Metagenomic Approaches for Optimising Hydrocarbon Pollution Rhizoremediation DOI Creative Commons
Oladayo Amed Idris, Mariana Erasmus

International Journal of Environmental Research, Journal Year: 2024, Volume and Issue: 19(2)

Published: Dec. 23, 2024

Abstract Increasing levels of pervasive harmful chemicals like polycyclic aromatic hydrocarbons (PAHs) have been linked to unprecedentedly high cases several illnesses, loss biodiversity, and environmental degradation, posing a threat the sustainability life. Several biodegradation procedures proposed for cleaning up contaminated sites, among which rhizoremediation, type phytoremediation, is perceived be one most cost-efficient methods has good public acceptance. To enhance effectiveness use transgenic plants deployed; however, many studies demonstrated that rhizosphere microbial communities are actively involved in degradation hydrocarbons. The plant thus facilitates formidable support cross-communication through root exudates, rhizodeposition. Unlike conventional microbiology procedures, throughput metagenomic approaches unveil both individual community functional capacities, novel species, gene molecular composition, allowing alteration growth promotion, resistance PAHs, metabolism contaminant compounds. This article presents an updated overview modifying soil effective enhanced rhizoremediation hydrocarbon-polluted soil. Graphical abstract

Language: Английский

Enhancing Dichlorobenzene Degradation in Sulfate-Rich Groundwater Using Yeast Extract: Performance and Microbial Responses DOI

Chunmei Ye,

Ouyang Ji,

Qingqing Li

et al.

Journal of environmental chemical engineering, Journal Year: 2025, Volume and Issue: unknown, P. 115433 - 115433

Published: Jan. 1, 2025

Language: Английский

Citations

0
Impact of antibiotic prophylaxis on gut microbiota in colorectal surgery: insights from an Eastern European stewardship study DOI Creative Commons

Irina Cezara Văcărean-Trandafir,

Roxana-Maria Amărandi, I Ivanov

et al.

Frontiers in Cellular and Infection Microbiology, Journal Year: 2025, Volume and Issue: 14

Published: Jan. 13, 2025

Introduction Antibiotic overuse is driving a global rise in antibiotic resistance, highlighting the need for robust antimicrobial stewardship (AMS) initiatives to improve prescription practices. While antimicrobials are essential treating sepsis and preventing surgical site infections (SSIs), they can inadvertently disrupt gut microbiota, leading postoperative complications. Treatment methods vary widely across nations due differences drug choice, dosage, therapy duration, affecting resistance rates, which reach up 51% some countries. In Romania Republic of Moldova, healthcare practices prophylaxis differ significantly despite similarities genetics, culture, diet. Romania's stricter regulations result more standardized protocols, whereas Moldova's limited funding leads less consistent greater variability treatment outcomes. Methods This study presents results prospective cross-border investigation involving 86 colorectal cancer patients from major oncological hospitals Moldova. We analyzed fecal samples collected before 7 days post-antibiotic treatment, focusing on V3–V4 region 16S rRNA gene. Results Our findings indicate that inconsistent policies—varying type, or duration—significantly impacted microbiota led frequent dysbiosis compared prophylactic (single dose, single product, time). Discussion emphasize protocols minimize its associated risks, promoting effective use, particularly low- middle-income countries (LMICs).

Language: Английский

Citations

0
Yeast mannans promote laxation and specifically modulate microbiota composition in older adults: An open-label pilot study. DOI Creative Commons
Matías Bedmar Moreno, Pieter Van den Abbeele, Aurélien Baudot

et al.

Nutrition Research, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 1, 2025

Language: Английский

Citations

0
Relationship Between Gut Microbiota and the Clinical Course of COVID-19 Disease DOI Creative Commons

Antonija Jonjić,

Ivan Dolanc, Goran Slivšek

et al.

