abundance estimates. RESULTS Our results show that long-read classifiers generally performed best. Several short-read classification and profiling methods produced many false positives (particularly at lower abundances), required heavy filtering to achieve acceptable precision (at the cost of reduced recall), and produced inaccurate abundance estimates. By contrast, two long-read methods (BugSeq, MEGAN-LR & DIAMOND) and one generalized method (sourmash) displayed high precision and recall without any filtering required. Furthermore, in the PacBio HiFi datasets these methods detected all species down to the 0.1% abundance level with high precision. Some long-read methods, such as MetaMaps and MMseqs2, required moderate filtering to reduce false positives to resemble the precision and recall of the top-performing methods. We found read quality affected performance for methods relying on protein prediction or exact k-mer matching, and these methods performed better with PacBio HiFi datasets. We also found that long-read datasets with a large proportion of shorter reads (< 2 kb length) resulted in lower precision and worse abundance estimates, relative to length-filtered datasets. Finally, for classification methods, we found that the long-read datasets produced significantly better results than short-read datasets, demonstrating clear advantages for long-read metagenomic sequencing. CONCLUSIONS Our critical assessment of available methods provides best-practice recommendations for current research using long reads and establishes a baseline for future benchmarking studies.
Collapse
Affiliation(s)
- Daniel M. Portik
- grid.423340.20000 0004 0640 9878Pacific Biosciences, 1305 O’Brien Dr, Menlo Park, CA 93025 USA
| | - C. Titus Brown
- grid.27860.3b0000 0004 1936 9684Department of Population Health and Reproduction, University of California Davis, Davis, CA USA
| | - N. Tessa Pierce-Ward
- grid.27860.3b0000 0004 1936 9684Department of Population Health and Reproduction, University of California Davis, Davis, CA USA
| |
Collapse
|
12
|
Vuong P, Wise MJ, Whiteley AS, Kaur P. Ten simple rules for investigating (meta)genomic data from environmental ecosystems. PLoS Comput Biol 2022; 18:e1010675. [PMID: 36480496 PMCID: PMC9731419 DOI: 10.1371/journal.pcbi.1010675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Paton Vuong
- UWA School of Agriculture & Environment, University of Western Australia, Perth, Australia
| | - Michael J. Wise
- School of Physics, Mathematics and Computing, University of Western Australia, Perth, Australia
- The Marshall Centre of Infectious Diseases, School of Biological Sciences, The University of Western Australia, Perth, Australia
| | - Andrew S. Whiteley
- Centre for Environment & Life Sciences, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Floreat, Australia
| | - Parwinder Kaur
- UWA School of Agriculture & Environment, University of Western Australia, Perth, Australia
- * E-mail:
| |
Collapse
|
13
|
Singh AK, Kumari M, Sharma N, Rai AK, Singh SP. Metagenomic views on taxonomic and functional profiles of the Himalayan Tsomgo cold lake and unveiling its deterzome potential. Curr Genet 2022; 68:565-579. [PMID: 35927361 DOI: 10.1007/s00294-022-01247-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 07/08/2022] [Accepted: 07/17/2022] [Indexed: 12/14/2022]
Abstract
Cold habitat is considered a potential source for detergent industry enzymes. This study aims at the metagenomic investigation of Tsomgo lake for taxonomic and functional annotation, unveiling the deterzome potential of the residing microbiota at this site. The present investigation revealed molecular profiling of microbial community structure and functional potential of the high-altitude Tsomgo lake samples of two different temperatures, harvested during March and August. Bacteria were found to be the most dominant phyla, with traces of genomic pieces of evidence belonging to archaea, viruses, and eukaryotes. Proteobacteria and Actinobacteria were noted to be the most abundant bacterial phyla in the cold lake. In-depth metagenomic investigation of the cold aquatic habitat revealed novel genes encoding detergent enzymes, amylase, protease, and lipase. Further, metagenome-assembled genomes (MAGs) belonging to the psychrophilic bacterium, Arthrobacter alpinus, were constructed from the metagenomic data. The annotation depicted the presence of detergent enzymes and genes for low-temperature adaptation in Arthrobacter alpinus. Psychrophilic microbial isolates were screened for lipase, protease, and amylase activities to further strengthen the metagenomic findings. A novel strain of Acinetobacter sp. was identified with the dual enzymatic activity of protease and amylase. The bacterial isolates exhibited hydrolyzing activity at low temperatures. This metagenomic study divulged novel genomic resources for detergent industry enzymes, and the bacterial isolates secreting cold-active amylase, lipase, and protease enzymes. The findings manifest that Tsomgo lake is a potential bioresource of cold-active enzymes, vital for various industrial applications.
Collapse
Affiliation(s)
- Ashutosh Kumar Singh
- Center of Innovative and Applied Bioprocessing (DBT-CIAB), Sector 81, SAS Nagar, Mohali, India
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Megha Kumari
- Institute of Bioresources and Sustainable Development (DBT-IBSD), Regional Centre, Tadong, Gangtok, Sikkim, India
| | - Nitish Sharma
- Center of Innovative and Applied Bioprocessing (DBT-CIAB), Sector 81, SAS Nagar, Mohali, India
| | - Amit Kumar Rai
- Institute of Bioresources and Sustainable Development (DBT-IBSD), Regional Centre, Tadong, Gangtok, Sikkim, India.
| | - Sudhir P Singh
- Center of Innovative and Applied Bioprocessing (DBT-CIAB), Sector 81, SAS Nagar, Mohali, India.
