Assessment of Fungal Diversity in the Environment using Metagenomics:a Decade in Review

Cuadros-Orellana, Sara

doi:10.4172/2165-8056.1000110

Cited by 37 publications

(24 citation statements)

References 185 publications

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“…The most widely used marker gene for amplicon sequencing is the small subunit ribosomal RNA (16S) locus, that is both a taxonomically and phylogenetically informative marker for both bacteria and archaea [10,11]. Other markers such as the small subunit 18S, the large subunit (LSU: 23S/25S/28S) and the highly variable spacers ITS1 and ITS2 of the internal transcribed spacer (ITS) region have also been used, in particular for fungi, higher plants, insects and microalgae [12][13][14].…”

Section: Amplicon Sequencingmentioning

confidence: 99%

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Machine learning for metagenomics: methods and tools

Soueidan¹,

Nikolski²

2017

Metagenomics

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Owing to the complexity and variability of metagenomic studies, modern machine learning approaches have seen increased usage to answer a variety of question encompassing the full range of metagenomic NGS data analysis. We review here the contribution of machine learning techniques for the eld of metagenomics, by presenting known successful approaches in a uni ed framework. This review focuses on ve important metagenomic problems: OTU-clustering, binning, taxonomic pro ing and assignment, comparative metagenomics and gene prediction. For each of these problems, we identify the most prominent methods, summarize the machine learning approaches used and put them into perspective of similar methods. We conclude our review looking further ahead at the challenge posed by the analysis of interactions within microbial communities and di erent environments, in a eld one could call "integrative metagenomics".

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Section: Amplicon Sequencingmentioning

confidence: 99%

“…Analysis of other communities, such as for example fungi, are often done by ad-hoc methods or by hijacking software tools designed for bacteria (see e.g. [12,14]). …”

Section: Binningmentioning

confidence: 99%

Machine learning for metagenomics: methods and tools

Soueidan¹,

Nikolski²

2017

Metagenomics

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“…Thus, enrichment of isolation media with fungal culture filtrates could offer interesting opportunities to enhance isolation success. Such symbioses might also, at least partially explain the descrepency in numbers of fungi isolated from various substrates and those known to be present as shown in contemporary metagenomic studies (Fierer et al 2007;Kemler et al 2013;Cuadros-Orellana et al 2013). …”

Section: Discussionmentioning

confidence: 92%

Cornuvesica: A little known mycophilic genus with a unique biology and unexpected new species

et al. 2015

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ABSTRACT:Little is known about the biology of the monotypic genus Cornuvesica (Microascales), apart from that isolates are notoriously difficult to culture on artificial media. A recent collection of material resembling this genus from freshly made wounds on Gmelina arborea in Indonesia, provided an opportunity to reconsider all available material of Cornuvesica falcata, type species of the genus. In addition to morphological comparisons, multigene phylogenetic analyses were made using sequences of the SSU, ITS, LSU and TEF1a genes. Our results showed that the holotype of Cor. falcata from pine in Canada differed from all other material previously considered to represent this species and also from the new Indonesian collections. The collections considered represented three additional species that we describe here as new. Three New Zealand isolates and an isolate from UK were respectively described as Cor. acuminata and Cor. crypta, while the Indonesian isolates were described as Cor. magnispora. Phylogenies based on the SSU and LSU data sets showed that Cornuvesica spp. do not belong in the Ceratocystidaceae as previously suggested, but represent a distinct lineage in the Microascales that has yet to be named. Results showed that culture filtrates from other fungi or ferric chloride markedly stimulated the growth of Cor. magnispora.

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“…Metagenomics are culture-independent methods for the study of microbial diversity, based on next generation sequencing (NGS) and allowing characterization of fungi in complex environmental systems, using specific molecular markers for identification 15 . Abundant metagenomic data are available in public databases such as Sequence Read Archive (SRA 16 ), Rast Server (MG-RAST 17 ), and EBI metagenomics (EMG 18 ).…”

Section: Introductionmentioning

confidence: 99%

Environmental prospecting of black yeast-like agents of human disease using culture-independent methodology

Costa

Silva

Voidaleski

et al. 2020

Sci Rep

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Melanized fungi and black yeasts in the family Herpotrichiellaceae (order chaetothyriales) are important agents of human and animal infectious diseases such as chromoblastomycosis and phaeohyphomycosis. the oligotrophic nature of these fungi enables them to survive in adverse environments where common saprobes are absent. Due to their slow growth, they lose competition with common saprobes, and therefore isolation studies yielded low frequencies of clinically relevant species in environmental habitats from which humans are thought to be infected. this problem can be solved with metagenomic techniques which allow recognition of microorganisms independent from culture. the present study aimed to identify species of the family Herpotrichiellaceae that are known to occur in Brazil by the use of molecular markers to screen public environmental metagenomic datasets from Brazil available in the Sequence Read Archive (SRA). Species characterization was performed with the BLASt comparison of previously described barcodes and padlock probe sequences. A total of 18,329 sequences was collected comprising the genera Cladophialophora, Exophiala, Fonsecaea, Rhinocladiella and Veronaea, with a focus on species related to the chromoblastomycosis. the data obtained in this study demonstrated presence of these opportunists in the investigated datasets. the used techniques contribute to our understanding of environmental occurrence and epidemiology of black fungi. A large number of species of black yeast-like fungi that belong to the ascomycetous order Chaetothyriales in the family Herpotrichiellaceae are renowned as opportunistic pathogens in immunocompetent vertebrate hosts 1,2. Agents are particularly involved in subcutaneous, and systemic or disseminated infections, known as chromoblastomycosis and phaeohyphomycosis, respectively 2-4. These infections are invariably chronic and can be severely mutilating or even fatal. Chromoblastomycosis is a relatively common disease in rural tropical climate zones around the world. This implantation disorder is characterized by the presence of a specialized tissue form of the fungus known as the muriform cell 2,5,6. Infection is hypothesized to take place via traumatic inoculation of environmental material such as plant thorns and/or wood fragments 7,8. Epidemiological data confirmed by studies using selective

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Assessment of Fungal Diversity in the Environment using Metagenomics:a Decade in Review

Cited by 37 publications

References 185 publications

Machine learning for metagenomics: methods and tools

Machine learning for metagenomics: methods and tools

Cornuvesica: A little known mycophilic genus with a unique biology and unexpected new species

Environmental prospecting of black yeast-like agents of human disease using culture-independent methodology

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