Comparative Analysis of Pasture Composition: DNA Metabarcoding Versus Quadrat‐Based Botanical Surveys in Experimental Grassland Plots

Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(4)

Published: March 27, 2025

ABSTRACT DNA metabarcoding provides a scalable alternative to traditional botanical surveys, which are often time‐consuming and reliant on taxonomic expertise. Here, we compare with quadrat‐based surveys assess plant species composition in experimental grassland plots under four defoliation regimes (continuous grazing, rotational frequent cutting conservation cutting). Botanical identified 16 taxa, while detected 25 including the dominant Holcus lanatus Lolium perenne . Despite detecting more there were some discrepancies identification, sequence data only able resolve taxa at genus level (e.g., Agrostis spp. instead of capillaris ) potential misidentifications Cardaminopsis helleri vs. Cardamine flexuosa ). However, both methods provided comparable results revealed statistically significant differences between treatments, higher diversity cut versus grazed plots. The semi‐quantitative nature limits its capacity accurately reflect abundance, posing challenges for ecological interpretations where precise quantification is required. it broader view biodiversity can complement methods, offering new opportunities efficient monitoring. findings support integration into assessments, particularly when used alongside techniques. Further refinement bioinformatics tools reference databases will enhance their accuracy reliability, enabling effective monitoring sustainable management practices. This study highlights as valuable tool understanding community responses interventions.

Language: Английский

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Protein Coding Low‐Copy rpb2 and ef1‐α Regions Are Viable Fungal Metabarcoding DNA Markers Which Can Supplement ITS for Better Accuracy

Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(4)

Published: April 1, 2025

ABSTRACT The nuclear ribosomal DNA Internal Transcribed Spacer (ITS) region is used as a universal fungal barcode marker, but often lacks significant barcoding gap between sister taxa. Here we tested the reliability of protein coding low‐copy genes alternative markers. Mock communities three unrelated agaric genera ( Dermoloma , Hodophilus and Russula ) representing lineages closely related species were sequenced by Illumina platform targeting ITS1, ITS2, second largest subunit RNA polymerase II gene rpb2 transcription elongation factor 1‐alpha ef1‐α regions. Species representation their relative abundances similar across all regions, despite lower copy number in ITS1 ITS2 required more sophisticated sequence filtering because they produced high chimeric sequences requiring reference‐based chimera removal had higher variants per species. Although clustering filtered ITS resulted an average correctly clustered units at optimal similarity thresholds, these thresholds varied substantially among genera. Best‐fitted markers consistent frequently lacked resolution due to low intraspecific variability. At some observed multiple lumped together, same time, split into partial clusters, which should be taken consideration when assessing best taxonomic identity clusters. To achieve improve detection, recommend combining different applying additional sorting current availability reference public databases far from being complete for groups, combined marker approach can group‐specific studies that build data own purposes.

Language: Английский

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Standardizing a microbiome pipeline for body fluid identification from complex crime scene stains

Applied and Environmental Microbiology, Journal Year: 2025, Volume and Issue: unknown

Published: April 30, 2025

ABSTRACT Recent advances in next-generation sequencing have opened up new possibilities for applying the human microbiome various fields, including forensics. Researchers capitalized on site-specific microbial communities found different parts of body to identify fluids from biological evidence. Despite promising results, microbiome-based methods not been integrated into forensic practice due lack standardized protocols and systematic testing forensically relevant samples. Our study addresses critical decisions establishing these protocols, focusing bioinformatics choices use machine learning present results case reports challenging In our study, we propose using operational taxonomic units (OTUs) read data processing generating heterogeneous training sets a random forest classifier. We incorporated six classes: saliva, semen, skin hand, penile skin, urine, vaginal/menstrual fluid, classifier achieved high weighted average F1 score 0.89. Systematic mock samples, mixed-source samples underwear, revealed reliable detection at least one component mixture identification vaginal fluid underwear substrates. Additionally, when investigating sexually shared (sexome) heterosexual couples, could potentially infer nature sexual activity. therefore highlight value sexome assessing activities investigations while delineating areas that warrant further research. IMPORTANCE Microbiome-based analyses combined with offer potential avenues science other applied yet remain lacking. Moreover, classifiers shown promise predicting sites forensics, but they systematically evaluated complex key and, knowledge, is first report classification uncontrolled (sexually microbiome) explore both strengths limitations classifying also providing options tackling limitations.

