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Loos D, Zhang L, Beemelmanns C, Kurzai O, Panagiotou G. DAnIEL: A User-Friendly Web Server for Fungal ITS Amplicon Sequencing Data. Front Microbiol 2021; 12:720513. [PMID: 34484161 PMCID: PMC8416086 DOI: 10.3389/fmicb.2021.720513] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/26/2021] [Indexed: 01/04/2023] Open
Abstract
Trillions of microbes representing all kingdoms of life are resident in, and on, humans holding essential roles for the host development and physiology. The last decade over a dozen online tools and servers, accessible via public domain, have been developed for the analysis of bacterial sequences; however, the analysis of fungi is still in its infancy. Here, we present a web server dedicated to the comprehensive analysis of the human mycobiome for (i) translating raw sequencing reads to data tables and high-standard figures, (ii) integrating statistical analysis and machine learning with a manually curated relational database and (iii) comparing the user’s uploaded datasets with publicly available from the Sequence Read Archive. Using 1,266 publicly available Internal transcribed spacers (ITS) samples, we demonstrated the utility of DAnIEL web server on large scale datasets and show the differences in fungal communities between human skin and soil sites.
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Affiliation(s)
- Daniel Loos
- Systems Biology and Bioinformatics Group, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Lu Zhang
- Systems Biology and Bioinformatics Group, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Christine Beemelmanns
- Chemical Biology of Microbe-Host Interactions Group, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Oliver Kurzai
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany.,National Reference Center for Invasive Fungal Infections NRZMyk, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Gianni Panagiotou
- Systems Biology and Bioinformatics Group, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany.,Systems Biology and Bioinformatics Group, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam, China
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2
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Gao B, Chi L, Zhu Y, Shi X, Tu P, Li B, Yin J, Gao N, Shen W, Schnabl B. An Introduction to Next Generation Sequencing Bioinformatic Analysis in Gut Microbiome Studies. Biomolecules 2021; 11:530. [PMID: 33918473 PMCID: PMC8066849 DOI: 10.3390/biom11040530] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/28/2021] [Accepted: 03/29/2021] [Indexed: 12/12/2022] Open
Abstract
The gut microbiome is a microbial ecosystem which expresses 100 times more genes than the human host and plays an essential role in human health and disease pathogenesis. Since most intestinal microbial species are difficult to culture, next generation sequencing technologies have been widely applied to study the gut microbiome, including 16S rRNA, 18S rRNA, internal transcribed spacer (ITS) sequencing, shotgun metagenomic sequencing, metatranscriptomic sequencing and viromic sequencing. Various software tools were developed to analyze different sequencing data. In this review, we summarize commonly used computational tools for gut microbiome data analysis, which extended our understanding of the gut microbiome in health and diseases.
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Affiliation(s)
- Bei Gao
- Department of Marine Science, School of Marine Sciences, Nanjing University of Information Science and Technology, Nanjing 210044, China;
| | - Liang Chi
- Metaorganism Immunity Section, Laboratory of Immune Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Yixin Zhu
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA;
| | - Xiaochun Shi
- Department of Environmental Ecological Engineering, School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing 210044, China; (X.S.); (W.S.)
| | - Pengcheng Tu
- Department of Food Science and Nutrition, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China;
| | - Bing Li
- Suzhou Industrial Park Environmental Law Enforcement Brigade (Environmental Monitoring Station), Suzhou 215021, China;
| | - Jun Yin
- Department of Hydrometeorology, School of Hydrology and Water Resources, Nanjing University of Information Science and Technology, Nanjing 210044, China;
| | - Nan Gao
- Department of Biotechnology, School of Biological and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China;
| | - Weishou Shen
- Department of Environmental Ecological Engineering, School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing 210044, China; (X.S.); (W.S.)
