Effects of Rare Microbiome Taxa Filtering on Statistical Analysis

Frontiers in Microbiology, Journal Year: 2021, Volume and Issue: 11

Published: Jan. 12, 2021

Background: The accuracy of microbial community detection in 16S rRNA marker-gene and metagenomic studies suffers from contamination sequencing errors that lead to either falsely identifying taxa were not the sample or misclassifying DNA fragment reads. Removing contaminants filtering rare features are two common approaches deal with this problem. While contaminant methods use auxiliary process information identify known contaminants, remove present a small number samples have counts where they observed. latter approach reduces extreme sparsity microbiome data has been shown correctly cultured “mock” datasets, true compositions known. Although is frequently used, careful evaluation its effect on analysis scientific conclusions remains unreported. Here, we assess alpha beta diversity estimation as well impact discriminate between disease states. Results: illustrated four datasets: mock quality control datasets same composition processed at different labs study datasets. Results show magnitude differences alleviates technical variability while preserving similarity (beta diversity). In DESeq2 linear discriminant Effect Size (LEfSe) used differentially abundant across groups samples, random forest models rank largest contribution toward classification. reveal retains significant preserves model classification ability measured by area under receiver operating characteristic curve (AUC). comparison removal method shows complementary effects advised be conjunction. Conclusions: Filtering complexity their integrity downstream analysis. This leads mitigation methods' sensitivity reduction variability, allowing researchers generate more reproducible comparable results

Language: Английский

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Unboxing the black box—one step forward to understand the soil microbiome: A systematic review

Microbial Ecology, Journal Year: 2022, Volume and Issue: 85(2), P. 669 - 683

Published: Feb. 2, 2022

Abstract Soil is one of the most important assets planet Earth, responsible for maintaining biodiversity and managing ecosystem services both managed natural ecosystems. It encompasses large proportion microscopic biodiversity, including prokaryotes eukaryotes. microbiome critical in soil functions, but their activities have diminutive recognition few systems like desert land forest highly dependent on abiotic biotic factors pH, carbon content, structure, texture, vegetation, it can notably vary with ecosystems respective inhabitants. Thus, unboxing this black box essential to comprehend basic components adding supported services. Recent advancements field molecular microbial ecology delivered commanding tools examine genetic trove biodiversity. Objective review provide a evaluation work microbiome, especially since advent NGS techniques. The also focuses advances our understanding communities, interactions, functional capabilities along role maneuvering biogeochemical cycle while underlining tapping unprecedented metagenomics data infer ecological attributes yet undiscovered microbiome. This key research directions that could shape future applied into has led us understand difficult generalize plays substantiated shaping networks indeed vital resource sustaining functioning. Exploring will help unlocking roles various network. be resourceful exploring forecasting its impacts dealing alleviating problems rapid climate change.

Language: Английский

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The Microbial Connection to Sustainable Agriculture

Plants, Journal Year: 2023, Volume and Issue: 12(12), P. 2307 - 2307

Published: June 14, 2023

Microorganisms are an important element in modeling sustainable agriculture. Their role soil fertility and health is crucial maintaining plants' growth, development, yield. Further, microorganisms impact agriculture negatively through disease emerging diseases. Deciphering the extensive functionality structural diversity within plant-soil microbiome necessary to effectively deploy these organisms Although both plant have been studied over decades, efficiency of translating laboratory greenhouse findings field largely dependent on ability inoculants or beneficial colonize maintain stability ecosystem. its environment two variables that influence microbiome's structure. Thus, recent years, researchers looked into engineering would enable them modify microbial communities order increase effectiveness inoculants. The environments believed support resistance biotic abiotic stressors, fitness, productivity. Population characterization manipulation, as well identification potential biofertilizers biocontrol agents. Next-generation sequencing approaches identify culturable non-culturable microbes associated with expanded our knowledge this area. Additionally, genome editing multidisciplinary omics methods provided scientists a framework engineer dependable high yield, resistance, nutrient cycling, management stressors. In review, we present overview agriculture, engineering, translation technology field, main used by laboratories worldwide study microbiome. These initiatives advancement green technologies

Language: Английский

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Key features and guidelines for the application of microbial alpha diversity metrics

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: Jan. 3, 2025

Language: Английский

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Enhancement of oral bioavailability of natural compounds and probiotics by mucoadhesive tailored biopolymer-based nanoparticles: A review

Food Hydrocolloids, Journal Year: 2021, Volume and Issue: 118, P. 106772 - 106772

Published: March 23, 2021

Encapsulation in polymer NPs (NPs) is a well-recognized way to improve the oral bioavailability of hydrophobic and hydrophilic compounds by enhancing their solubility aqueous medium, protect them from acid enzymatic degradation gastrointestinal tract, favour permeability across mucosal membranes. Nanostructures rather than larger delivery systems are also proposed encapsulate prebiotics, probiotics natural antimicrobial compounds, as they allow greater penetration mucous layer, well lower longer dosages. The with mucoadhesive capacity designed specifically increase residence time at intestinal absorption sites due ability adhere mucosa. However, should be able penetrate through mucosa reach enterocytes or absorptive cells. By using appropriate materials, size surface properties can routed towards particular mucus-interaction mechanism. Polymer widely employed for applications pharmaceutical industry, since easily tunable mucus penetrating ability. Due biodegradability, biocompatibility non-toxicity, biopolymer have gained interest recent years potential food applications. This review aims promote attention use food-grade based on potential, facilitate antimicrobials along tract. includes previous brief introduction complex mucoadhesion mechanism common evaluation methods determining mucoadhesiveness nanoparticulate systems.

