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Nanopore Long-Read Metagenomics Reveals Pollution-Driven Antibiotic Resistance and Xenobiotic Degradation in Urban Beach Microbiomes.

Λεπτομέρειες βιβλιογραφικής εγγραφής
Τίτλος: Nanopore Long-Read Metagenomics Reveals Pollution-Driven Antibiotic Resistance and Xenobiotic Degradation in Urban Beach Microbiomes.
Συγγραφείς: de Oliveira AFB; Laboratório de Engenharia Biológica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil., Carneiro BS; Instituto Evandro Chagas, Ananindeua, Pará, Brazil., de Carvalho JB; Laboratório de Engenharia Biológica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil., de Oliveira AR; Laboratório de Engenharia Biológica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil., da Costa da Silva AL; Laboratório de Engenharia Biológica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil., de Oliveira Veras AA; Laboratório de Engenharia Biológica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil., Baraúna RA; Laboratório de Engenharia Biológica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil., das Graças DA; Laboratório de Engenharia Biológica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil.
Πηγή: Environmental microbiology reports [Environ Microbiol Rep] 2026 Aug; Vol. 18 (4), pp. e70396.
Τύπος έκδοσης: Journal Article
Γλώσσα: English
Στοιχεία περιοδικού: Publisher: Society for Applied Microbiology and Blackwell Pub Country of Publication: United States NLM ID: 101499207 Publication Model: Print Cited Medium: Internet ISSN: 1758-2229 (Electronic) Linking ISSN: 17582229 NLM ISO Abbreviation: Environ Microbiol Rep Subsets: MEDLINE
Imprint Name(s): Original Publication: [Hoboken, N.J.] : Society for Applied Microbiology and Blackwell Pub., c2009-
Ιατρικοί όροι (MeSH): Microbiota*/genetics , Bacteria*/genetics , Bacteria*/classification , Bacteria*/isolation & purification , Bacteria*/metabolism , Bacteria*/drug effects , Xenobiotics*/metabolism , Metagenomics* , Bathing Beaches* , Drug Resistance, Bacterial* , Drug Resistance, Microbial*, Brazil ; Biodiversity ; Phylogeny ; Biodegradation, Environmental ; Cities
Περίληψη: Coastal ecosystems are vital for biodiversity but are increasingly threatened by urbanisation and pollution, which significantly alter local microbial communities. This study assessed bacterial diversity and functional profiles in urban and island beaches in Belém, Brazil. Urban beaches showed significantly higher microbial diversity and evenness, alongside functional plasticity due to pollutant input, while island beaches hosted more specialised and stable communities. Taxonomic analysis revealed the significant enrichment of opportunistic genera such as Comamonas, Clostridium and Paenibacillus in urban areas, and the massive dominance of Prochlorococcus and Candidatus Pelagibacter in island sites. Furthermore, shotgun metagenomics identified a robust genomic potential for xenobiotic degradation and antibiotic resistance in urban microbiomes, whereas island microbiomes were significantly enriched in genes for energy production and biosynthesis. These results underscore the ecological divergence between anthropogenically impacted and natural coastal environments, highlighting the importance of microbiome monitoring for sustainable coastal management.
(© 2026 The Author(s). Environmental Microbiology Reports published by John Wiley & Sons Ltd.)
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Cantalapiedra, C. P., A. Hernández‐Plaza, I. Letunic, P. Bork, and J. Huerta‐Cepas. 2021. “eggNOG‐Mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale.” Molecular Biology and Evolution 38: 5825–5829. https://doi.org/10.1093/molbev/msab293.
Carini, P., L. Steindler, S. Beszteri, and S. J. Giovannoni. 2012. “Nutrient Requirements for Growth of the Extreme Oligotroph “Candidatus Pelagibacter ubique” HTCC1062 on a Defined Medium.” ISME Journal 7: 592–602.
Chrairi, M., S. Barrijal, A. Castellano‐Hinojosa, et al. 2024. “Metagenomic Analysis of Microbial Diversity in the Moroccan Coastal Water of the Gibraltar Strait.” Water 16: 3202.
Danecek, P., J. K. Bonfield, J. Liddle, et al. 2021. “Twelve Years of SAMtools and BCFtools.” GigaScience 10: giab008.
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Eltokhy, M. A., B. T. Saad, W. N. Eltayeb, I. S. Yahia, K. M. Aboshanab, and E. Ashour. 2021. “Exploring the Nature of the Antimicrobial Metabolites Produced by Paenibacillus ehimensis Soil Isolate MZ921932 Using a Metagenomic Nanopore Sequencing Coupled With LC‐Mass Analysis.” Antibiotics (Basel, Switzerland) 11: 12.