| |
Collapse
|
14
|
Matharu D, Ponsero AJ, Dikareva E, Korpela K, Kolho KL, de Vos WM, Salonen A. Bacteroides abundance drives birth mode dependent infant gut microbiota developmental trajectories. Front Microbiol 2022; 13:953475. [PMID: 36274732 PMCID: PMC9583133 DOI: 10.3389/fmicb.2022.953475] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 09/07/2022] [Indexed: 11/13/2022] Open
Abstract
Background and aims Birth mode and other early life factors affect a newborn's microbial colonization with potential long-term health effects. Individual variations in early life gut microbiota development, especially their effects on the functional repertoire of microbiota, are still poorly characterized. This study aims to provide new insights into the gut microbiome developmental trajectories during the first year of life. Methods Our study comprised 78 term infants sampled at 3 weeks, 3 months, 6 months, and 12 months (n = 280 total samples), and their mothers were sampled in late pregnancy (n = 50). Fecal DNA was subjected to shotgun metagenomic sequencing. Infant samples were studied for taxonomic and functional maturation, and maternal microbiota was used as a reference. Hierarchical clustering on taxonomic profiles was used to identify the main microbiota developmental trajectories in the infants, and their associations with perinatal and postnatal factors were assessed. Results In line with previous studies, infant microbiota composition showed increased alpha diversity and decreased beta diversity by age, converging toward an adult-like profile. However, we did not observe an increase in functional alpha diversity, which was stable and comparable with the mother samples throughout all the sampling points. Using a de novo clustering approach, two main infant microbiota clusters driven by Bacteroidaceae and Clostridiaceae emerged at each time point. The clusters were associated with birth mode and their functions differed mainly in terms of biosynthetic and carbohydrate degradation pathways, some of which consistently differed between the clusters for all the time points. The longitudinal analysis indicated three main microbiota developmental trajectories, with the majority of the infants retaining their characteristic cluster until 1 year. As many as 40% of vaginally delivered infants were grouped with infants delivered by C-section due to their clear and persistent depletion in Bacteroides. Intrapartum antibiotics, any perinatal or postnatal factors, maternal microbiota composition, or other maternal factors did not explain the depletion in Bacteroides in the subset of vaginally born infants. Conclusion Our study provides an enhanced understanding of the compositional and functional early life gut microbiota trajectories, opening avenues for investigating elusive causes that influence non-typical microbiota development.
Collapse
Affiliation(s)
- Dollwin Matharu
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Alise J. Ponsero
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Biosystems Engineering and BIO5 Institute, University of Arizona, Tucson, AZ, United States
| | - Evgenia Dikareva
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Katri Korpela
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Kaija-Leena Kolho
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Children's Hospital, Pediatric Research Center, University of Helsinki and HUS, Helsinki, Finland
- Faculty of Medicine and Health Technology, University of Tampere, Tampere, Finland
| | - Willem M. de Vos
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | - Anne Salonen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| |
Collapse
|
15
|
Escudeiro P, Henry CS, Dias RP. Functional characterization of prokaryotic dark matter: the road so far and what lies ahead. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100159. [PMID: 36561390 PMCID: PMC9764257 DOI: 10.1016/j.crmicr.2022.100159] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 07/18/2022] [Accepted: 08/05/2022] [Indexed: 12/25/2022] Open
Abstract
Eight-hundred thousand to one trillion prokaryotic species may inhabit our planet. Yet, fewer than two-hundred thousand prokaryotic species have been described. This uncharted fraction of microbial diversity, and its undisclosed coding potential, is known as the "microbial dark matter" (MDM). Next-generation sequencing has allowed to collect a massive amount of genome sequence data, leading to unprecedented advances in the field of genomics. Still, harnessing new functional information from the genomes of uncultured prokaryotes is often limited by standard classification methods. These methods often rely on sequence similarity searches against reference genomes from cultured species. This hinders the discovery of unique genetic elements that are missing from the cultivated realm. It also contributes to the accumulation of prokaryotic gene products of unknown function among public sequence data repositories, highlighting the need for new approaches for sequencing data analysis and classification. Increasing evidence indicates that these proteins of unknown function might be a treasure trove of biotechnological potential. Here, we outline the challenges, opportunities, and the potential hidden within the functional dark matter (FDM) of prokaryotes. We also discuss the pitfalls surrounding molecular and computational approaches currently used to probe these uncharted waters, and discuss future opportunities for research and applications.
Collapse
Affiliation(s)
- Pedro Escudeiro
- BioISI - Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal
| | - Christopher S. Henry
- Argonne National Laboratory, Lemont, Illinois, USA,University of Chicago, Chicago, Illinois, USA
| | - Ricardo P.M. Dias
- BioISI - Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal,iXLab - Innovation for National Biological Resilience, Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal,Corresponding author.
| |
Collapse
|
16
|
Sharon I, Quijada NM, Pasolli E, Fabbrini M, Vitali F, Agamennone V, Dötsch A, Selberherr E, Grau JH, Meixner M, Liere K, Ercolini D, de Filippo C, Caderni G, Brigidi P, Turroni S. The Core Human Microbiome: Does It Exist and How Can We Find It? A Critical Review of the Concept. Nutrients 2022; 14:nu14142872. [PMID: 35889831 PMCID: PMC9323970 DOI: 10.3390/nu14142872] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/06/2022] [Accepted: 07/08/2022] [Indexed: 11/16/2022] Open
Abstract
The core microbiome, which refers to a set of consistent microbial features across populations, is of major interest in microbiome research and has been addressed by numerous studies. Understanding the core microbiome can help identify elements that lead to dysbiosis, and lead to treatments for microbiome-related health states. However, defining the core microbiome is a complex task at several levels. In this review, we consider the current state of core human microbiome research. We consider the knowledge that has been gained, the factors limiting our ability to achieve a reliable description of the core human microbiome, and the fields most likely to improve that ability. DNA sequencing technologies and the methods for analyzing metagenomics and amplicon data will most likely facilitate higher accuracy and resolution in describing the microbiome. However, more effort should be invested in characterizing the microbiome’s interactions with its human host, including the immune system and nutrition. Other components of this holobiontic system should also be emphasized, such as fungi, protists, lower eukaryotes, viruses, and phages. Most importantly, a collaborative effort of experts in microbiology, nutrition, immunology, medicine, systems biology, bioinformatics, and machine learning is probably required to identify the traits of the core human microbiome.
Collapse
Affiliation(s)
- Itai Sharon
- Migal-Galilee Research Institute, P.O. Box 831, Kiryat Shmona 11016, Israel
- Faculty of Sciences and Technology, Tel-Hai Academic College, Upper Galilee 1220800, Israel
- Correspondence:
| | - Narciso Martín Quijada
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, A-1210 Vienna, Austria; (N.M.Q.); (E.S.)
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, FFoQSI GmbH, A-3430 Tulln an der Donau, Austria
| | - Edoardo Pasolli
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, 80055 Portici, Italy; (E.P.); (D.E.)
- Task Force on Microbiome Studies, University of Naples Federico II, 80055 Portici, Italy
| | - Marco Fabbrini
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy; (M.F.); (S.T.)
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy;
| | - Francesco Vitali
- Institute of Agricultural Biology and Biotechnology (IBBA), National Research Council (CNR), Via Moruzzi 1, 56124 Pisa, Italy; (F.V.); (C.d.F.)
| | - Valeria Agamennone
- Microbiology and Systems Biology, Netherlands Organization for Applied Scientific Research (TNO), Utrechtseweg 48, 3704 HE Zeist, The Netherlands;
| | - Andreas Dötsch
- Department of Physiology and Biochemistry of Nutrition, Max Rubner-Institut (MRI)-Federal Research Institute of Nutrition and Food, 76131 Karlsruhe, Germany;
| | - Evelyne Selberherr
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, A-1210 Vienna, Austria; (N.M.Q.); (E.S.)
| | - José Horacio Grau
- Amedes Genetics, Amedes Medizinische Dienstleistungen GmbH, 10117 Berlin, Germany; (J.H.G.); (M.M.); (K.L.)