Language: Английский

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Exploring the human hair follicle microbiome*

British Journal of Dermatology, Journal Year: 2020, Volume and Issue: 184(5), P. 802 - 815

Published: Aug. 7, 2020

Human hair follicles (HFs) carry complex microbial communities that differ from the skin surface microbiota. This likely reflects HF epithelium differs epidermal barrier in it provides a moist, less acidic, and relatively ultraviolet light-protected environment, part of which is immune-privileged, thus facilitating survival. Here we review current understanding human microbiome its potential physiological pathological functions, including folliculitis, acne vulgaris, hidradenitis suppurativa, alopecia areata cicatricial alopecias. While reviewing main bacteria (such as Propionibacteria, Corynebacteria, Staphylococci Streptococci), viruses, fungi parasites constituents, advocate broad view an integral holobiont. Specifically, explore how may manage via regulated production antimicrobial peptides cathelicidin, psoriasin, RNAse7 dermcidin) by keratinocytes, impact on cytokine chemokine release HF, examine growth-modulatory effects antibiotics, ask whether affects growth turn. We highlight major open questions novel approaches to management diseases targeting microbiome.

Language: Английский

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The complexities of the diet-microbiome relationship: advances and perspectives

Genome Medicine, Journal Year: 2021, Volume and Issue: 13(1)

Published: Jan. 20, 2021

Personalised dietary modulation of the gut microbiota may be key to disease management. Current investigations provide a broad understanding impact diet on composition and activity microbiota, yet detailed knowledge in applying as an actionable tool remains limited. Further relative novelty field, approaches are standardised extremely heterogeneous research outcomes have ensued. This related confounders associated with complexities capturing accurate representation both microbiota. review discusses intricacies current methodologies diet-microbial relations, implications limitations these investigative approaches, future considerations that assist accelerating applications. New should consider improved collection data, further characterisation mechanistic interactions, increased focus -omic technologies such metabolomics describe bacterial metabolic food degradation, together its crosstalk host. Furthermore, clinical evidence health is required before therapeutic strategies for microbial amelioration can made. The potential reach diet-microbiota relations depend re-evaluation, progression, unification methodologies, which interactions.

Language: Английский

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Leveraging Human Microbiome Features to Diagnose and Stratify Children with Irritable Bowel Syndrome

Journal of Molecular Diagnostics, Journal Year: 2019, Volume and Issue: 21(3), P. 449 - 461

Published: April 17, 2019

Accurate diagnosis and stratification of children with irritable bowel syndrome (IBS) remain challenging. Given the central role recurrent abdominal pain in IBS, we evaluated relationships pediatric IBS intestinal microbes fecal metabolites using a comprehensive clinical characterization multiomics strategy. Using rigorous phenotyping, identified preadolescent (aged 7 to 12 years) Rome III (n = 23) healthy controls 22) characterized their microbial communities whole-genome shotgun metagenomics global unbiased metabolomic profiling. Correlation-based approaches machine learning algorithms associations between microbes, metabolites, pain. cases differed from respect key bacterial taxa (eg, Flavonifractor plautii Lachnospiraceae bacterium 7_1_58FAA), metagenomic functions carbohydrate metabolism amino acid metabolism), higher-order secondary bile acids, sterols, steroid-like compounds). Significant frequency severity features were identified. A random forest classifier built on metabolic markers successfully distinguished (area under curve, 0.93). Leveraging multiple lines evidence, genes/pathways, associated these capable distinguishing children. These multi-omics features, links childhood coupled nutritional interventions, may lead new microbiome-guided diagnostic therapeutic strategies.

Language: Английский

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Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions

Frontiers in Microbiology, Journal Year: 2021, Volume and Issue: 12

Published: Feb. 22, 2021

The human microbiome has emerged as a central research topic in biology and biomedicine. Current studies generate high-throughput omics data across different body sites, populations, life stages. Many of the challenges are similar to other studies, quantitative analyses need address heterogeneity data, specific statistical properties, remarkable variation composition individuals sites. This led broad spectrum machine learning that range from study design, processing, standardization analysis, modeling, cross-study comparison, prediction, science ecosystems, reproducible reporting. Nevertheless, although many statistics approaches tools have been developed, new techniques needed deal with emerging applications vast data. We review discuss introduce COST Action CA18131 "ML4Microbiome" brings together researchers experts current such analysis pipelines for reproducibility results, benchmarking, improvement, or development existing ontologies.

Language: Английский

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Dysbiosis From a Microbial and Host Perspective Relative to Oral Health and Disease

Frontiers in Microbiology, Journal Year: 2021, Volume and Issue: 12

Published: March 5, 2021

The significance of microbiology and immunology with regard to caries periodontal disease gained substantial clinical or research consideration in the mid 1960's. This enhanced emphasis related several simple but elegant experiments illustrating relevance bacteria oral infections. Since that point, understanding diseases has become increasingly sophisticated many original hypotheses causality have either been abandoned amplified. COVID pandemic reminded us importance history relative infectious words Churchill “those who fail learn from are condemned repeat it.” review is designed present an overview broad general directions over last 60 years immunology, reviewing significant contributions, indicating emerging foci interest, proposing future based on technical advances new understandings. Our goal this rich (standard immunology) point potential (omics) can lead a better disease. Over years, scientists moved position downplaying role one implicating as true pathogens cause More recently it proposed form ecological first line defense against “foreign” invaders also serve train immune system acquired host defensive stimulus. While early immunological was focused exposure modulator disease, “hygiene hypothesis,” now “old friends hypothesis” suggest response could be trained by for long-term health. Advanced “omics” technologies currently being used address changes occur microbiome methodologies shaped detection quantifiable biomarkers define human physiology pathologies. In summary, will emphasize commensals pathobionts play their interaction status host, prediction current “omic” allow researchers understand future.

Language: Английский

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