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Aplakidou E, Vergoulidis N, Chasapi M, Venetsianou NK, Kokoli M, Panagiotopoulou E, Iliopoulos I, Karatzas E, Pafilis E, Georgakopoulos-Soares I, Kyrpides NC, Pavlopoulos GA, Baltoumas FA. Visualizing metagenomic and metatranscriptomic data: A comprehensive review. Comput Struct Biotechnol J 2024; 23:2011-2033. [PMID: 38765606 PMCID: PMC11101950 DOI: 10.1016/j.csbj.2024.04.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/22/2024] Open
Abstract
The fields of Metagenomics and Metatranscriptomics involve the examination of complete nucleotide sequences, gene identification, and analysis of potential biological functions within diverse organisms or environmental samples. Despite the vast opportunities for discovery in metagenomics, the sheer volume and complexity of sequence data often present challenges in processing analysis and visualization. This article highlights the critical role of advanced visualization tools in enabling effective exploration, querying, and analysis of these complex datasets. Emphasizing the importance of accessibility, the article categorizes various visualizers based on their intended applications and highlights their utility in empowering bioinformaticians and non-bioinformaticians to interpret and derive insights from meta-omics data effectively.
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Affiliation(s)
- Eleni Aplakidou
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Department of Informatics and Telecommunications, Data Science and Information Technologies program, University of Athens, 15784 Athens, Greece
| | - Nikolaos Vergoulidis
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
| | - Maria Chasapi
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Department of Informatics and Telecommunications, Data Science and Information Technologies program, University of Athens, 15784 Athens, Greece
| | - Nefeli K. Venetsianou
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
| | - Maria Kokoli
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
| | - Eleni Panagiotopoulou
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Department of Informatics and Telecommunications, Data Science and Information Technologies program, University of Athens, 15784 Athens, Greece
| | - Ioannis Iliopoulos
- Department of Basic Sciences, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Evangelos Karatzas
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Evangelos Pafilis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Greece
| | - Ilias Georgakopoulos-Soares
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Nikos C. Kyrpides
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Georgios A. Pavlopoulos
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
- Center of New Biotechnologies & Precision Medicine, Department of Medicine, School of Health Sciences, National and Kapodistrian University of Athens, Greece
- Hellenic Army Academy, 16673 Vari, Greece
| | - Fotis A. Baltoumas
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari, Greece
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Bai X, Sönnerborg A, Nowak P. Elite controllers microbiome: unraveling the mystery of association and causation. Curr Opin HIV AIDS 2024; 19:261-267. [PMID: 38874425 DOI: 10.1097/coh.0000000000000867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
PURPOSE OF REVIEW To unravel the current knowledge and possible link between the gut microbiome and HIV-1 virological control in elite controllers (EC), who can suppress viral replication in the absence of antiretroviral therapy. In addition, to discuss the limitations of current research and propose future research directions. RECENT FINDINGS EC possess a different gut bacterial microbiota profile in composition and functionality from that of treatment-naive HIV-1 viremic progressors (VP). Specifically, EC have a richer bacterial microbiota as compared to VP, which closely resembles the microbiota in HIV-1 negative healthy controls (HC). Differentially abundant bacteria are found between EC and VP or HC, though results vary among the few existing studies. These data imply that the gut microbiome could contribute to the natural suppression of HIV-1 infection. SUMMARY An association between the gut microbiome and HIV-1 virological control is evidenced by recent studies. Yet, there are substantial knowledge gaps, and the underlying mechanism of how the microbiome influences the EC phenotype is far from clarified. Future research should consider diverse microbial communities, the complex microbe-host interactions, as well as yet-unidentified causal links between microbiome alterations and HIV-1 disease progression.
