Current challenges and best-practice protocols for microbiome analysis

Briefings in Bioinformatics, Journal Year: 2019, Volume and Issue: 22(1), P. 178 - 193

Published: Nov. 7, 2019

Analyzing the microbiome of diverse species and environments using next-generation sequencing techniques has significantly enhanced our understanding on metabolic, physiological ecological roles environmental microorganisms. However, analysis is affected by experimental conditions (e.g. errors genomic repeats) computationally intensive cumbersome downstream quality control, assembly, binning statistical analyses). Moreover, introduction new technologies protocols led to a flood methodologies, which also have an immediate effect results analyses. The aim this work review most important workflows for 16S rRNA shotgun long-read metagenomics, as well provide best-practice design, sample processing, sequencing, binning, annotation visualization. To simplify standardize computational analysis, we set metagenomic data (available at https://github.com/grimmlab/MicrobiomeBestPracticeReview).

Language: Английский

---

Morphological approaches in studying fungi: collection, examination, isolation, sporulation and preservation

Mycosphere, Journal Year: 2020, Volume and Issue: 11(1), P. 2678 - 2754

Published: Jan. 1, 2020

Traditionally, fungal taxonomy was based on observable phenotypic characters.Recent advances have driven taxonomic conclusions towards DNA-based approaches and these techniques corresponding pros cons.Species concepts must therefore rely incorporated of genotypic, physiological characters chemotaxonomy.Examination interpretation morphological however vary from person to person.Standardized procedures are used in the study fungi general practices herein outlined.It is not possible detail all for thus, this paper emphasizes microfungi.Specimen collection initial step any

Language: Английский

---

Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

IMA Fungus, Journal Year: 2020, Volume and Issue: 11(1)

Published: July 10, 2020

True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of based on global richness estimates, with around 3 million predicted species. Compared to plants animals, have simple body plans often morphologically ecologically obscure structures. This poses challenges for accurate precise identifications. Here we provide a conceptual framework identification fungi, encouraging approach integrative (polyphasic) taxonomy species delimitation, i.e. combination genealogy (phylogeny), phenotype (including autecology), reproductive biology (when feasible). allows objective evaluation diagnostic characters, either phenotypic or molecular both. Verification identifications is crucial but neglected. Because clade-specific evolutionary histories, there currently no single tool although DNA barcoding using internal transcribed spacer (ITS) remains first diagnosis, particularly in metabarcoding studies. Secondary barcodes are increasingly implemented groups where ITS does not sufficient precision. Issues pairwise sequence similarity-based OTU clustering discussed, multiple alignment-based phylogenetic approaches subsequent verification recommended as more alternatives. In approaches, trade-off between speed accuracy precision must be carefully considered. Intragenomic variation other markers should properly documented, phylotype diversity necessarily proxy richness. Important strategies improve are: (1) broadly document intraspecific intragenomic markers; (2) substantially expand repositories, focusing undersampled clades missing taxa; (3) curation labels primary repositories increase number sequences verified material; (4) link data digital information voucher specimens including imagery. parallel, technological improvements genome sequencing offer promising alternatives future. Despite prevalence DNA-based fungal taxonomy, phenotype-based remain an important strategy catalog establish initial hypotheses.

Language: Английский

---

Secondary metabolism in the lichen symbiosis

Chemical Society Reviews, Journal Year: 2017, Volume and Issue: 47(5), P. 1730 - 1760

Published: Nov. 2, 2017

Lichens, which are defined by a core symbiosis between mycobiont (fungal partner) and photobiont (photoautotrophic partner), in fact complex assemblages of microorganisms that constitute largely untapped source bioactive secondary metabolites. Historically, compounds isolated from lichens have predominantly been those produced the dominant fungal partner, these continue to be great interest for their unique chemistry biotechnological potential. In recent years it has become apparent many photobionts lichen-associated bacteria also produce range potentially valuable molecules. There is evidence suggest nature played substantial role shaping aspects lichen chemistry, example driving metabolites do not bring them direct benefit but useful as whole. This most evident studies cyanobacterial photobionts, differ free living cyanobacteria symbiotic organisms. The roles other lichen-derived molecules may play communication maintaining poorly understood at present. Nonetheless, advances genomics, mass spectrometry analytical technologies continuing illuminate wealth biological chemical diversity present within holobiome. Implementation novel biodiscovery strategies such metagenomic screening, coupled with synthetic biology approaches reconstitute, re-engineer heterologously express biosynthetic gene clusters cultivable host, offer promising means tapping into this hitherto inaccessible natural products.

Language: Английский

---

Diversity of biologically active secondary metabolites from endophytic and saprotrophic fungi of the ascomycete order Xylariales

Natural Product Reports, Journal Year: 2018, Volume and Issue: 35(9), P. 992 - 1014

Published: Jan. 1, 2018

The diversity of secondary metabolites in the fungal order Xylariales is reviewed with special emphasis on correlations between chemical and biodiversity as inferred from recent taxonomic phylogenetic studies.

