How micro(nano)plastics interact with human gut microbiota Dysbiosis Food Inflammation Microbiome Gut biodegradation MicrobialBiote1 CIAL_CSIC_UAM
The consequences of plastic waste on the environment and human, animal, and plant health have risen as a global concern, with microplastics serving as the primary focus. The presence of MNPs in the food chain has resulted in an increase in human consumption. They have been identified in the majority of consumable food categories, potable, and even human fecal matter. Therefore, oral intake is the primary route of exposure to MNPs.
The impact of MNPs on the microbiota of the gut Over the past two decades, the significance of gut microbiome–host relationships has been increasingly recognized, with scientific evidence indicating the central function of the gut microbiota in proper host development, with consequences for host physiology and health maintenance. Importantly, the gut microbiota is regarded as an "organ" exposed to environmental alterations and trauma as the first line of defense.
At realistic concentrations, the effects of exposure to PS MPs in untreated and seawater on the gut microbiota present in marine bivalve blue mussels have been reported. Potential human pathogens displayed elevated abundance after MP exposure for six weeks, while some maintained higher abundance after eight days of depuration. MNP-induced effects on intestinal microbiota may also be conceivable due to the biofilm present on their surfaces, which has significant consequences on aquatic species.
Intestinal dysbiosis can alter the thick mucus layer, which may result in aberrant mucus invasion and epithelial adherence of pathogens, or may permit the interaction of MNPs with the epithelial layer and damage the gut epithelium, thus altering the intestinal milieu. Mucus-associated bacterial biofilms may contribute to these conditions.
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Investigating the impact of database choice on the accuracy of metagenomic read classification for the rumen microbiome - Animal MicrobiomeMicrobiome analysis is quickly moving towards high-throughput methods such as metagenomic sequencing. Accurate taxonomic classification of metagenomic data relies on reference sequence databases, and their associated taxonomy. However, for understudied environments such as the rumen microbiome many sequences will be derived from novel or uncultured microbes that are not present in reference databases. As a result, taxonomic classification of metagenomic data from understudied environments may be inaccurate. To assess the accuracy of taxonomic read classification, this study classified metagenomic data that had been simulated from cultured rumen microbial genomes from the Hungate collection. To assess the impact of reference databases on the accuracy of taxonomic classification, the data was classified with Kraken 2 using several reference databases. We found that the choice and composition of reference database significantly impacted on taxonomic classification results, and accuracy. In particular, NCBI RefSeq proved to be a poor choice of database. Our results indicate that inaccurate read classification is likely to be a significant problem, affecting all studies that use insufficient reference databases. We observed that adding cultured reference genomes from the rumen to the reference database greatly improved classification rate and accuracy. We also demonstrated that metagenome-assembled genomes (MAGs) have the potential to further enhance classification accuracy by representing uncultivated microbes, sequences of which would otherwise be unclassified or incorrectly classified. However, classification accuracy was strongly dependent on the taxonomic labels assigned to these MAGs. We therefore highlight the importance of accurate reference taxonomic information and suggest that, with formal taxonomic lineages, MAGs have the potential to improve classification rate and accuracy, particularly in environments such as the rumen that are understudied or contain many
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