- Center for Species Survival, Smithsonian Conservation Biology Institute, Washington, DC 20008, USA
| | - Martin Meixner
- Amedes Genetics, Amedes Medizinische Dienstleistungen GmbH, 10117 Berlin, Germany; (J.H.G.); (M.M.); (K.L.)
| | - Karsten Liere
- Amedes Genetics, Amedes Medizinische Dienstleistungen GmbH, 10117 Berlin, Germany; (J.H.G.); (M.M.); (K.L.)
| | - Danilo Ercolini
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, 80055 Portici, Italy; (E.P.); (D.E.)
- Task Force on Microbiome Studies, University of Naples Federico II, 80055 Portici, Italy
| | - Carlotta de Filippo
- Institute of Agricultural Biology and Biotechnology (IBBA), National Research Council (CNR), Via Moruzzi 1, 56124 Pisa, Italy; (F.V.); (C.d.F.)
| | - Giovanna Caderni
- NEUROFARBA Department, Pharmacology and Toxicology Section, University of Florence, Viale Pieraccini 6, 50139 Florence, Italy;
| | - Patrizia Brigidi
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy;
| | - Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy; (M.F.); (S.T.)
| |
Collapse
|
17
|
Hoarfrost A, Aptekmann A, Farfañuk G, Bromberg Y. Deep learning of a bacterial and archaeal universal language of life enables transfer learning and illuminates microbial dark matter. Nat Commun 2022; 13:2606. [PMID: 35545619 PMCID: PMC9095714 DOI: 10.1038/s41467-022-30070-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 03/30/2022] [Indexed: 12/22/2022] Open
Abstract
The majority of microbial genomes have yet to be cultured, and most proteins identified in microbial genomes or environmental sequences cannot be functionally annotated. As a result, current computational approaches to describe microbial systems rely on incomplete reference databases that cannot adequately capture the functional diversity of the microbial tree of life, limiting our ability to model high-level features of biological sequences. Here we present LookingGlass, a deep learning model encoding contextually-aware, functionally and evolutionarily relevant representations of short DNA reads, that distinguishes reads of disparate function, homology, and environmental origin. We demonstrate the ability of LookingGlass to be fine-tuned via transfer learning to perform a range of diverse tasks: to identify novel oxidoreductases, to predict enzyme optimal temperature, and to recognize the reading frames of DNA sequence fragments. LookingGlass enables functionally relevant representations of otherwise unknown and unannotated sequences, shedding light on the microbial dark matter that dominates life on Earth. Computational methods to analyse microbial systems rely on reference databases which do not capture their full functional diversity. Here the authors develop a deep learning model and apply it using transfer learning, creating biologically useful models for multiple different tasks.
Collapse
Affiliation(s)
- A Hoarfrost
- Department of Marine and Coastal Sciences, Rutgers University, 71 Dudley Road, New Brunswick, NJ, 08873, USA. .,NASA Ames Research Center, Moffett Field, CA, 94035, USA.
| | - A Aptekmann
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ, 08901, USA
| | - G Farfañuk
- Department of Biological Chemistry, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Y Bromberg
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Dr, New Brunswick, NJ, 08901, USA.
| |
Collapse
|
18
|
Inferring Species Compositions of Complex Fungal Communities from Long- and Short-Read Sequence Data. mBio 2022; 13:e0244421. [PMID: 35404122 PMCID: PMC9040722 DOI: 10.1128/mbio.02444-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Our study is unique in that it provides an in-depth comparative study of a real-life complex fungal community analyzed with multiple long- and short-read sequencing approaches. These technologies and their application are currently of great interest to diverse biologists as they seek to characterize the community compositions of microbiomes.
Collapse
|
19
|
Frey B, Varliero G, Qi W, Stierli B, Walthert L, Brunner I. Shotgun Metagenomics of Deep Forest Soil Layers Show Evidence of Altered Microbial Genetic Potential for Biogeochemical Cycling. Front Microbiol 2022; 13:828977. [PMID: 35300488 PMCID: PMC8921678 DOI: 10.3389/fmicb.2022.828977] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 02/11/2022] [Indexed: 11/29/2022] Open
Abstract
Soil microorganisms such as Bacteria and Archaea play important roles in the biogeochemical cycling of soil nutrients, because they act as decomposers or are mutualistic or antagonistic symbionts, thereby influencing plant growth and health. In the present study, we investigated the vertical distribution of soil metagenomes to a depth of 1.5 m in Swiss forests of European beech and oak species on calcareous bedrock. We explored the functional genetic potential of soil microorganisms with the aim to disentangle the effects of tree genus and soil depth on the genetic repertoire, and to gain insight into the microbial C and N cycling. The relative abundance of reads assigned to taxa at the domain level indicated a 5–10 times greater abundance of Archaea in the deep soil, while Bacteria showed no change with soil depth. In the deep soil there was an overrepresentation of genes for carbohydrate-active enzymes, which are involved in the catalyzation of the transfer of oligosaccharides, as well as in the binding of carbohydrates such as chitin or cellulose. In addition, N-cycling genes (NCyc) involved in the degradation and synthesis of N compounds, in nitrification and denitrification, and in nitrate reduction were overrepresented in the deep soil. Consequently, our results indicate that N-transformation in the deep soil is affected by soil depth and that N is used not only for assimilation but also for energy conservation, thus indicating conditions of low oxygen in the deep soil. Using shotgun metagenomics, our study provides initial findings on soil microorganisms and their functional genetic potential, and how this may change depending on soil properties, which shift with increasing soil depth. Thus, our data provide novel, deeper insight into the “dark matter” of the soil.
