A novel method to assess the integrity of frozen archival DNA samples: Alpha‐diversity ratios of short‐ and long‐read 16S rRNA gene sequences DOI Creative Commons
Krista M. Sumby, J. Stephen, Jeremy J. Austin

et al.

Methods in Ecology and Evolution, Journal Year: 2024, Volume and Issue: 15(10), P. 1804 - 1813

Published: Sept. 2, 2024

Abstract Archival DNA samples collected and analysed for a range of research applied questions have accumulated in the laboratories universities, government agencies commercial service providers decades. These archives represent valuable, yet largely un‐tapped repository genomic information. With lowering costs of, increasing access to, high‐throughput sequencing, we predict an increase retrospective to explore wealth information that resides these archival samples. However, this occur, need confidence integrity samples, often stored under suboptimal conditions their fitness purpose downstream analysis. Here, borrow from well‐established concept ancient evaluate sample integrity, defined as loss content recovered amplicons, frozen based on ratio ⍺‐diversity short‐ long‐read 16S rRNA gene sequences. The variable region 87 extracted soil, western southern agricultural regions Australia between 2001 2021 were sequenced using both PacBio full length reads (V1–V9, 1.5 kbp) Illumina short‐reads (V3–V4, 200–450 bp). When ratios calculated long short assess degradation, did not decrease older versus younger We suggest novel method confirm before embarking large‐scale diversity profiling projects DNA.

Language: Английский

A Systematic Review and Meta-Analysis of 16S rRNA and Cancer Microbiome Atlas Datasets to Characterize Microbiota Signatures in Normal Breast, Mastitis, and Breast Cancer DOI Creative Commons
Sima Kianpour Rad, Kenny Yeo, F. Wu

et al.

Microorganisms, Journal Year: 2025, Volume and Issue: 13(2), P. 467 - 467

Published: Feb. 19, 2025

The breast tissue microbiome has been increasingly recognized as a potential contributor to cancer development and progression. However, inconsistencies in microbial composition across studies have hindered the identification of definitive signatures. We conducted systematic review meta-analysis 11 using 16S rRNA sequencing characterize bacterial 1260 fresh samples, including normal, mastitis-affected, benign, cancer-adjacent, cancerous tissues. Studies published until 31 December 2023 were included if they analyzed human Illumina short-read with sufficient metadata, while non-human non-breast tissues, non-English articles, those lacking metadata or alternative methods excluded. also incorporated data from Cancer Genome Atlas (TCGA-BRCA) cohort enhance our analyses. Our identified Proteobacteria, Firmicutes, Actinobacteriota, Bacteroidota dominant phyla tissue, Staphylococcus Corynebacterium frequently detected studies. While diversity was similar between cancer-adjacent both exhibited lower compared normal mastitis-affected Variability genera observed primer sets studies, emphasizing need for standardized methodologies research. An analysis TCGA-BRCA confirmed dominance Corynebacterium, which associated proliferation-related gene expression programs. Notably, high abundance 4.1-fold increased mortality risk. These findings underscore clinical relevance tumor progression emphasize importance methodological consistency. Future establish causal relationships, elucidate underlying mechanisms, assess microbiome-targeted interventions are warranted.

Language: Английский

Citations

1
Edgeworthia gardneri (Wall.) Meisn Mitigates CCL4-induced liver injury in mice by modulating gut microbiota, boosting antioxidant defense, and reducing inflammation DOI Creative Commons

Jiashu Hu,

Jitao Sun,

Qiu Zhong

et al.