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Affiliation(s)
- Xiangning Bai
- Department of Microbiology, Division of Laboratory Medicine, Oslo University Hospital, Oslo, Norway
- Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm
| | - Anders Sönnerborg
- Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm
- Department of Infectious Diseases, Karolinska University Hospital, Huddinge, Sweden
| | - Piotr Nowak
- Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm
- Department of Infectious Diseases, Karolinska University Hospital, Huddinge, Sweden
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Garrison EC, Brown AMV, Salazar MM, Barr B, Moustaid-Moussa N, Gollahon LS. Microbiome Taxonomic and Functional Differences in C3H/HeJ Mice Fed a Long-Term High-Fat Diet with Beef Protein ± Ammonium Hydroxide Supplementation. Nutrients 2024; 16:1613. [PMID: 38892546 PMCID: PMC11174526 DOI: 10.3390/nu16111613] [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: 03/26/2024] [Revised: 05/17/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024] Open
Abstract
Studies have suggested that alkalinized foods may reduce the effects of the acidogenic Western diet in promoting obesity, metabolic syndrome, type 2 diabetes, cancer, and coronary heart disease. Indeed, a recent study in mice fed a high-fat diet containing dietary beef supplemented with ammonium hydroxide showed improvement in a suite of metabolic outcomes. However, the effects of dietary protein ammonium supplementation on the microbiome remain unknown. In this study, the effects of ammonium supplementation on beef protein towards microbiome taxa and function in a high-fat diet were analyzed. Fecal microbiomes were characterized using a shotgun metagenomic approach for 16-month-old male and female mice after long-term diet treatments. The results for ammoniated diets showed that several bacteria known to be associated with health benefits increased significantly, including Romboutsia, Oscillospiraceae, and Lactococcus cremoris. The beneficial mucin-degrader Akkermansia was especially abundant, with a high prevalence (~86%) in females. Concurrently, the phyla Actinomycetota (Actinobacteria) and Bacteroidota (Bacteroidetes) were significantly reduced. While sex was a confounding factor affecting microbiome responses to ammonium supplementation in dietary protein, it is worth noting that several putatively beneficial microbiome functions increased with ammonium supplementation, such as glycine betaine transport, xenobiotic detoxification, enhanced defense, and others. Conversely, many disease-associated microbiome functions reduced. Importantly, modifying protein pH alone via ammonium supplementation induced beneficial microbiota changes. Taken together, these results suggest that ammonium-supplemented proteins may mediate some negative microbiome-associated effects of high-fat/Western diets.
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Affiliation(s)
- Emily C. Garrison
- Department of Biological Sciences, Texas Tech University, 2500 Broadway, Lubbock, TX 79409, USA; (E.C.G.); (A.M.V.B.); (M.M.S.); (B.B.)
| | - Amanda M. V. Brown
- Department of Biological Sciences, Texas Tech University, 2500 Broadway, Lubbock, TX 79409, USA; (E.C.G.); (A.M.V.B.); (M.M.S.); (B.B.)
| | - McKinlee M. Salazar
- Department of Biological Sciences, Texas Tech University, 2500 Broadway, Lubbock, TX 79409, USA; (E.C.G.); (A.M.V.B.); (M.M.S.); (B.B.)
| | - Benjamin Barr
- Department of Biological Sciences, Texas Tech University, 2500 Broadway, Lubbock, TX 79409, USA; (E.C.G.); (A.M.V.B.); (M.M.S.); (B.B.)
| | - Naima Moustaid-Moussa
- Department of Nutritional Sciences, Texas Tech University, 2500 Broadway, Lubbock, TX 79409, USA;
- Obesity Research Institute, Texas Tech University, 2500 Broadway, Lubbock, TX 79409, USA
| | - Lauren S. Gollahon
- Department of Biological Sciences, Texas Tech University, 2500 Broadway, Lubbock, TX 79409, USA; (E.C.G.); (A.M.V.B.); (M.M.S.); (B.B.)