Collapse
Affiliation(s)
- Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Gilda Varliero
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland.,Centre for Microbial Ecology and Genomics, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Weihong Qi
- Functional Genomics Center Zurich (FGCZ), ETH Zürich/University of Zurich, Zurich, Switzerland
| | - Beat Stierli
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Lorenz Walthert
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Ivano Brunner
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| |
Collapse
|
20
|
Gao Y, Zhu Z, Sun F. Increasing prediction performance of colorectal cancer disease status using random forests classification based on metagenomic shotgun sequencing data. Synth Syst Biotechnol 2022; 7:574-585. [PMID: 35155839 PMCID: PMC8801753 DOI: 10.1016/j.synbio.2022.01.005] [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] [Received: 11/01/2021] [Revised: 12/14/2021] [Accepted: 01/19/2022] [Indexed: 12/14/2022] Open
Abstract
Dysfunction of microbial communities in various human body sites has been shown to be associated with a variety of diseases raising the possibility of predicting diseases based on metagenomic samples. Although many studies have investigated this problem, there are no consensus on the optimal approaches for predicting disease status based on metagenomic samples. Using six human gut metagenomic datasets consisting of large numbers of colorectal cancer patients and healthy controls from different countries, we investigated different software packages for extracting relative abundances of known microbial genomes and for integrating mapping and assembly approaches to obtain the relative abundance profiles of both known and novel genomes. The random forests (RF) classification algorithm was then used to predict colorectal cancer status based on the microbial relative abundance profiles. Based on within data cross-validation and cross-dataset prediction, we show that the RF prediction performance using the microbial relative abundance profiles estimated by Centrifuge is generally higher than that using the microbial relative abundance profiles estimated by MetaPhlAn2 and Bracken. We also develop a novel method to integrate the relative abundance profiles of both known and novel microbial organisms to further increase the prediction performance for colorectal cancer from metagenomes.
Collapse
|
21
|
Vuong P, Wise MJ, Whiteley AS, Kaur P. Small investments with big returns: environmental genomic bioprospecting of microbial life. Crit Rev Microbiol 2022; 48:641-655. [PMID: 35100064 DOI: 10.1080/1040841x.2021.2011833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Microorganisms and their natural products are major drivers of ecological processes and industrial applications. Microbial bioprospecting has been critical for the advancement in various fields such as pharmaceuticals, sustainable industries, food security and bioremediation. Next generation sequencing has been paramount in the exploration of diverse environmental microbiomes. It presents a culture-independent approach to investigating hitherto uncultured taxa, resulting in the creation of massive sequence databases, which are available in the public domain. Genome mining searches available (meta)genomic data for target biosynthetic genes, and combined with the large-scale public data, this in-silico bioprospecting method presents an efficient and extensive way to uncover microbial bioproducts. Bioinformatic tools have progressed to a stage where we can recover genomes from the environment; these metagenome-assembled genomes present a way to understand the metabolic capacity of microorganisms in a physiological and ecological context. Environmental sampling been extensive across various ecological settings, including microbiomes with unique physicochemical properties that could influence the discovery of novel functions and metabolic pathways. Although in-silico methods cannot completely substitute in-vitro studies, the contextual information it provides is invaluable for understanding the ecological and taxonomic distribution of microbial genotypes and to form effective strategies for future microbial bioprospecting efforts.
Collapse
Affiliation(s)
- Paton Vuong
- UWA School of Agriculture & Environment, University of Western Australia, Perth, Australia
| | - Michael J Wise
- School of Physics, Mathematics and Computing, University of Western Australia, Perth, Australia
| | - Andrew S Whiteley
- Centre for Environment & Life Sciences, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Floreat, Australia
| | - Parwinder Kaur
- UWA School of Agriculture & Environment, University of Western Australia, Perth, Australia
| |
Collapse
|
22
|
Complex marine microbial communities partition metabolism of scarce resources over the diel cycle. Nat Ecol Evol 2022; 6:218-229. [DOI: 10.1038/s41559-021-01606-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/01/2021] [Indexed: 12/20/2022]
|
23
|
Pust MM, Tümmler B. Bacterial low-abundant taxa are key determinants of a healthy airway metagenome in the early years of human life. Comput Struct Biotechnol J 2021; 20:175-186. [PMID: 35024091 PMCID: PMC8713036 DOI: 10.1016/j.csbj.2021.12.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 12/06/2021] [Accepted: 12/06/2021] [Indexed: 11/17/2022] Open
Abstract
The default removal of low-abundance (rare) taxa from microbial community analyses may lead to an incomplete picture of the taxonomic and functional microbial potential within the human habitat. Publicly available shotgun metagenomics data of healthy children and children with cystic fibrosis (CF) were reanalysed to study the development of the rare species biosphere, which was here defined by either the 15th, 25th or 35th species abundance percentile. We found that healthy children contained an age-independent network of abundant (core) and rare species with both entities being essential in maintaining the network structure. The protein sequence usage for more than 100 bacterial metabolic pathways differed between the core and rare species biosphere. In CF children, the background structure was underdeveloped and random forest bootstrapping based on all constituents of the early airway metagenome and host-associated factors indicated that rare taxa were the most important variables in deciding whether a child was healthy or suffered from the life-limiting CF disease. Attempts failed to make the age-independent CF network as robust as the healthy structure when an increasing number of bacterial taxa from the healthy network was incorporated into the CF structure by computer-based model simulations. However, the transfer of a key combination of taxa from the healthy to the CF network structure with high species diversity and low species dominance, correlated with a more robust CF network and a topological approximation of CF and healthy graph structures. Rothia mucilaginosa, Streptococci and rare species were essential in improving the underdeveloped CF network.
Collapse
Affiliation(s)
- Marie-Madlen Pust
- Department of Paediatric Pneumology, Allergology, and Neonatology, Hannover Medical School (MHH), Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Germany
| | - Burkhard Tümmler
- Department of Paediatric Pneumology, Allergology, and Neonatology, Hannover Medical School (MHH), Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Germany
| |
Collapse
|
24
|
Yan L, Tang L, Zhou Z, Lu W, Wang B, Sun Z, Jiang X, Hu D, Li J, Zhang D. Metagenomics reveals contrasting energy utilization efficiencies of captive and wild camels (Camelus ferus). Integr Zool 2021; 17:333-345. [PMID: 34520120 DOI: 10.1111/1749-4877.12585] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Captive conditions can affect the symbiotic microbiome of animals. In this study, we compared the structural and functional differences of the gastrointestinal microbiomes of wild Bactrian camels (Camelus ferus) between wild and captive populations, as well as their different host energy utilization performances through metagenomics. The results showed that wild-living camels harbored more microbial taxa related to the production of volatile fatty acids, fewer methanogens, and fewer genes encoding enzymes involved in methanogenesis, leading to higher energy utilization efficiency compared to that of captive-living camels. These findings suggest that the wild-living camel fecal microbiome demonstrates a series of adaptive characteristics that enable the host to adjust to a relatively barren field environment. Our study provides novel insights into the mechanisms of wildlife adaptations to habitats from the perspective of the microbiome.