Ecotoxicology and Environmental Safety, Journal Year: 2025, Volume and Issue: 293, P. 118042 - 118042

Published: March 1, 2025

Herbal medicine has become an area of growing global scientific interest. The prime objective this study was to investigate the protective role Edgeworthia gardneri (Wall.) Meisn (EGM polysaccharide) against carbon tetrachloride (CCl4)-induced liver injury in mice. Forty-five ICR mice were randomly divided into three groups (n = 15): IC, IM, and IT. IT group received EGM polysaccharide solution (50 mg/kg) daily, while IC IM administered equivalent volume normal saline. intraperitoneally injected with a mixture CCl4 olive oil at 1:1 (v/v) (2 mL/kg) every 3 days. Our results showed that significantly (p < 0.05) reduced pathological hepatic alterations increased index caused by CCl4. Moreover, therapy 0.001) levels antioxidant enzymes, such as glutathione peroxidase (GSH-Px), superoxide dismutase (SOD), total capacity (T-AOC) malondialdehyde (MDA) content dose-dependent manner. Notably, alleviated inflammatory cascades evidenced decreased serum interleukin-6 (IL-6), interleukin-1β (IL-1β), tumor necrosis factor- α (TNF-α) under administration. Furthermore, 16 s rRNA gene sequencing exhibited abundance probiotics bacteria, Unclassified_Lachnospiraceae, pathogenic bacterial texas like Brevundimonas Candidatus_Nitrocosmicu. Conclusively, protects CCl4-induced oxidative stress inflammation alleviates through beneficial gut microbiota modulations. current suggests is effective agent counteracting damage.

Language: Английский

Citations

1
Galactooligosaccharide-Metabolism-Related Genes of Bifidobacterium pseudocatenulatum Contribute to the Regulation of Glucose and Lipid Metabolism in Type 2 Diabetic Mice DOI
Guopeng Lin, Bo Zhang,

Zhihao Qu

et al.

Journal of Agricultural and Food Chemistry, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 12, 2025

This study investigated whether the galactooligosaccharide (GOS)-metabolism-related genes (GOS-cluster) in

Language: Английский

Citations

0
Comparative analysis of Illumina, PacBio, and nanopore for 16S rRNA gene sequencing of rabbit’s gut microbiota DOI Creative Commons

Iliyass Biada,

M. A. Santacreu, Ó. González-Recio

et al.

Frontiers in Microbiomes, Journal Year: 2025, Volume and Issue: 4

Published: May 15, 2025

This research aims to assess whether sequencing the full length of 16S rRNA gene using PacBio HiFi and Oxford Nanopore Technology (ONT) platforms outperform Illumina MiSeq platform in providing detailed specie level insights. Moreover, it compare similarities microbial communities detected across three platforms. The study employed DNA from four rabbit does’ soft feces, sequenced for specific regions V3-V4, complete ONT MinION. Results highlight different levels taxonomic resolution. At species level, exhibited better resolutions with 63% 76% respectively, while 48% Illumina. However, all platforms, classification output at was mainly labeled as “ Uncultured_bacterium ” most classified sequences, which does not improve understanding gut microbiota composition rabbits. although high correlations between relative abundances taxa were observed, diversity analysis showed significant differences compositions These findings suggest that offer improvements species-level resolution compared Illumina, due references databases ambiguous annotation, still fall short a precise characterization Additionally, disparities observed results these impact platform, especially when primers are used. consideration is particularly important comparing or analyzing sequences derived technologies.

Language: Английский

Citations

0
Advances in Sinonasal Microbiome Analysis DOI Creative Commons
Cristian Roca, Yasine Mirmozaffari,

William Martin

et al.

Ear Nose & Throat Journal, Journal Year: 2025, Volume and Issue: unknown

Published: May 19, 2025

Language: Английский

Citations

0
Comparative evaluation of sequencing technologies and primer sets for mouse gut microbiota profiling DOI Creative Commons

Aleksandra Strokach,

Polina Y. Zoruk,

Daria I. Boldyreva

et al.

