⚙
AI-generated deep summary
by claude@2026-07, 2026-07-03
· read from full text
ⓘ
This study compared Illumina short-read versus Pacific Biosciences long-read 16S rRNA gene sequencing for assessing archaeal and bacterial diversity in 42 river biofilm samples from seven sites in England. The authors found that PacBio longer reads provided higher taxonomic resolution and enabled classification of taxa that were unassigned in the Illumina datasets, improving species-level identification for ecological monitoring, while both platforms yielded comparable bacterial community structures in terms of relative abundance. A key caveat is that the work focuses on river biofilm microbiomes using 16S targeting, so results are specific to this marker and sampling context. The paper does not explicitly discuss endometriosis or adenomyosis; it was included in the corpus via a keyword match in the upstream search index.
Abstract
Freshwater ecosystems are under increasing pressure from pollution, habitat degradation, and climate change, highlighting the need for reliable biomonitoring approaches to assess ecosystem health and identify the causes of biodiversity and ecosystem service loss. Characterisation of freshwater microbiomes has the potential to be an important tool for understanding freshwater ecology, ecosystem health and ecosystem function. High-throughput sequencing technologies, such as Illumina short-read and Pacific Biosciences long-read sequencing, are widely used for microbial community analysis. However, the relative performance of these approaches for monitoring freshwater microbiomes has not been well explored. In this study, we compared the performance of long- and short-read sequencing approaches to assess archaeal and bacterial diversity in 42 river biofilm samples across seven distinct river sites in England by targeting the 16S ribosomal RNA gene. Our findings demonstrated that longer reads generated by PacBio sequencing provide a higher taxonomic resolution, enabling the classification of taxa that remained unassigned in the short-read Illumina datasets. This enhanced resolution is particularly beneficial for biodiversity assessments because it improves species-level identification, which is crucial for ecological monitoring. Despite this, both sequencing methods produced comparable bacterial community structures regarding taxon relative abundance, suggesting that the sequencing approach does not profoundly affect the comparative assessment of community composition. However, while Illumina offers higher throughput and cost efficiency, PacBio’s ability to resolve complex microbial communities highlights its potential for studies requiring precise taxonomic identification.
Full text
2,152 characters
· extracted from
oa-html
· click to expand
Abstract
Freshwater ecosystems are under increasing pressure from pollution, habitat degradation, and climate change, highlighting the need for reliable biomonitoring approaches to assess ecosystem health and identify the causes of biodiversity and ecosystem service loss. Characterisation of freshwater microbiomes has the potential to be an important tool for understanding freshwater ecology, ecosystem health and ecosystem function. High-throughput sequencing technologies, such as Illumina short-read and Pacific Biosciences long-read sequencing, are widely used for microbial community analysis. However, the relative performance of these approaches for monitoring freshwater microbiomes has not been well explored. In this study, we compared the performance of long- and short-read sequencing approaches to assess archaeal and bacterial diversity in 42 river biofilm samples across seven distinct river sites in England by targeting the 16S ribosomal RNA gene.
Our findings demonstrated that longer reads generated by PacBio sequencing provide a higher taxonomic resolution, enabling the classification of taxa that remained unassigned in the short-read Illumina datasets. This enhanced resolution is particularly beneficial for biodiversity assessments because it improves species-level identification, which is crucial for ecological monitoring. Despite this, both sequencing methods produced comparable bacterial community structures regarding taxon relative abundance, suggesting that the sequencing approach does not profoundly affect the comparative assessment of community composition. However, while Illumina offers higher throughput and cost efficiency, PacBio’s ability to resolve complex microbial communities highlights its potential for studies requiring precise taxonomic identification.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
Author emails: merand{at}ceh.ac.uk, m.a.j.anderson{at}pgr.reading.ac.uk, amytho{at}ceh.ac.uk, susbus{at}ceh.ac.uk, h.s.gweon{at}reading.ac.uk, Jonathan.Warren{at}environment-agency.gov.uk, kerry.walsh{at}environment-agency.gov.uk, daniel.read{at}ceh.ac.uk
Text is read by the "Ask this paper" AI Q&A widget below.
Extraction quality varies by source — PMC NXML preserves structure
cleanly, OA-HTML may include some navigation residue, and OA-PDF can
have broken hyphenation. The publisher copy
(via DOI)
is the canonical version.