Viruses, Journal Year: 2025, Volume and Issue: 17(4), P. 520 - 520

Published: April 2, 2025

Possible early detection of people at increased risk for severe COVID-19 clinical course is extremely important so that appropriate therapy can be initiated promptly to prevent numerous deaths. Our study included 45 patients treated Dubrava University Hospital, with analysed from medical records and stool samples collected determination the gut microbiota diversity using 16S rRNA analysis. Sequencing was successful 41 belonging four groups (WHO guidelines): 12 samples—critical, 12—severe, 9—moderate 8—mild group. Microbial composition assessed between two approaches—ANCOM (QIIME2) Kruskal–Wallis (MicrobiomeAnalyst). On genus level, taxa were found differentially abundant: archaeal Halococcus Coprococcus (for both W = 37)—the most abundant in critical group (10% 0.94% entire abundance, respectively). catus only species identified by methods Alpha indicated greater evenness features Beta showed clustering A relationship disease indicated, pointing towards specific distinct In a broader sense, our findings might useful combating potential future similar pandemics emerging virus outbreaks.

Language: Английский

Citations

0
Microbial ecology of drinking water biofiltration based on 16S rRNA sequencing: a meta-analysis DOI Creative Commons
Fabien Cholet, Marta Vignola, Dominic Quinn

et al.

Water Research, Journal Year: 2025, Volume and Issue: 281, P. 123684 - 123684

Published: April 19, 2025

Biofiltration, a sustainable water treatment technology relying on microbial processes to remove contaminants, offers promising approach achieving the United Nations Sustainable Goal 6 of universal access clean and sanitation by 2030. However, key barrier optimising biofiltration is incomplete understanding biological mechanisms governing its performance. Despite numerous studies examining how engineering decisions impact biofilter performance associated microbiome, significant influence geographical location communities raises question whether these findings are universally applicable or location-specific. To address this, we conducted meta-analysis 15 microbiomes using 16S rRNA high-throughput sequencing (HTS) data, mainly originating from rapid gravity and/or granular activated carbon (GAC) filters. different types scales, results highlight as major contributor microbiome dissimilarity in samples (Top Bottom) (R2∼ 0.5; p-value<0.001). The same was observed for influent waters (PERMANOVA R2= 0.76; p-value<0.001), indicating location-specific opposed differences driven operating parameters. Irrespective location, higher percentage assembled through deterministic (∼55 %) compared stochastic (∼45 %). Finally, our suggest that depth stratification may be with enrichment taxa capable metabolising more complex organic deeper filter layers (10 enriched pathways Bottom 3 at Top). These insights provide broader offer possible research avenues targeted effective design strategies.

Language: Английский

Citations

0
Do we need a standardized 16S rRNA gene amplicon sequencing analysis protocol for poultry microbiota research? DOI Creative Commons
Joshua M. Lyte, Mitiku Mihiret Seyoum, Diana E. Ayala

et al.

Poultry Science, Journal Year: 2025, Volume and Issue: unknown, P. 105242 - 105242

Published: May 1, 2025

Language: Английский

Citations

0
Resistome Signature and Antibiotic Resistance Mechanisms in Rhizospheric Soil Bacteriomes of Mecca Region, Saudi Arabia: Insights into Impact on Human Health DOI Creative Commons
Rewaa S. Jalal, Hana Sonbol