Collapse
Affiliation(s)
- Liping Yan
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Liping Tang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Zhichao Zhou
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Wei Lu
- Gansu Endangered Animals Protection Center, Wuwei, China
| | - Bo Wang
- Gansu Endangered Animals Protection Center, Wuwei, China
| | - Zhicheng Sun
- Administrative Bureau of Dunhuang Xihu National Nature Reserve, Dunhuang, China
| | - Xue Jiang
- Administrative Bureau of Dunhuang Xihu National Nature Reserve, Dunhuang, China
| | - Defu Hu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Junqing Li
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Dong Zhang
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| |
Collapse
|
25
|
Montes-Carreto LM, Aguirre-Noyola JL, Solís-García IA, Ortega J, Martinez-Romero E, Guerrero JA. Diverse methanogens, bacteria and tannase genes in the feces of the endangered volcano rabbit ( Romerolagus diazi). PeerJ 2021; 9:e11942. [PMID: 34458021 PMCID: PMC8378336 DOI: 10.7717/peerj.11942] [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: 04/21/2021] [Accepted: 07/19/2021] [Indexed: 12/27/2022] Open
Abstract
Background The volcano rabbit is the smallest lagomorph in Mexico, it is monotypic and endemic to the Trans-Mexican Volcanic Belt. It is classified as endangered by Mexican legislation and as critically endangered by the IUCN, in the Red List. Romerolagus diazi consumes large amounts of grasses, seedlings, shrubs, and trees. Pines and oaks contain tannins that can be toxic to the organisms which consume them. The volcano rabbit microbiota may be rich in bacteria capable of degrading fiber and phenolic compounds. Methods We obtained the fecal microbiome of three adults and one young rabbit collected in Coajomulco, Morelos, Mexico. Taxonomic assignments and gene annotation revealed the possible roles of different bacteria in the rabbit gut. We searched for sequences encoding tannase enzymes and enzymes associated with digestion of plant fibers such as cellulose and hemicellulose. Results The most representative phyla within the Bacteria domain were: Proteobacteria, Firmicutes and Actinobacteria for the young rabbit sample (S1) and adult rabbit sample (S2), which was the only sample not confirmed by sequencing to correspond to the volcano rabbit. Firmicutes, Actinobacteria and Cyanobacteria were found in adult rabbit samples S3 and S4. The most abundant phylum within the Archaea domain was Euryarchaeota. The most abundant genera of the Bacteria domain were Lachnoclostridium (Firmicutes) and Acinetobacter (Proteobacteria), while Methanosarcina predominated from the Archaea. In addition, the potential functions of metagenomic sequences were identified, which include carbohydrate and amino acid metabolism. We obtained genes encoding enzymes for plant fiber degradation such as endo 1,4 β-xylanases, arabinofuranosidases, endoglucanases and β-glucosidases. We also found 18 bacterial tannase sequences.
Collapse
Affiliation(s)
- Leslie M Montes-Carreto
- Facultad de Ciencias Biológicas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - José Luis Aguirre-Noyola
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de Mexico, Cuernavaca, Morelos, Mexico
| | - Itzel A Solís-García
- Red de Estudios Moleculares Avanzados, Instituto de Ecología, A.C., Xalapa, Veracruz, Mexico
| | - Jorge Ortega
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de Mexico, Mexico
| | | | - José Antonio Guerrero
- Facultad de Ciencias Biológicas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| |
Collapse
|
26
|
Kobiyama A, Rashid J, Reza MS, Ikeda Y, Yamada Y, Kudo T, Mizusawa N, Yanagisawa S, Ikeda D, Sato S, Ogata T, Ikeo K, Kaga S, Watanabe S, Naiki K, Kaga Y, Segawa S, Tada Y, Musashi T, Mineta K, Gojobori T, Watabe S. Seasonal and annual changes in the microbial communities of Ofunato Bay, Japan, based on metagenomics. Sci Rep 2021; 11:17277. [PMID: 34446773 PMCID: PMC8390468 DOI: 10.1038/s41598-021-96641-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 08/12/2021] [Indexed: 02/07/2023] Open
Abstract
Five years of datasets from 2015 to 2019 of whole genome shotgun sequencing for cells trapped on 0.2-µm filters of seawater collected monthly from Ofunato Bay, an enclosed bay in Japan, were analysed, which included the 2015 data that we had reported previously. Nucleotide sequences were determined for extracted DNA from three locations for both the upper (1 m) and deeper (8 or 10 m) depths. The biotic communities analysed at the domain level comprised bacteria, eukaryotes, archaea and viruses. The relative abundance of bacteria was over 60% in most months for the five years. The relative abundance of the SAR86 cluster was highest in the bacterial group, followed by Candidatus Pelagibacter and Planktomarina. The relative abundance of Ca. Pelagibacter showed no relationship with environmental factors, and those of SAR86 and Planktomarina showed positive correlations with salinity and dissolved oxygen, respectively. The bacterial community diversity showed seasonal changes, with high diversity around September and low diversity around January for all five years. Nonmetric multidimensional scaling analysis also revealed that the bacterial communities in the bay were grouped in a season-dependent manner and linked with environmental variables such as seawater temperature, salinity and dissolved oxygen.
Collapse
Affiliation(s)
- Atsushi Kobiyama
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Jonaira Rashid
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
- Bangladesh Fisheries Research Institute, Freshwater Station, Mymensingh, 2201, Bangladesh
| | - Md Shaheed Reza
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
- Department of Fisheries Technology, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Yuri Ikeda
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Yuichiro Yamada
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Toshiaki Kudo
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Nanami Mizusawa
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Saki Yanagisawa
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Daisuke Ikeda
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Shigeru Sato
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Takehiko Ogata
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Kazuho Ikeo
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
- National Institute of Genetics, Yata, Mishima, Shizuoka, 411-8540, Japan
| | - Shinnosuke Kaga
- Iwate Fisheries Technology Center, Kamaishi, Iwate, 026-0001, Japan
| | - Shiho Watanabe
- Iwate Fisheries Technology Center, Kamaishi, Iwate, 026-0001, Japan
| | - Kimiaki Naiki
- Iwate Inland Fisheries Technology Center, Hachimantai, Iwate, 028-7302, Japan
| | - Yoshimasa Kaga
- Iwate Inland Fisheries Technology Center, Hachimantai, Iwate, 028-7302, Japan
| | - Satoshi Segawa
- Iwate Fisheries Technology Center, Kamaishi, Iwate, 026-0001, Japan
| | - Yumiko Tada
- Iwate Fisheries Technology Center, Kamaishi, Iwate, 026-0001, Japan
| | - Tatsuya Musashi
- Iwate Fisheries Technology Center, Kamaishi, Iwate, 026-0001, Japan
| | - Katsuhiko Mineta
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Takashi Gojobori
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia.