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Grant Information: 445350/2024-5 Conselho Nacional de Desenvolvimento Científico e Tecnológico
Substance Nomenclature: 0 (Xenobiotics)
Entry Date(s): Date Created: 20260810 Date Completed: 20260810 Latest Revision: 20260818
Update Code: 20260818
PubMed Central ID: PMC13456970
DOI: 10.1111/1758-2229.70396
PMID: 42575708
Βάση Δεδομένων: MEDLINE
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  Data: Nanopore Long-Read Metagenomics Reveals Pollution-Driven Antibiotic Resistance and Xenobiotic Degradation in Urban Beach Microbiomes.
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  Data: <searchLink fieldCode="AU" term="%22de+Oliveira+AFB%22">de Oliveira AFB</searchLink>; Laboratório de Engenharia Biológica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil.<br /><searchLink fieldCode="AU" term="%22Carneiro+BS%22">Carneiro BS</searchLink>; Instituto Evandro Chagas, Ananindeua, Pará, Brazil.<br /><searchLink fieldCode="AU" term="%22de+Carvalho+JB%22">de Carvalho JB</searchLink>; Laboratório de Engenharia Biológica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil.<br /><searchLink fieldCode="AU" term="%22de+Oliveira+AR%22">de Oliveira AR</searchLink>; Laboratório de Engenharia Biológica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil.<br /><searchLink fieldCode="AU" term="%22da+Costa+da+Silva+AL%22">da Costa da Silva AL</searchLink>; Laboratório de Engenharia Biológica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil.<br /><searchLink fieldCode="AU" term="%22de+Oliveira+Veras+AA%22">de Oliveira Veras AA</searchLink>; Laboratório de Engenharia Biológica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil.<br /><searchLink fieldCode="AU" term="%22Baraúna+RA%22">Baraúna RA</searchLink>; Laboratório de Engenharia Biológica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil.<br /><searchLink fieldCode="AU" term="%22das+Graças+DA%22">das Graças DA</searchLink>; Laboratório de Engenharia Biológica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil.
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  Data: <i>Original Publication</i>: [Hoboken, N.J.] : Society for Applied Microbiology and Blackwell Pub., c2009-
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  Data: <searchLink fieldCode="MM" term="%22Microbiota%22">Microbiota*</searchLink>/<searchLink fieldCode="MM" term="%22Microbiota+genetics%22">genetics</searchLink> <br /><searchLink fieldCode="MM" term="%22Bacteria%22">Bacteria*</searchLink>/<searchLink fieldCode="MM" term="%22Bacteria+genetics%22">genetics</searchLink> <br /><searchLink fieldCode="MM" term="%22Bacteria%22">Bacteria*</searchLink>/<searchLink fieldCode="MM" term="%22Bacteria+classification%22">classification</searchLink> <br /><searchLink fieldCode="MM" term="%22Bacteria%22">Bacteria*</searchLink>/<searchLink fieldCode="MM" term="%22Bacteria+isolation+%26+purification%22">isolation & purification</searchLink> <br /><searchLink fieldCode="MM" term="%22Bacteria%22">Bacteria*</searchLink>/<searchLink fieldCode="MM" term="%22Bacteria+metabolism%22">metabolism</searchLink> <br /><searchLink fieldCode="MM" term="%22Bacteria%22">Bacteria*</searchLink>/<searchLink fieldCode="MM" term="%22Bacteria+drug+effects%22">drug effects</searchLink> <br /><searchLink fieldCode="MM" term="%22Xenobiotics%22">Xenobiotics*</searchLink>/<searchLink fieldCode="MM" term="%22Xenobiotics+metabolism%22">metabolism</searchLink> <br /><searchLink fieldCode="MM" term="%22Metagenomics%22">Metagenomics*</searchLink> <br /><searchLink fieldCode="MM" term="%22Bathing+Beaches%22">Bathing Beaches*</searchLink> <br /><searchLink fieldCode="MM" term="%22Drug+Resistance%2C+Bacterial%22">Drug Resistance, Bacterial*</searchLink> <br /><searchLink fieldCode="MM" term="%22Drug+Resistance%2C+Microbial%22">Drug Resistance, Microbial*</searchLink><br /><searchLink fieldCode="MH" term="%22Brazil%22">Brazil</searchLink> ; <searchLink fieldCode="MH" term="%22Biodiversity%22">Biodiversity</searchLink> ; <searchLink fieldCode="MH" term="%22Phylogeny%22">Phylogeny</searchLink> ; <searchLink fieldCode="MH" term="%22Biodegradation%2C+Environmental%22">Biodegradation, Environmental</searchLink> ; <searchLink fieldCode="MH" term="%22Cities%22">Cities</searchLink>
– Name: Abstract
  Label: Abstract
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  Data: Coastal ecosystems are vital for biodiversity but are increasingly threatened by urbanisation and pollution, which significantly alter local microbial communities. This study assessed bacterial diversity and functional profiles in urban and island beaches in Belém, Brazil. Urban beaches showed significantly higher microbial diversity and evenness, alongside functional plasticity due to pollutant input, while island beaches hosted more specialised and stable communities. Taxonomic analysis revealed the significant enrichment of opportunistic genera such as Comamonas, Clostridium and Paenibacillus in urban areas, and the massive dominance of Prochlorococcus and Candidatus Pelagibacter in island sites. Furthermore, shotgun metagenomics identified a robust genomic potential for xenobiotic degradation and antibiotic resistance in urban microbiomes, whereas island microbiomes were significantly enriched in genes for energy production and biosynthesis. These results underscore the ecological divergence between anthropogenically impacted and natural coastal environments, highlighting the importance of microbiome monitoring for sustainable coastal management.<br /> (© 2026 The Author(s). Environmental Microbiology Reports published by John Wiley & Sons Ltd.)