Language: Английский

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BioInformatics Agent (BIA): Unleashing the Power of Large Language Models to Reshape Bioinformatics Workflow

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: May 22, 2024

Abstract Bioinformatics plays a crucial role in understanding biological phenomena, yet the exponential growth of data and rapid technological advancements have heightened barriers to in-depth exploration this domain. Thereby, we propose B io- I nformatics A gent ( BIA ), an intelligent agent leveraging Large Language Models (LLMs) technology, facilitate autonomous bioinformatic analysis through natural language. The primary functionalities encompass extraction processing raw metadata, querying both locally deployed public databases for information. It further undertakes formulation workflow designs, generates executable code, delivers comprehensive reports. Focused on single-cell RNA sequencing (scRNA-seq) data, paper demonstrates ’s remarkable proficiency information analysis, as well executing sophisticated tasks interactions. Additionally, analyzed failed executions from demonstrate prospective enhancement strategies including selfrefinement domain adaptation. future outlook includes expanding practical implementations across multi-omics alleviating workload burden bioinformatics community empowering more profound investigations into mysteries life sciences. is available at: https://github.com/biagent-dev/biagent .

Language: Английский

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Advancing ecological assessment of the Arabian Gulf through eDNA metabarcoding: opportunities, prospects, and challenges

Frontiers in Marine Science, Journal Year: 2024, Volume and Issue: 11

Published: March 18, 2024

The Arabian Gulf (hereafter ‘the Gulf’) is renowned for its unique ecological characteristics and distinct marine life. It offers a diverse range of ecosystems that have adapted to the impacts posed by natural stress human activities. Regular biomonitoring diversity assessments are necessary document health ecosystem implement appropriate measures effective conservation management. Recently, environmental DNA (eDNA), total pool isolated from samples, has emerged as highly tool studies. This review explores opportunities, prospects, challenges associated with employing eDNA metabarcoding in assessment Gulf. provides an overview status discusses potential applications assessing biodiversity, monitoring invasive species, evaluating health. Additionally, investigation addresses inherent implementing this technique, considering complexities, methodological intricacies, data interpretation. Overall, emphasizes immense advancing calls further research collaboration harness benefits ecosystem.

Language: Английский

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A Comprehensive View of Food Microbiota: Introducing FoodMicrobionet v5

Foods, Journal Year: 2024, Volume and Issue: 13(11), P. 1689 - 1689

Published: May 28, 2024

Amplicon-targeted metagenomics is now the standard approach for study of composition and dynamics food microbial communities. Hundreds papers on this subject have been published in scientific journals information dispersed a variety sources, while raw sequences their metadata are available public repositories some, but not all, studies. A limited number web resources databases allow scientists to access wealth level annotation studies samples varies. Here, we report release FoodMicrobionet v5, comprehensive database metataxonomic bacterial fungal communities foods. The current version includes 251 (11 focusing microbiota, 230 10 providing data both microbiota) 14,035 with bacteria 1114 fungi. new structure compatible interactive apps scripts developed previous versions allows scientists, R&D personnel industries regulators

Language: Английский

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Transforming gastrointestinal helminth parasite identification in vertebrate hosts with metabarcoding: a systematic review

Parasites & Vectors, Journal Year: 2024, Volume and Issue: 17(1)