| | - Shugo Watabe
- Kitasato University School of Marine Biosciences, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan.
| |
Collapse
|
27
|
Kumar R, Pandit P, Kumar D, Patel Z, Pandya L, Kumar M, Joshi C, Joshi M. Landfill microbiome harbour plastic degrading genes: A metagenomic study of solid waste dumping site of Gujarat, India. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 779:146184. [PMID: 33752005 DOI: 10.1016/j.scitotenv.2021.146184] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 05/21/2023]
Abstract
Globally, environmental pollution by plastic waste has become a severe ecological and social problem worldwide. The present study aimed to analyse the bacterial community structure and functional potential of the landfill site using high throughput shotgun metagenomic approach to understand plastic degrading capabilities present in the municipal solid waste (MSW) dumping site. In this study, soil, leachate and compost samples were collected from various locations (height and depth) of the Pirana landfill site in Ahmedabad city Gujarat, India. In total 30 phyla, 58 class, 125 order, 278 families, 793 genera, and 2468 species were predicted. The most dominant phyla detected were Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria in the soil and compost samples. Whereas, in leachate samples, the predominant phyla belonged to Firmicutes (54.24%) followed by Actinobacteria (43.67%) and Proteobacteria (1.02%). The functional profiling revealed the presence of enzymatic groups and pathways involved in biodegradation of xenobiotics. The results also demonstrated the presence of potential genes that is associated with the biodegradation of different types of plastics such as polyethylene (PE), polyethylene terephthalate (PET), and polystyrene (PS). Present study extablishes the relationship between microbial community structure and rich sources of gene pool, which are actively involved in biodegradation of plastic waste in landfill sites.
Collapse
Affiliation(s)
- Raghawendra Kumar
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat 382011, India
| | - Priti Pandit
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat 382011, India
| | - Dinesh Kumar
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat 382011, India
| | - Zarna Patel
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat 382011, India
| | - Labdhi Pandya
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat 382011, India
| | - Manish Kumar
- Discipline of Earth Sciences, Indian Institute of Technology Gandhinagar, Gujarat 382355, India.
| | - Chaitanya Joshi
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat 382011, India
| | - Madhvi Joshi
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat 382011, India.
| |
Collapse
|
28
|
Using RNA-Sequencing Data to Examine Tissue-Specific Garlic Microbiomes. Int J Mol Sci 2021; 22:ijms22136791. [PMID: 34202675 PMCID: PMC8268838 DOI: 10.3390/ijms22136791] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/16/2021] [Accepted: 06/21/2021] [Indexed: 12/30/2022] Open
Abstract
Garlic (Allium sativum) is a perennial bulbous plant. Due to its clonal propagation, various diseases threaten the yield and quality of garlic. In this study, we conducted in silico analysis to identify microorganisms, bacteria, fungi, and viruses in six different tissues using garlic RNA-sequencing data. The number of identified microbial species was the highest in inflorescences, followed by flowers and bulb cloves. With the Kraken2 tool, 57% of identified microbial reads were assigned to bacteria and 41% were assigned to viruses. Fungi only made up 1% of microbial reads. At the species level, Streptomyces lividans was the most dominant bacteria while Fusarium pseudograminearum was the most abundant fungi. Several allexiviruses were identified. Of them, the most abundant virus was garlic virus C followed by shallot virus X. We obtained a total of 14 viral genome sequences for four allexiviruses. As we expected, the microbial community varied depending on the tissue types, although there was a dominant microorganism in each tissue. In addition, we found that Kraken2 was a very powerful and efficient tool for the bacteria using RNA-sequencing data with some limitations for virome study.
Collapse
|
29
|
Gerner SM, Graf AB, Rattei T. Tamock: simulation of habitat-specific benchmark data in metagenomics. BMC Bioinformatics 2021; 22:227. [PMID: 33932979 PMCID: PMC8088724 DOI: 10.1186/s12859-021-04154-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 04/26/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Simulated metagenomic reads are widely used to benchmark software and workflows for metagenome interpretation. The results of metagenomic benchmarks depend on the assumptions about their underlying ecosystems. Conclusions from benchmark studies are therefore limited to the ecosystems they mimic. Ideally, simulations are therefore based on genomes, which resemble particular metagenomic communities realistically. RESULTS We developed Tamock to facilitate the realistic simulation of metagenomic reads according to a metagenomic community, based on real sequence data. Benchmarks samples can be created from all genomes and taxonomic domains present in NCBI RefSeq. Tamock automatically determines taxonomic profiles from shotgun sequence data, selects reference genomes accordingly and uses them to simulate metagenomic reads. We present an example use case for Tamock by assessing assembly and binning method performance for selected microbiomes. CONCLUSIONS Tamock facilitates automated simulation of habitat-specific benchmark metagenomic data based on real sequence data and is implemented as a user-friendly command-line application, providing extensive additional information along with the simulated benchmark data. Resulting benchmarks enable an assessment of computational methods, workflows, and parameters specifically for a metagenomic habitat or ecosystem of a metagenomic study. AVAILABILITY Source code, documentation and install instructions are freely available at GitHub ( https://github.com/gerners/tamock ).
Collapse
Affiliation(s)
- Samuel M Gerner
- Division of Computational System Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
- Department Bioengineering, University of Applied Sciences FH Campus Wien, Vienna, Austria
| | - Alexandra B Graf
- Department Bioengineering, University of Applied Sciences FH Campus Wien, Vienna, Austria
| | - Thomas Rattei
- Division of Computational System Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.
| |
Collapse
|
30
|
Pust MM, Tümmler B. Identification of core and rare species in metagenome samples based on shotgun metagenomic sequencing, Fourier transforms and spectral comparisons. ISME COMMUNICATIONS 2021; 1:2. [PMID: 37938695 PMCID: PMC9645229 DOI: 10.1038/s43705-021-00010-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/23/2021] [Accepted: 03/01/2021] [Indexed: 04/27/2023]
Abstract
In shotgun metagenomic sequencing applications, low signal-to-noise ratios may complicate species-level differentiation of genetically similar core species and impede high-confidence detection of rare species. However, core and rare species can take pivotal roles in their habitats and should hence be studied as one entity to gain insights into the total potential of microbial communities in terms of taxonomy and functionality. Here, we offer a solution towards increased species-level specificity, decreased false discovery and omission rates of core and rare species in complex metagenomic samples by introducing the rare species identifier (raspir) tool. The python software is based on discrete Fourier transforms and spectral comparisons of biological and reference frequency signals obtained from real and ideal distributions of short DNA reads mapping towards circular reference genomes. Simulation-based testing of raspir enabled the detection of rare species with genome coverages of less than 0.2%. Species-level differentiation of rare Escherichia coli and Shigella spp., as well as the clear delineation between human Streptococcus spp. was feasible with low false discovery (1.3%) and omission rates (13%). Publicly available human placenta sequencing data were reanalysed with raspir. Raspir was unable to identify placental microbial communities, reinforcing the sterile womb paradigm.