- Obesity Research Institute, Texas Tech University, 2500 Broadway, Lubbock, TX 79409, USA
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Valles-Colomer M, Manghi P, Cumbo F, Masetti G, Armanini F, Asnicar F, Blanco-Miguez A, Pinto F, Punčochář M, Garaventa A, Amoroso L, Ponzoni M, Corrias MV, Segata N. Neuroblastoma is associated with alterations in gut microbiome composition subsequent to maternal microbial seeding. EBioMedicine 2024; 99:104917. [PMID: 38104504 PMCID: PMC10731604 DOI: 10.1016/j.ebiom.2023.104917] [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: 07/12/2023] [Revised: 11/21/2023] [Accepted: 12/01/2023] [Indexed: 12/19/2023] Open
Abstract
BACKGROUND Neuroblastoma is the most frequent extracranial solid tumour in children, accounting for ∼15% of deaths due to cancer in childhood. The most common clinical presentation are abdominal tumours. An altered gut microbiome composition has been linked to multiple cancer types, and reported in murine models of neuroblastoma. Whether children with neuroblastoma display alterations in gut microbiome composition remains unexplored. METHODS We assessed gut microbiome composition by shotgun metagenomic profiling in an observational cross-sectional study on 288 individuals, consisting of patients with a diagnosis of neuroblastoma at disease onset (N = 63), healthy controls matching the patients on the main covariates of microbiome composition (N = 94), healthy siblings of the patients (N = 13), mothers of patients (N = 59), and mothers of the controls (N = 59). We examined taxonomic and functional microbiome composition and mother-infant strain transmission patterns. FINDINGS Patients with neuroblastoma displayed alterations in gut microbiome composition characterised by reduced microbiome richness, decreased relative abundances of 18 species (including Phocaeicola dorei and Bifidobacterium bifidum), enriched protein fermentation and reduced carbohydrate fermentation potential. Using machine learning, we could successfully discriminate patients from controls (AUC = 82%). Healthy siblings did not display such alterations but resembled the healthy control group. No significant differences in maternal microbiome composition nor mother-to-offspring transmission were detected. INTERPRETATION Patients with neuroblastoma display alterations in taxonomic and functional gut microbiome composition, which cannot be traced to differential maternal seeding. Follow-up research should include investigating potential causal links. FUNDING Italian Ministry of Health Ricerca Corrente and Ricerca Finalizzata 5 per mille (to MPonzoni); Fondazione Italiana Neuroblastoma (to MPonzoni); European Research Council (ERC-StG project MetaPG-716575 and ERC-CoG microTOUCH-101045015 to NS); the European H2020 program ONCOBIOME-825410 project (to NS); the National Cancer Institute of the National Institutes of Health 1U01CA230551 (to NS); the Premio Internazionale Lombardia e Ricerca 2019 (to NS); the MIUR Progetti di Ricerca di Rilevante Interesse Nazionale (PRIN) Bando 2017 Grant 2017J3E2W2 (to NS); EMBO ALTF 593-2020 and Knowledge Generation Project from the Spanish Ministry of Science and Innovation (PID2022-139328OA-I00) (to MV-C).
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Affiliation(s)
- Mireia Valles-Colomer
- Department CIBIO, University of Trento, Trento, Italy; MELIS Department, Pompeu Fabra University, Barcelona, Spain.
| | - Paolo Manghi
- Department CIBIO, University of Trento, Trento, Italy
| | - Fabio Cumbo
- Department CIBIO, University of Trento, Trento, Italy
| | | | | | | | | | | | | | | | | | - Mirco Ponzoni
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Maria Valeria Corrias
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy; Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy.
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Zadra N, Tatti A, Silverj A, Piccinno R, Devilliers J, Lewis C, Arnoldi D, Montarsi F, Escuer P, Fusco G, De Sanctis V, Feuda R, Sánchez-Gracia A, Rizzoli A, Rota-Stabelli O. Shallow Whole-Genome Sequencing of Aedes japonicus and Aedes koreicus from Italy and an Updated Picture of Their Evolution Based on Mitogenomics and Barcoding. INSECTS 2023; 14:904. [PMID: 38132578 PMCID: PMC10743467 DOI: 10.3390/insects14120904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023]
Abstract
Aedes japonicus and Aedes koreicus are two invasive mosquitoes native to East Asia that are quickly establishing in temperate regions of Europe. Both species are vectors of arboviruses, but we currently lack a clear understanding of their evolution. Here, we present new short-read, shallow genome sequencing of A. japonicus and A. koreicus individuals from northern Italy, which we used for downstream phylogenetic and barcode analyses. We explored associated microbial DNA and found high occurrences of Delftia bacteria in both samples, but neither Asaia nor Wolbachia. We then assembled complete mitogenomes and used these data to infer divergence times estimating the split of A. japonicus from A. koreicus in the Oligocene, which was more recent than that previously reported using mitochondrial markers. We recover a younger age for most other nodes within Aedini and other Culicidae. COI barcoding and phylogenetic analyses indicate that A. japonicus yaeyamensis, A. japonicus amamiensis, and the two A. koreicus sampled from Europe should be considered as separate species within a monophyletic species complex. Our studies further clarify the evolution of A. japonicus and A. koreicus, and indicate the need to obtain whole-genome data from putative species in order to disentangle their complex patterns of evolution.
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Affiliation(s)
- Nicola Zadra
- Center Agriculture Food Environment (C3A), University of Trento, 38010 San Michele all’Adige, Italy; (N.Z.); (A.T.); (A.S.); (R.P.)