Published: July 19, 2024

Abstract Background Gastrointestinal helminths are a very widespread group of intestinal parasites that can cause major health issues in their hosts, including severe illness or death. Traditional methods helminth parasite identification using microscopy time-consuming and poor terms taxonomic resolution, require skilled observers. DNA metabarcoding has emerged as powerful alternative for assessing community composition variety sample types over the last few decades. While approaches have been reviewed use other research areas, only recently become widespread. As such, there is need to synthesize methodology highlight considerations be taken into account when developing protocol. Methods We published literature utilized identify gastrointestinal vertebrate hosts. extracted information from 62 peer-reviewed papers between 2014 2023 created stepwise guide process. Results found studies our review varied technique methodology, such type utilized, genetic marker regions targeted bioinformatic databases used. The main limitations abundance data may not reliably attained sequence read numbers, representative species present host cost expertise required utilize this method prohibitive some groups. Conclusions Overall, assess communities preferable traditional methods, yielding higher throughput increased versatility due its utility any geographical location, with types, virtually species. Additionally, potential exciting new discoveries regarding evolution. Graphical

Language: Английский

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Metacommunity theory and metabarcoding reveal the environmental, spatial, and biotic drivers of meiofaunal communities in sandy beaches

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 22, 2024

Abstract Sandy beaches are important ecosystems providing coastal protection and recreation, but they face significant threats from human activities sea level rise. They inhabited by meiofauna, small benthic invertebrates that highly abundant diverse, commonly understudied biotic components of beach ecosystems. Here, we investigate the factors shaping meiofaunal metacommunities employing Generalised Dissimilarity Modelling (GDM) Joint Species Distribution (JSDM) to study community turnover assembly processes. We analysed over 550 meiofauna samples a >650 km stretch southern North Sea coastline using metabarcoding approach. Our findings reveal environmental factors, especially Distance Low Tide Sediment Grain Size, drivers turnover. This highlights influence gradient marine terrestrial habitats sediment conditions. Spatial which indicate dispersal limitations, also significantly impact composition, challenging view have broad geographic distributions. The JSDM results show species sorting conditions is dominant process in with increasing differences between sampling sites, associations, or similar preferences, major driver at sites Further, find spatial across region. By facilitating inference ecological niches for high number taxa, provides powerful framework understanding ecology these animals. highlight importance considering gradients limitations ecosystem research, future research should aim adding information on functional traits interactions under varying understand dynamics resilience.

Language: Английский

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New insights into biologic interpretation of bioinformatic pipelines for fish eDNA metabarcoding: A case study in Pearl River estuary

Journal of Environmental Management, Journal Year: 2024, Volume and Issue: 368, P. 122136 - 122136

Published: Aug. 11, 2024

Language: Английский

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Comparison of commonly used software pipelines for analyzing fungal metabarcoding data

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: Nov. 14, 2024

Abstract Background Metabarcoding targeting the internal transcribed spacer (ITS) region is commonly used to characterize fungal communities of various environments. Given their size and complexity, raw ITS sequences are necessarily processed quality-filtered with bioinformatic pipelines. However, such pipelines not yet standardized, especially for communities, those available may produce contrasting results. While some cluster based on a specified percentage base pair similarity into operational taxonomic units (OTUs), others utilize denoising techniques infer amplicon sequencing variants (ASVs). ASVs now considered more accurate representation diversity prokaryote 16S rRNA sequencing, applicability this method still debated. Results Here we compared performance two DADA2 (inferring ASVs) mothur (clustering OTUs) metabarcoding originating from different environmental sample types (fresh bovine feces pasture soil). At 99% OTU threshold, consistently identified higher richness DADA2. In addition, generated homogenous relative abundances across multiple technical replicates ( n = 18), while results same were highly heterogeneous. Conclusions Our study highlights potential pipeline-associated bias in data analysis samples. Based homogeneity capacity detect OTUs/ASVs, suggest using clustering 97% as most appropriate option processing data.

Language: Английский

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