Collapse
Affiliation(s)
- Marie-Madlen Pust
- Clinic for Paediatric Pneumology, Allergology, and Neonatology, Hannover Medical School (MHH), Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Hannover, Germany
| | - Burkhard Tümmler
- Clinic for Paediatric Pneumology, Allergology, and Neonatology, Hannover Medical School (MHH), Hannover, Germany.
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Hannover, Germany.
| |
Collapse
|
31
|
Shen J, McFarland AG, Young VB, Hayden MK, Hartmann EM. Toward Accurate and Robust Environmental Surveillance Using Metagenomics. Front Genet 2021; 12:600111. [PMID: 33747038 PMCID: PMC7973286 DOI: 10.3389/fgene.2021.600111] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 01/21/2021] [Indexed: 01/23/2023] Open
Abstract
Environmental surveillance is a critical tool for combatting public health threats represented by the global COVID-19 pandemic and the continuous increase of antibiotic resistance in pathogens. With its power to detect entire microbial communities, metagenomics-based methods stand out in addressing the need. However, several hurdles remain to be overcome in order to generate actionable interpretations from metagenomic sequencing data for infection prevention. Conceptually and technically, we focus on viability assessment, taxonomic resolution, and quantitative metagenomics, and discuss their current advancements, necessary precautions and directions to further development. We highlight the importance of building solid conceptual frameworks and identifying rational limits to facilitate the application of techniques. We also propose the usage of internal standards as a promising approach to overcome analytical bottlenecks introduced by low biomass samples and the inherent lack of quantitation in metagenomics. Taken together, we hope this perspective will contribute to bringing accurate and consistent metagenomics-based environmental surveillance to the ground.
Collapse
Affiliation(s)
- Jiaxian Shen
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, United States
| | - Alexander G. McFarland
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, United States
| | - Vincent B. Young
- Division of Infectious Diseases, Department of Internal Medicine, The University of Michigan Medical School, Ann Arbor, MI, United States
| | - Mary K. Hayden
- Division of Infectious Diseases, Department of Internal Medicine, Rush University Medical Center, Chicago, IL, United States
| | - Erica M. Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, United States
| |
Collapse
|
32
|
Moreno-Indias I, Lahti L, Nedyalkova M, Elbere I, Roshchupkin G, Adilovic M, Aydemir O, Bakir-Gungor B, Santa Pau ECD, D’Elia D, Desai MS, Falquet L, Gundogdu A, Hron K, Klammsteiner T, Lopes MB, Marcos-Zambrano LJ, Marques C, Mason M, May P, Pašić L, Pio G, Pongor S, Promponas VJ, Przymus P, Saez-Rodriguez J, Sampri A, Shigdel R, Stres B, Suharoschi R, Truu J, Truică CO, Vilne B, Vlachakis D, Yilmaz E, Zeller G, Zomer AL, Gómez-Cabrero D, Claesson MJ. Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions. Front Microbiol 2021; 12:635781. [PMID: 33692771 PMCID: PMC7937616 DOI: 10.3389/fmicb.2021.635781] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/28/2021] [Indexed: 12/23/2022] Open
Abstract
The human microbiome has emerged as a central research topic in human biology and biomedicine. Current microbiome studies generate high-throughput omics data across different body sites, populations, and life stages. Many of the challenges in microbiome research are similar to other high-throughput studies, the quantitative analyses need to address the heterogeneity of data, specific statistical properties, and the remarkable variation in microbiome composition across individuals and body sites. This has led to a broad spectrum of statistical and machine learning challenges that range from study design, data processing, and standardization to analysis, modeling, cross-study comparison, prediction, data science ecosystems, and reproducible reporting. Nevertheless, although many statistics and machine learning approaches and tools have been developed, new techniques are needed to deal with emerging applications and the vast heterogeneity of microbiome data. We review and discuss emerging applications of statistical and machine learning techniques in human microbiome studies and introduce the COST Action CA18131 "ML4Microbiome" that brings together microbiome researchers and machine learning experts to address current challenges such as standardization of analysis pipelines for reproducibility of data analysis results, benchmarking, improvement, or development of existing and new tools and ontologies.
Collapse
Affiliation(s)
- Isabel Moreno-Indias
- Instituto de Investigación Biomédica de Málaga (IBIMA), Unidad de Gestión Clìnica de Endocrinologìa y Nutrición, Hospital Clìnico Universitario Virgen de la Victoria, Universidad de Málaga, Málaga, Spain
- Centro de Investigación Biomeìdica en Red de Fisiopatologtìa de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
| | - Leo Lahti
- Department of Computing, University of Turku, Turku, Finland
| | - Miroslava Nedyalkova
- Human Genetics and Disease Mechanisms, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Ilze Elbere
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | | | - Muhamed Adilovic
- Department of Genetics and Bioengineering, International University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Onder Aydemir
- Department of Electrical and Electronics Engineering, Karadeniz Technical University, Trabzon, Turkey
| | - Burcu Bakir-Gungor
- Department of Computer Engineering, Abdullah Gul University, Kayseri, Turkey
| | | | - Domenica D’Elia
- Department for Biomedical Sciences, Institute for Biomedical Technologies, National Research Council, Bari, Italy
| | - Mahesh S. Desai
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
- Odense Research Center for Anaphylaxis, Department of Dermatology and Allergy Center, Odense University Hospital, University of Southern Denmark, Odense, Denmark
| | - Laurent Falquet
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Aycan Gundogdu
- Department of Microbiology and Clinical Microbiology, Faculty of Medicine, Erciyes University, Kayseri, Turkey
- Metagenomics Laboratory, Genome and Stem Cell Center (GenKök), Erciyes University, Kayseri, Turkey
| | - Karel Hron
- Department of Mathematical Analysis and Applications of Mathematics, Palacký University, Olomouc, Czechia
| | | | - Marta B. Lopes
- NOVA Laboratory for Computer Science and Informatics (NOVA LINCS), FCT, UNL, Caparica, Portugal
- Centro de Matemática e Aplicações (CMA), FCT, UNL, Caparica, Portugal
| | - Laura Judith Marcos-Zambrano
- Computational Biology Group, Precision Nutrition and Cancer Research Program, IMDEA Food Institute, Madrid, Spain
| | - Cláudia Marques
- CINTESIS, NOVA Medical School, NMS, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Michael Mason