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, Nanjing 210044, China
| | - Bernd Schnabl
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA;
- Department of Medicine, VA San Diego Healthcare System, San Diego, CA 92161, USA
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Hupfauf S, Etemadi M, Fernández-Delgado Juárez M, Gómez-Brandón M, Insam H, Podmirseg SM. CoMA - an intuitive and user-friendly pipeline for amplicon-sequencing data analysis. PLoS One 2020; 15:e0243241. [PMID: 33264369 PMCID: PMC7710066 DOI: 10.1371/journal.pone.0243241] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 11/17/2020] [Indexed: 12/23/2022] Open
Abstract
In recent years, there has been a veritable boost in next-generation sequencing (NGS) of gene amplicons in biological and medical studies. Huge amounts of data are produced and need to be analyzed adequately. Various online and offline analysis tools are available; however, most of them require extensive expertise in computer science or bioinformatics, and often a Linux-based operating system. Here, we introduce "CoMA-Comparative Microbiome Analysis" as a free and intuitive analysis pipeline for amplicon-sequencing data, compatible with any common operating system. Moreover, the tool offers various useful services including data pre-processing, quality checking, clustering to operational taxonomic units (OTUs), taxonomic assignment, data post-processing, data visualization, and statistical appraisal. The workflow results in highly esthetic and publication-ready graphics, as well as output files in standardized formats (e.g. tab-delimited OTU-table, BIOM, NEWICK tree) that can be used for more sophisticated analyses. The CoMA output was validated by a benchmark test, using three mock communities with different sample characteristics (primer set, amplicon length, diversity). The performance was compared with that of Mothur, QIIME and QIIME2-DADA2, popular packages for NGS data analysis. Furthermore, the functionality of CoMA is demonstrated on a practical example, investigating microbial communities from three different soils (grassland, forest, swamp). All tools performed well in the benchmark test and were able to reveal the majority of all genera in the mock communities. Also for the soil samples, the results of CoMA were congruent to those of the other pipelines, in particular when looking at the key microbial players.
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Affiliation(s)
- Sebastian Hupfauf
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Mohammad Etemadi
- Department of Horticultural Science, School of Agriculture, Shiraz University, Shiraz, Iran
| | | | - María Gómez-Brandón
- Department of Ecology and Animal Biology, GEA Group, University of Vigo, Vigo, Spain
| | - Heribert Insam
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
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4
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Sundaresan N, Sahu AK, Jagan EG, Pandi M. Evaluation of ITS2 molecular morphometrics effectiveness in species delimitation of Ascomycota - A pilot study. Fungal Biol 2019; 123:517-527. [PMID: 31196521 DOI: 10.1016/j.funbio.2019.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 04/01/2019] [Accepted: 05/02/2019] [Indexed: 01/19/2023]
Abstract
Exploring the secondary structure information of nuclear ribosomal internal transcribed spacer 2 (ITS2) has been a promising approach in species delimitation. However, Compensatory base changes (CBC) concept employed in this approach turns futile when CBC is absent. This prompted us to investigate the utility of insertion/deletion (INDELs) and substitutions in fungal delineation at species level. Upon this rationale, 116 strains representing 97 species, belonging to 6 genera (Colletotrichum, Boeremia, Leptosphaeria, Peyronellaea, Plenodomus and Stagonosporopsis) of Ascomycota were retrieved from Q-bank for molecular morphometric analysis. CBC, INDELs and substitutions between the species of their respective genus were recorded. Most species combinations lacked CBC. Among the substitution events, transitions were predominant. INDELs were less frequent than the substitutions. These evolutionary events were mapped upon the helices to discern species specific variation sites. In 68 species unique variation sites were recognised. The remaining 29 species shared absolute similarity with distinctly named species. The variation sites catalogued in them overlapped with other distinct species and resulted in the blurring of species boundaries. Species specific variation sites recognized in this study are the preliminary results and they could be discerned with absolute confidence when larger datasets encompassing all described species of genera were investigated. They could be of potential use in barcoding fungi at species level. This study also concludes that the ITS2 molecular morphometric analysis is an efficient third dimensional study of the fungal species delimitation. This may help to avoid the false positives in species delimitations and to alleviate the challenges in molecular characterization.
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Affiliation(s)
- Natesan Sundaresan
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, India
| | - Amit Kumar Sahu
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, India
| | - Enthai Ganeshan Jagan
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, India
| | - Mohan Pandi
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, India.
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Shamim M, Kumar P, Kumar RR, Kumar M, Kumar RR, Singh KN. Assessing Fungal Biodiversity Using Molecular Markers. Fungal Biol 2017. [DOI: 10.1007/978-3-319-34106-4_15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Duarte APM, Ferro M, Rodrigues A, Bacci M, Nagamoto NS, Forti LC, Pagnocca FC. Prevalence of the genus Cladosporium on the integument of leaf-cutting ants characterized by 454 pyrosequencing. Antonie van Leeuwenhoek 2016; 109:1235-43. [PMID: 27307255 DOI: 10.1007/s10482-016-0724-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 06/08/2016] [Indexed: 11/30/2022]
Abstract
The relationship of attine ants with their mutualistic fungus and other microorganisms has been studied during the last two centuries. However, previous studies about the diversity of fungi in the ants' microenvironment are based mostly on culture-dependent approaches, lacking a broad characterization of the fungal ant-associated community. Here, we analysed the fungal diversity found on the integument of Atta capiguara and Atta laevigata alate ants using 454 pyrosequencing. We obtained 35,453 ITS reads grouped into 99 molecular operational taxonomic units (MOTUs). Data analysis revealed that A. capiguara drones had the highest diversity of MOTUs. Besides the occurrence of several uncultured fungi, the mycobiota analysis revealed that the most abundant taxa were the Cladosporium-complex, Cryptococcus laurentii and Epicoccum sp. Taxa in the genus Cladosporium were predominant in all samples, comprising 67.9 % of all reads. The remarkable presence of the genus Cladosporium on the integument of leaf-cutting ants alates from distinct ant species suggests that this fungus is favored in this microenvironment.
