Navigating the seven challenges of taxonomic reference databases in metabarcoding analyses

Molecular Ecology Resources, Год журнала: 2022, Номер 23(4), С. 742 - 755

Опубликована: Дек. 8, 2022

Assessment of biodiversity using metabarcoding data, such as from bulk or environmental DNA sampling, is becoming increasingly relevant in ecology, sciences and monitoring. Thereby, the taxonomic identification species their sequences relies strongly on reference databases that link genetic to names. These vary completeness availability, depending group studied region targeted. The incompleteness an important argument explain nondetection by supposedly present. However, there exist further generally overlooked problems with can lead false inaccurate inferences assignment. Here, we synthesize all possible inherent databases. In particular, identify a complete, mutually nonexclusive list seven classes challenges when it comes selecting, developing database for are: (i) mislabelling, (ii) sequencing errors, (iii) sequence conflict, (iv) (v) low resolution, (vi) missing taxa (vii) intraspecific variants. For each problem identified, provide description consequences assignment process. We illustrate respective examples taken literature obtained quantitative analyses public databases, GenBank BOLD. Finally, discuss solutions identified how navigate them. Only raising users' awareness limitations data will adequate interpretations these be achieved.

Язык: Английский

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Fecal microbiota transplantation improves anti-PD-1 inhibitor efficacy in unresectable or metastatic solid cancers refractory to anti-PD-1 inhibitor

Cell Host & Microbe, Год журнала: 2024, Номер 32(8), С. 1380 - 1393.e9

Опубликована: Июль 25, 2024

Язык: Английский

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A conserved interdomain microbial network underpins cadaver decomposition despite environmental variables

Nature Microbiology, Год журнала: 2024, Номер 9(3), С. 595 - 613

Опубликована: Фев. 12, 2024

Abstract Microbial breakdown of organic matter is one the most important processes on Earth, yet controls decomposition are poorly understood. Here we track 36 terrestrial human cadavers in three locations and show that a phylogenetically distinct, interdomain microbial network assembles during despite selection effects location, climate season. We generated metagenome-assembled genome library from cadaver-associated soils integrated it with metabolomics data to identify links between taxonomy function. This universal decomposers characterized by cross-feeding metabolize labile products. The key bacterial fungal rare across non-decomposition environments appear unique decaying flesh, including humans, swine, mice cattle, insects as likely vectors for dispersal. observed lockstep interactions further underlies robust forensic tool potential aid predictions time since death.

Язык: Английский

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Information storage across a microbial community using universal RNA barcoding

Nature Biotechnology, Год журнала: 2025, Номер unknown

Опубликована: Март 18, 2025

Язык: Английский

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Escherichia/Shigella, SCFAs, and Metabolic Pathways—The Triad That Orchestrates Intestinal Dysbiosis in Patients with Decompensated Alcoholic Cirrhosis from Western Mexico

Microorganisms, Год журнала: 2022, Номер 10(6), С. 1231 - 1231

Опубликована: Июнь 16, 2022

Gut microbiota undergoes profound alterations in alcohol cirrhosis. Microbiota-derived products, e.g., short chain fatty acids (SCFA), regulate the homeostasis of gut-liver axis. The objective was to evaluate composition and functions intestinal patients with alcohol-decompensated Fecal samples 18 healthy controls (HC) were obtained. Microbial characterized by 16S rRNA amplicon sequencing, SCFA quantification performed gas chromatography (GC), metagenomic predictive profiles analyzed PICRUSt2. cirrhosis group revealed a significant increase pathogenic/pathobionts genera Escherichia/Shigella Prevotella, decrease beneficial bacteria, such as Blautia, Faecalibacterium, decreased α-diversity (p < 0.001) compared HC. concentrations significantly reduced 0.001). PICRUSt2 analysis indicated acetyl-CoA fermentation butyrate, well an pathways related antibiotics resistance, aromatic amino acid biosynthesis. These metabolic have been poorly described progression alcohol-related decompensated gut these possesses pathogenic/inflammatory environment; therefore, future strategies balance dysbiosis should be implemented. findings are for first time population western Mexico.

Язык: Английский

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A Comparison of Six DNA Extraction Protocols for 16S, ITS and Shotgun Metagenomic Sequencing of Microbial Communities

BioTechniques, Год журнала: 2022, Номер 73(1), С. 34 - 46

Опубликована: Июнь 17, 2022

Microbial communities contain a broad phylogenetic diversity of organisms; however, the majority methods center on describing bacteria and archaea. Fungi are important symbionts in many ecosystems potentially members human microbiome, beyond those that can cause disease. To expand our analysis microbial to include data from fungal internal transcribed spacer (ITS) region, five candidate DNA extraction kits were compared against standardized protocol for archaea using 16S rRNA gene amplicon- shotgun metagenomics sequencing. The results presented considering diverse panel host-associated environmental sample types comparing cost, processing time, well-to-well contamination, yield, limit detection community composition among protocols. Across all criteria, MagMAX Microbiome kit was found perform best. PowerSoil Pro performed comparably but with increased cost per overall time. Zymo MagBead, NucleoMag Food Norgen Stool included.