Life, Journal Year: 2024, Volume and Issue: 14(8), P. 928 - 928

Published: July 24, 2024

The objective of this investigation is to ascertain the distinctive profile rhizospheric soil resistome within Mecca region, while also evaluating potential risks associated with horizontal transfer determinants open environment and human clinical isolates. We have made metagenomic whole-genome shotgun sequencing for microbiomes two endemic plants, namely Moringa oleifera Abutilon fruticosum. resistomes plants abundance antibiotic resistance genes (ARGs) were identified by cross-referencing encoded proteins comprehensive database (CARD). ARGs then analyzed their antimicrobial (AMR) mechanisms. Predominantly are bacterial species Pseudomonas aeruginosa Mycobacterium tuberculosis. These opportunistic pathogens implicated in respiratory infections correlated heightened mortality rates. most prevalent array existing comprises mexA, mexC, mexE, cpxR, mechanisms active efflux, along ACC(2), ACC(3), AAC(6), APH(6), addition arr1, arr3, arr4, iri, rphA, rphB, inactivation. Furthermore, vanS, vanR, vanJ target alteration, rpoB2 RbpA noted replacement protection, respectively. confer against a diverse spectrum drug classes encompassing fluoroquinolones, aminoglycosides, glycopeptides, rifampicins. This study underscores hazards posed health presence these pathogenic bacteria particularly scenarios where novel populations harbored subsequently transmitted through food chain Consequently, stringent adherence good agricultural transportation practices imperative, regard edible plant parts those utilized folkloric medicine.

Language: Английский

Citations

2
A Targeted Reference Database for Improved Analysis of Environmental 16S rRNA Oxford Nanopore Sequencing Data DOI Creative Commons
Melcy Philip,

Tonje Nilsen,

Sanna Majaneva

et al.

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

Published: Oct. 3, 2024

Abstract The Oxford Nanopore Technologies (ONT) sequencing platform is compact and efficient, making it suitable for rapid biodiversity assessments in remote areas. Despite its long reads, ONT has a higher error rate compared to other platforms, necessitating high-quality reference databases accurate taxonomic assignments. However, the absence of targeted underexplored habitats, such as seafloor, limits ONT’s broader applicability exploratory analysis. To address this, we have developed strategy build environmentally-targeted enhance 16S rRNA gene(16S) analysis using ONT. We start by Illumina short-read data create database full-length or near sequences from seafloor samples. Initially, amplicons are mapped SILVA database, with matches added our database. Unmatched reconstructed METASEED Barrnap methodologies amplicon metagenome data. Finally, if previous strategies did not succeed, included This resulted AQUAeD-DB, which contains 14 545 clustered at 95% identity. Comparative relative abundance correlation studies reveal that AQUAeD-DB provides consistent results both read assignments (median coefficient: 0.50), whereas standard showed substantially weaker correlation. These findings also emphasis potential recognize high low-abundance taxa, could be key indicators environmental studies. work highlights necessity analysis, especially ONT-based studies, lays foundations future extension

Language: Английский

Citations

2
The microwave bacteriome: biodiversity of domestic and laboratory microwave ovens DOI Creative Commons
Alba Iglesias, Lorena Martinez‐Gamboa, Daniel Torrent

et al.

Frontiers in Microbiology, Journal Year: 2024, Volume and Issue: 15

Published: Aug. 8, 2024

Microwaves have become an essential part of the modern kitchen, but their potential as a reservoir for bacterial colonization and microbial composition within them remain largely unexplored. In this study, we investigated communities in microwave ovens compared domestic microwaves, microwaves used shared large spaces, laboratory using next-generation sequencing culturing techniques. The oven population was dominated by

Language: Английский

Citations

1
Assessment of Skimmed Milk Flocculation for Bacterial Enrichment from Water Samples, and Benchmarking of DNA Extraction and 16S rRNA Databases for Metagenomics DOI Open Access
Deyan Donchev, Ivan Stoikov, Antonia Diukendjieva

et al.

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(19), P. 10817 - 10817

Published: Oct. 8, 2024

Water samples for bacterial microbiome studies undergo biomass concentration, DNA extraction, and taxonomic identification steps. Through benchmarking, we studied the applicability of skimmed milk flocculation (SMF) enrichment, an adapted in-house extraction protocol, six 16S rRNA databases (16S-DBs). Surface water from two rivers were treated with SMF vacuum filtration (VF) subjected to amplicon or shotgun metagenomics. A microbial community standard underwent five protocols, taxonomical different 16S-DBs, evaluation by Measurement Integrity Quotient (MIQ) score. In samples, was metabolized members lactic acid bacteria genera such as

Language: Английский

Citations

0