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Affiliation(s)
- A P M Duarte
- Center for the Study of Social Insects, UNESP - São Paulo State University, Avenida 24-A, n. 1515, Bela Vista, Rio Claro, SP, 13.506-900, Brazil.
| | - M Ferro
- Center for the Study of Social Insects, UNESP - São Paulo State University, Avenida 24-A, n. 1515, Bela Vista, Rio Claro, SP, 13.506-900, Brazil
| | - A Rodrigues
- Center for the Study of Social Insects, UNESP - São Paulo State University, Avenida 24-A, n. 1515, Bela Vista, Rio Claro, SP, 13.506-900, Brazil.,Department of Biochemistry and Microbiology, UNESP - São Paulo State University, Rio Claro, SP, Brazil
| | - M Bacci
- Center for the Study of Social Insects, UNESP - São Paulo State University, Avenida 24-A, n. 1515, Bela Vista, Rio Claro, SP, 13.506-900, Brazil.,Department of Biochemistry and Microbiology, UNESP - São Paulo State University, Rio Claro, SP, Brazil
| | - N S Nagamoto
- Department of Plant Protection, UNESP - São Paulo State University, Botucatu, SP, Brazil
| | - L C Forti
- Department of Plant Protection, UNESP - São Paulo State University, Botucatu, SP, Brazil
| | - F C Pagnocca
- Center for the Study of Social Insects, UNESP - São Paulo State University, Avenida 24-A, n. 1515, Bela Vista, Rio Claro, SP, 13.506-900, Brazil.,Department of Biochemistry and Microbiology, UNESP - São Paulo State University, Rio Claro, SP, Brazil
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Gweon HS, Oliver A, Taylor J, Booth T, Gibbs M, Read DS, Griffiths RI, Schonrogge K. PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform. Methods Ecol Evol 2015; 6:973-980. [PMID: 27570615 PMCID: PMC4981123 DOI: 10.1111/2041-210x.12399] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 04/16/2015] [Indexed: 11/28/2022]
Abstract
Studying fungal biodiversity using data generated from Illumina MiSeq sequencing platforms poses a number of bioinformatic challenges with the analysis typically involving a large number of tools for each analytical step from quality filtering to generating identified operational taxonomic unit (OTU) abundance tables.Here, we introduce PIPITS, an open-source stand-alone suite of software for automated processing of Illumina MiSeq sequences for fungal community analysis. PIPITS exploits a number of state of the art applications to process paired-end reads from quality filtering to producing OTU abundance tables.We provide detailed descriptions of the pipeline and show its utility in the analysis of 9 396 092 sequences generated on the MiSeq platform from Illumina MiSeq. PIPITS is the first automated bioinformatics pipeline dedicated for fungal ITS sequences which incorporates ITSx to extract subregions of ITS and exploits the latest RDP Classifier to classify sequences against the curated UNITE fungal data set.
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Affiliation(s)
- Hyun S Gweon
- Centre for Ecology & Hydrology Maclean Building Benson Lane Crowmarsh Gifford Wallingford, Oxon OX10 8BB UK
| | - Anna Oliver
- Centre for Ecology & Hydrology Maclean Building Benson Lane Crowmarsh Gifford Wallingford, Oxon OX10 8BB UK
| | - Joanne Taylor
- Royal Botanic Garden Edinburgh 20A Inverleith Row Edinburgh EH3 5LR UK
| | - Tim Booth
- Centre for Ecology & Hydrology Maclean Building Benson Lane Crowmarsh Gifford Wallingford, Oxon OX10 8BB UK
| | - Melanie Gibbs
- Centre for Ecology & Hydrology Maclean Building Benson Lane Crowmarsh Gifford Wallingford, Oxon OX10 8BB UK
| | - Daniel S Read
- Centre for Ecology & Hydrology Maclean Building Benson Lane Crowmarsh Gifford Wallingford, Oxon OX10 8BB UK
| | - Robert I Griffiths
- Centre for Ecology & Hydrology Maclean Building Benson Lane Crowmarsh Gifford Wallingford, Oxon OX10 8BB UK
| | - Karsten Schonrogge
- Centre for Ecology & Hydrology Maclean Building Benson Lane Crowmarsh Gifford Wallingford, Oxon OX10 8BB UK
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