- CIBIO Department, University of Trento, 38123 Trento, Italy;
- Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy; (D.A.); (A.R.)
| | - Alessia Tatti
- Center Agriculture Food Environment (C3A), University of Trento, 38010 San Michele all’Adige, Italy; (N.Z.); (A.T.); (A.S.); (R.P.)
- Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy; (D.A.); (A.R.)
- Department of Biology, University of Padova, 35121 Padova, Italy;
- University School for Advanced Studies IUSS Pavia, 27100 Pavia, Italy
| | - Andrea Silverj
- Center Agriculture Food Environment (C3A), University of Trento, 38010 San Michele all’Adige, Italy; (N.Z.); (A.T.); (A.S.); (R.P.)
- CIBIO Department, University of Trento, 38123 Trento, Italy;
- Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy; (D.A.); (A.R.)
| | - Riccardo Piccinno
- Center Agriculture Food Environment (C3A), University of Trento, 38010 San Michele all’Adige, Italy; (N.Z.); (A.T.); (A.S.); (R.P.)
- Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy; (D.A.); (A.R.)
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Julien Devilliers
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK; (J.D.); (C.L.); (R.F.)
| | - Clifton Lewis
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK; (J.D.); (C.L.); (R.F.)
| | - Daniele Arnoldi
- Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy; (D.A.); (A.R.)
| | - Fabrizio Montarsi
- Istituto Zooprofilattico Sperimentale Delle Venezie, 35020 Legnaro, Italy;
| | - Paula Escuer
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, 08028 Barcelona, Spain; (P.E.); (A.S.-G.)
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08007 Barcelona, Spain
| | - Giuseppe Fusco
- Department of Biology, University of Padova, 35121 Padova, Italy;
| | | | - Roberto Feuda
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK; (J.D.); (C.L.); (R.F.)
| | - Alejandro Sánchez-Gracia
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, 08028 Barcelona, Spain; (P.E.); (A.S.-G.)
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08007 Barcelona, Spain
| | - Annapaola Rizzoli
- Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy; (D.A.); (A.R.)
| | - Omar Rota-Stabelli
- Center Agriculture Food Environment (C3A), University of Trento, 38010 San Michele all’Adige, Italy; (N.Z.); (A.T.); (A.S.); (R.P.)
- CIBIO Department, University of Trento, 38123 Trento, Italy;
- Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy; (D.A.); (A.R.)
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Hansen ZA, Vasco K, Rudrik JT, Scribner KT, Zhang L, Manning SD. Recovery of the gut microbiome following enteric infection and persistence of antimicrobial resistance genes in specific microbial hosts. Sci Rep 2023; 13:15524. [PMID: 37726374 PMCID: PMC10509190 DOI: 10.1038/s41598-023-42822-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 09/15/2023] [Indexed: 09/21/2023] Open
Abstract
Enteric pathogens cause widespread foodborne illness and are increasingly resistant to important antibiotics yet their ecological impact on the gut microbiome and resistome is not fully understood. Herein, shotgun metagenome sequencing was applied to stool DNA from 60 patients (cases) during an enteric bacterial infection and after recovery (follow-ups). Overall, the case samples harbored more antimicrobial resistance genes (ARGs) with greater resistome diversity than the follow-up samples (p < 0.001), while follow-ups had more diverse gut microbiota (p < 0.001). Although cases were primarily defined by genera Escherichia, Salmonella, and Shigella along with ARGs for multi-compound and multidrug resistance, follow-ups had a greater abundance of Bacteroidetes and Firmicutes phyla and resistance genes for tetracyclines, macrolides, lincosamides, and streptogramins, and aminoglycosides. A host-tracking analysis revealed that Escherichia was the primary bacterial host of ARGs in both cases and follow-ups, with a greater abundance occurring during infection. Eleven distinct extended spectrum beta-lactamase (ESBL) genes were identified during infection, with some detectable upon recovery, highlighting the potential for gene transfer within the community. Because of the increasing incidence of disease caused by foodborne pathogens and their role in harboring and transferring resistance determinants, this study enhances our understanding of how enteric infections impact human gut ecology.
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Affiliation(s)
- Zoe A Hansen
- Departments of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
| | - Karla Vasco
- Departments of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
| | - James T Rudrik
- Bureau of Laboratories, The Michigan Department of Health and Human Services, Lansing, MI, 48906, USA
| | - Kim T Scribner
- Fisheries and Wildlife, Michigan State University, East Lansing, MI, 48824, USA
| | - Lixin Zhang
- Departments of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
- Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, 48824, USA
| | - Shannon D Manning
- Departments of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA.
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