Язык: Английский

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Rhizosheath–root system changes exopolysaccharide content but stabilizes bacterial community across contrasting seasons in a desert environment

Environmental Microbiome, Год журнала: 2022, Номер 17(1)

Опубликована: Апрель 1, 2022

In hot deserts daily/seasonal fluctuations pose great challenges to the resident organisms. However, these extreme ecosystems host unique microenvironments, such as rhizosheath-root system of desert speargrasses in which biological activities and interactions are facilitated by milder conditions reduced fluctuations. Here, we examined bacterial microbiota associated with this structure its surrounding sand speargrass Stipagrostis pungens under contrasting environmental summer winter Sahara Desert.The belowground has higher nutrient humidity contents, cooler temperatures than sand. The plant responds harsh increasing abundance diversity extracellular polymeric substances (EPS) compared winter. On contrary, community interactome remain stable and, unlike bulk sand, unaffected seasonal variations. communities consistently dominated Actinobacteria Alphaproteobacteria form distinct bacteria from those two seasons. microbiome-stabilization mediated acts retain beneficial multiple growth promoting functions, including capable produce EPS, increase water holding capacity ameliorating rhizosheath micro-environment.Our results reveal capability plants stabilize their below ground microbial conditions, minimizing heterogeneity contributing overall holobiont resilience poly-extreme conditions.

Язык: Английский

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The fate of sulfonamide resistance genes and anthropogenic pollution marker intI1 after discharge of wastewater into a pristine river stream

Frontiers in Microbiology, Год журнала: 2023, Номер 14

Опубликована: Янв. 25, 2023

Currently there are sparse regulations regarding the discharge of antibiotics from wastewater treatment plants (WWTP) into river systems, making surface waters a latent reservoir for and antibiotic resistance genes (ARGs). To better understand factors that influence fate ARGs in environment to foster surveillance spreading such habitats, several indicator have been proposed, including integrase gene intI1 sulfonamide sul1 sul2.Here we used quantitative PCR long-read nanopore sequencing monitor abundance these present as class 1 integron cassettes system pristine source WWTP-impacted water. ARG was compared with dynamics microbial communities determined via 16S rRNA amplicon sequencing, conventional water parameters concentration sulfamethoxazole (SMX), sulfamethazine (SMZ) sulfadiazine (SDZ).Our results show WWTP effluent principal all three sulfonamides highest concentrations SMX (median 8.6 ng/l), sul1, sul2 median relative 0.55, 0.77 0.65%, respectively. Downstream WWTP, quality improved constantly, lower concentrations, decreasing abundances numbers diversity integron. The riverine community partially recovered after receiving effluent, which consolidated by microbiome recovery model. Surprisingly, increased 3-fold over 13 km stretch, suggesting an internal multiplication.We found no evidence low amounts aquatic stimulate maintenance or even spread corresponding ARGs. Nevertheless, integrons carrying various were still downstream WWTP. Therefore, limiting release ARG-harboring microorganisms may be more crucial restricting environmental antimicrobial than attenuating ng/L antibiotics.

Язык: Английский

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From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools

Microbial Genomics, Год журнала: 2023, Номер 9(3)

Опубликована: Март 3, 2023

In metagenomic analyses of microbiomes, one the first steps is usually taxonomic classification reads by comparison to a database previously taxonomically classified genomes. While different studies comparing methods have determined that tools are 'best', there two been used most to-date: Kraken (

Язык: Английский

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A critical role of a eubiotic microbiota in gating proper immunocompetence in Arabidopsis

Nature Plants, Год журнала: 2023, Номер 9(9), С. 1468 - 1480

Опубликована: Авг. 17, 2023

Although many studies have shown that microbes can ectopically stimulate or suppress plant immune responses, the fundamental question of whether entire preexisting microbiota is indeed required for proper development response remains unanswered. Using a recently developed peat-based gnotobiotic growth system, we found Arabidopsis grown in absence natural lacked age-dependent maturation and were defective several aspects pattern-triggered immunity. Axenic plants exhibited hypersusceptibility to infection by bacterial pathogen Pseudomonas syringae pv. tomato DC3000 fungal Botrytis cinerea. Microbiota-mediated immunocompetence was suppressed rich nutrient conditions, indicating tripartite interaction between host, abiotic environment. A synthetic composed 48 culturable strains from leaf endosphere healthy able substantially restore similar inoculated with soil-derived community. In contrast, 52-member dysbiotic overstimulated transcriptome. Together, these results provide evidence causal role eubiotic gating immunity plants.

Язык: Английский

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