– Name: Ref
  Label: References
  Group: RefInfo
  Data: Alanzi, A. R. 2024. “Exploring Microbial Dark Matter for the Discovery of Novel Natural Products: Characteristics, Abundance Challenges and Methods.” Journal of Microbiology and Biotechnology 35: e2407064. https://doi.org/10.4014/jmb.2407.07064.<br />Albuquerque, U. P., P. H. S. Gonçalves, W. S. Ferreira Júnior, et al. 2018. “Humans as Niche Constructors: Revisiting the Concept of Chronic Anthropogenic Disturbances in Ecology.” Perspectives in Ecology and Conservation 16: 1–11.<br />Antonelli, P., S. Grizard, F. H. Tran, et al. 2024. “Bioaccumulation of Polycyclic Aromatic Hydrocarbons and Microbiota Dynamics Across Developmental Stages of the Asian Tiger Mosquito, Aedes albopictus Exposed to Urban Pollutants.” Ecotoxicology and Environmental Safety 286: 117214.<br />Behrendt, U., P. Schumann, M. Stieglmeier, et al. 2010. “Characterization of Heterotrophic Nitrifying Bacteria With Respiratory Ammonification and Denitrification Activity – Description of Paenibacillus uliginis sp. nov., an Inhabitant of Fen Peat Soil and Paenibacillus purispatii sp. nov., Isolated From a Spacecraft Assembly Clean Room.” Systematic and Applied Microbiology 33: 328–336.<br />Braz, V. S., K. Melchior, and C. G. Moreira. 2020. “Escherichia coli as a Multifaceted Pathogenic and Versatile Bacterium.” Frontiers in Cellular and Infection Microbiology 10: 548492.<br />Buchfink, B., K. Reuter, and H.‐G. Drost. 2021. “Sensitive Protein Alignments at Tree‐Of‐Life Scale Using DIAMOND.” Nature Methods 18: 366–368.<br />Callahan, B. J., K. Sankaran, J. A. Fukuyama, P. J. McMurdie, and S. P. Holmes. 2016. “Bioconductor Workflow for Microbiome Data Analysis: From Raw Reads to Community Analyses.” F1000Research 5: 1492.<br />Cantalapiedra, C. P., A. Hernández‐Plaza, I. Letunic, P. Bork, and J. Huerta‐Cepas. 2021. “eggNOG‐Mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale.” Molecular Biology and Evolution 38: 5825–5829. https://doi.org/10.1093/molbev/msab293.<br />Carini, P., L. Steindler, S. Beszteri, and S. J. Giovannoni. 2012. “Nutrient Requirements for Growth of the Extreme Oligotroph “Candidatus Pelagibacter ubique” HTCC1062 on a Defined Medium.” ISME Journal 7: 592–602.<br />Chrairi, M., S. Barrijal, A. Castellano‐Hinojosa, et al. 2024. “Metagenomic Analysis of Microbial Diversity in the Moroccan Coastal Water of the Gibraltar Strait.” Water 16: 3202.<br />Danecek, P., J. K. Bonfield, J. Liddle, et al. 2021. “Twelve Years of SAMtools and BCFtools.” GigaScience 10: giab008.<br />Dang, H., T. Li, M. Chen, and G. Huang. 2008. “Cross‐Ocean Distribution of Rhodobacterales Bacteria as Primary Surface Colonizers in Temperate Coastal Marine Waters.” Applied and Environmental Microbiology 74: 52–60.<br />De Coster, W., S. 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        Type: general
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              Text: 2026 Aug
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