- Computational Oncology, Sage Bionetworks, Seattle, WA, United States
| | - Patrick May
- Bioinformatics Core, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Lejla Pašić
- Sarajevo Medical School, University Sarajevo School of Science and Technology, Sarajevo, Bosnia and Herzegovina
| | - Gianvito Pio
- Department of Computer Science, University of Bari Aldo Moro, Bari, Italy
| | - Sándor Pongor
- Faculty of Information Tehnology and Bionics, Pázmány University, Budapest, Hungary
| | - Vasilis J. Promponas
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Piotr Przymus
- Faculty of Mathematics and Computer Science, Nicolaus Copernicus University, Toruñ, Poland
| | - Julio Saez-Rodriguez
- Institute of Computational Biomedicine, Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Heidelberg, Germany
| | - Alexia Sampri
- Division of Informatics, Imaging and Data Sciences, School of Health Sciences, University of Manchester, Manchester, United Kingdom
| | - Rajesh Shigdel
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Blaz Stres
- Jozef Stefan Institute, Ljubljana, Slovenia
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
- Faculty of Civil and Geodetic Engineering, University of Ljubljana, Ljubljana, Slovenia
| | - Ramona Suharoschi
- Molecular Nutrition and Proteomics Lab, Faculty of the Food Science and Technology, Institute of Life Sciences, University of Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, Cluj-Napoca, Romania
| | - Jaak Truu
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Ciprian-Octavian Truică
- Department of Computer Science and Engineering, Faculty of Automatic Control and Computers, University Politehnica of Bucharest, Bucharest, Romania
| | - Baiba Vilne
- Bioinformatics Research Unit, Riga Stradins University, Riga, Latvia
| | - Dimitrios Vlachakis
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Ercument Yilmaz
- Department of Computer Technologies, Karadeniz Technical University, Trabzon, Turkey
| | - Georg Zeller
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Aldert L. Zomer
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - David Gómez-Cabrero
- Navarrabiomed, Complejo Hospitalario de Navarra (CHN), IdiSNA, Universidad Pública de Navarra (UPNA), Pamplona, Spain
| | - Marcus J. Claesson
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| |
Collapse
|
33
|
de Abreu VAC, Perdigão J, Almeida S. Metagenomic Approaches to Analyze Antimicrobial Resistance: An Overview. Front Genet 2021; 11:575592. [PMID: 33537056 PMCID: PMC7848172 DOI: 10.3389/fgene.2020.575592] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 12/04/2020] [Indexed: 11/13/2022] Open
Abstract
Antimicrobial resistance is a major global public health problem, which develops when pathogens acquire antimicrobial resistance genes (ARGs), primarily through genetic recombination between commensal and pathogenic microbes. The resistome is a collection of all ARGs. In microorganisms, the primary method of ARG acquisition is horizontal gene transfer (HGT). Thus, understanding and identifying HGTs, can provide insight into the mechanisms of antimicrobial resistance transmission and dissemination. The use of high-throughput sequencing technologies has made the analysis of ARG sequences feasible and accessible. In particular, the metagenomic approach has facilitated the identification of community-based antimicrobial resistance. This approach is useful, as it allows access to the genomic data in an environmental sample without the need to isolate and culture microorganisms prior to analysis. Here, we aimed to reflect on the challenges of analyzing metagenomic data in the three main approaches for studying antimicrobial resistance: (i) analysis of microbial diversity, (ii) functional gene analysis, and (iii) searching the most complete and pertinent resistome databases.
Collapse
Affiliation(s)
- Vinicius A C de Abreu
- Laboratório de Bioinformática e Computação de Alto Desempenho (LaBioCad), Faculdade de Computação (FACOMP), Universidade Federal do Pará, Belém, Brazil
| | - José Perdigão
- Laboratório de Bioinformática e Computação de Alto Desempenho (LaBioCad), Faculdade de Computação (FACOMP), Universidade Federal do Pará, Belém, Brazil
| | - Sintia Almeida
- Central de Genômica e Bioinformática (CeGenBio), Núcleo de Pesquisa e Desenvolvimento de Medicamentos (NPDM), Departamento de Fisiologia e Farmacologia, Universidade Federal do Ceará, Fortaleza, Brazil
| |
Collapse
|
34
|
Pust MM, Wiehlmann L, Davenport C, Rudolf I, Dittrich AM, Tümmler B. The human respiratory tract microbial community structures in healthy and cystic fibrosis infants. NPJ Biofilms Microbiomes 2020; 6:61. [PMID: 33319812 PMCID: PMC7738502 DOI: 10.1038/s41522-020-00171-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 11/13/2020] [Indexed: 02/06/2023] Open
Abstract
The metagenome development of the human respiratory tract was investigated by shotgun metagenome metagenomic sequencing of cough swabs from healthy children and children with cystic fibrosis (CF) between 3 weeks and 6 years of age. A healthy microbial community signature was associated with increased absolute abundances in terms of bacterial–human cell ratios of core and rare species across all age groups, with a higher diversity of rare species and a tightly interconnected species co-occurrence network, in which individual members were found in close proximity to each other and negative correlations were absent. Even without typical CF pathogens, the CF infant co-occurrence network was found to be less stable and prone to fragmentation due to fewer connections between species, a higher number of bridging species and the presence of negative species correlations. Detection of low-abundant DNA of the CF hallmark pathogen Pseudomonas aeruginosa was neither disease- nor age-associated in our cohort. Healthy and CF children come into contact with P. aeruginosa on a regular basis and from early on.
Collapse
Affiliation(s)
- Marie-Madlen Pust
- Clinic for Paediatric Pneumology, Allergology, and Neonatology, Hannover Medical School, Hannover, Germany.,Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Hannover, Germany
| | - Lutz Wiehlmann
- Research Core Unit Genomics, Hannover Medical School, Hannover, Germany
| | - Colin Davenport
- Research Core Unit Genomics, Hannover Medical School, Hannover, Germany
| | - Isa Rudolf
- Clinic for Paediatric Pneumology, Allergology, and Neonatology, Hannover Medical School, Hannover, Germany.,Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Hannover, Germany
| | - Anna-Maria Dittrich
- Clinic for Paediatric Pneumology, Allergology, and Neonatology, Hannover Medical School, Hannover, Germany.,Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Hannover, Germany
| | - Burkhard Tümmler
- Clinic for Paediatric Pneumology, Allergology, and Neonatology, Hannover Medical School, Hannover, Germany. .,Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Hannover Medical School, Hannover, Germany.
| |
Collapse
|