Language: Английский

---

Comparison of antifungal activity of essential oils from different plants against three fungi

Food and Chemical Toxicology, Journal Year: 2019, Volume and Issue: 134, P. 110821 - 110821

Published: Sept. 15, 2019

Language: Английский

---

Trichoderma: Advent of Versatile Biocontrol Agent, Its Secrets and Insights into Mechanism of Biocontrol Potential

Sustainability, Journal Year: 2022, Volume and Issue: 14(19), P. 12786 - 12786

Published: Oct. 7, 2022

Trichoderma is an important biocontrol agent for managing plant diseases. species are members of the fungal genus hyphomycetes, which widely distributed in soil. It can function as a well growth promoter. now frequently used biological control agents (BCAs) to combat wide range Major diseases have been successfully managed due their application. spp. being extensively researched order enhance its effectiveness top agent. The activation numerous regulatory mechanisms major factor ability manage Trichoderma-based methods include nutrient competition, mycoparasitism, synthesis antibiotic and hydrolytic enzymes, induced resistance. may synthesize variety secondary metabolites that inhibit activity GPCRs (G protein-coupled receptors) membrane-bound receptors sense transmit environmental inputs affect metabolism. Related intracellular signalling pathways also play role this process. Secondary produced by activate disease-fighting within plants protect against pathogens. β- Glucuronidase (GUS), green fluorescent protein (gfp), hygromycin B phosphotransferase (hygB), producing genes examples exogenous markers could be identify track specific isolates agro-ecosystems. More than sixty percent biofungicides on market derived from species. These fungi harmful developing Additionally, they solubilize nutrients boost bioremediate contaminants through mechanisms, including mycoparasitism antibiosis. Enzymes industry. This review article intends provide overview update (from 1975 2022) fungi, information key metabolites, genes, interactions with

Language: Английский

---

Fungal Mushrooms: A Natural Compound With Therapeutic Applications

Frontiers in Pharmacology, Journal Year: 2022, Volume and Issue: 13

Published: July 13, 2022

Fungi are extremely diverse in terms of morphology, ecology, metabolism, and phylogeny. Approximately, 130 medicinal activities like antitumor, immunomodulation, antioxidant, radical scavenging, cardioprotective antiviral actions assumed to be produced by the various varieties mushrooms. The polysaccharides, present mushrooms β-glucans, micronutrients, antioxidants glycoproteins, triterpenoids, flavonoids, ergosterols can help establish natural resistance against infections toxins.. Clinical trials have been performed on Agaricus blazei Murrill Kyowa for their anticancer effect , A. its antihypertensive effects, some other had also evaluated neurological effects. human evaluation dose studies toxicity was from literature number All were found safe at a 2000 mg/kg but with mild side safety therapeutic effectiveness fungal shifted interest biotechnologists toward nanobiotechnology as drug delivery system due vast advantages nanotechnology systems. In complement vital nutritional significance mushrooms, numerous species identified sources bioactive chemicals. Moreover, there unanswered queries regarding safety, efficacy, critical issues that affect future mushroom medicine development, could jeopardize usage twenty-first century.

Language: Английский

---

A genomic compendium of cultivated human gut fungi characterizes the gut mycobiome and its relevance to common diseases

Cell, Journal Year: 2024, Volume and Issue: 187(12), P. 2969 - 2989.e24

Published: May 21, 2024

Language: Английский

---

Significance of precise documentation of hosts and geospatial data of fungal collections, with an emphasis on plant-associated fungi

New Zealand Journal of Botany, Journal Year: 2024, Volume and Issue: unknown, P. 1 - 28

Published: July 28, 2024

In taxonomy, precision of species collection data is a cornerstone for advancing research and its diverse applications. Despite the widespread recognition significance these data, researchers have frequently neglected some important details in published taxonomic studies. Historically, fungal studies leaned heavily on morphological delineation taxa. contrast, methods currently employ synthesis combination morpho-molecular markers, chemical attributes both ecological geographic data. Even with new methods, mycologists value derived from old records as essential guides current future Therefore, this underscores importance careful documentation habits habitats parallel collection. While collecting specimens fungi, it to record metadata such sampling location, habitat (host/substrate), season (date or specific season) physical information specimen itself. These datasets will provide rich source ecology conservation resources. Understanding distribution patterns possible explanations real challenge conserving biodiversity, lack data-recording creates substantial obstacles. Accurate fungarium are basic understanding richness assessing red-listed invasive species. This paper explores additions recording, emphasising hosts locations. We also discuss significant roles seemingly insignificant recording enhance about relationships

Language: Английский

---