Frontiers in Microbiology, Journal Year: 2025, Volume and Issue: 16

Published: May 20, 2025

Advancements in sequencing technologies, such as Illumina and Oxford Nanopore Technologies (ONT), have significantly improved microbiome research. However, variations platforms, primer selection, DNA quality may influence microbial diversity assessments, particularly studies of gut microbiota. This study systematically evaluates these factors mouse microbiota analysis, comparing 16S rRNA gene metagenome (MS) across both platforms. Our findings highlight the critical selection on results, with certain combinations detecting unique taxa that others miss. Despite taxonomic resolution, all tested sets consistently revealed significant differences between experimental groups, indicating key shifts induced by bacterial cultures remain detectable regardless choice. A comparative analysis ONT notable profiling, capturing a broader range taxa. In contrast, MS platforms showed high degree correlation, errors minimal impact estimations. Furthermore, type extracted (high molecular weight vs. standard DNA) had little outcomes, underscoring robustness technologies. These results advantages limitations different strategies While remains cost-effective tool for assessing diversity, provides superior resolution more precise species identification. advocates hybrid approach combines multiple technologies to achieve comprehensive accurate representation communities.

Language: Английский

Citations

0
Is Short-Read 16S rRNA Sequencing of Oral Microbiome Sampling a Suitable Diagnostic Tool for Head and Neck Cancer? DOI Open Access
Kenny Yeo,

Fangmeinuo Wu,

Runhao Li

et al.

Published: Aug. 27, 2024

The oral microbiome, studied by sampling the saliva or rinse, has been long thought to have diagnostic capacity for head and neck cancers (HNC). However, previous reports on HNC microbiome provide inconsistent results. aim of this study is consolidate these datasets determine microbial composition between patients healthy premalignant individuals. We analyzed 16 published cancer (HNC) short-read 16S rRNA sequencing datasets, specifically targeting V3V4, V4 V4V5 regions. These included rinse samples from donors with HNC, as well donors. Differences in diversities abundance were determined. displayed lower alpha diversity than In contrast, opposite trend was observed samples. Beta largely similar across different patient types. Similar phyla detected all samples, but proportions dependent sample type (i.e. rinse) primer set utilised sequencing. Neisseria, Leptotrichia Megasphaera elevated saliva, while Mycoplasma saliva. Oral enrichment Fusobacterium, Veillonella, Alloprevotella, Campylobacter had conflicting sparse partial least squares discriminant analysis model performed effectively discriminating using V3V4 (AUC = 0.888), 0.928), poor discriminative 0.688). conclusion, our meta-analysis highlighted limitations sequencing, particularly due variations batches, sets V4), Hence, caution should be exercised when interpreting results studies, especially types are used.

Language: Английский

Citations

2
Is Short-Read 16S rRNA Sequencing of Oral Microbiome Sampling a Suitable Diagnostic Tool for Head and Neck Cancer? DOI Creative Commons
Kenny Yeo,

Fangmeinuo Wu,

Runhao Li

et al.

Pathogens, Journal Year: 2024, Volume and Issue: 13(10), P. 826 - 826

Published: Sept. 24, 2024

The oral microbiome, studied by sampling the saliva or rinse, has been long thought to have diagnostic capacity for head and neck cancers (HNC). However, previous reports on HNC microbiome provide inconsistent results. aim of this study is consolidate these datasets determine microbial composition between patients healthy premalignant individuals. We analyzed 16 published cancer (HNC) short-read 16S rRNA sequencing datasets, specifically targeting V3V4, V4 V4V5 regions. These included rinse samples from donors with HNC, as well donors. Differences in diversities abundance were determined. displayed lower alpha diversity than In contrast, opposite trend was observed samples. Beta scores largely similar across different patient types. Similar phyla detected all samples, but proportions dependent sample type (i.e., rinse) primer set utilized sequencing.

Language: Английский

Citations

2
A novel method to assess the integrity of frozen archival DNA samples: Alpha‐diversity ratios of short‐ and long‐read 16S rRNA gene sequences DOI Creative Commons
Krista M. Sumby, J. Stephen, Jeremy J. Austin

et al.

Methods in Ecology and Evolution, Journal Year: 2024, Volume and Issue: 15(10), P. 1804 - 1813

Published: Sept. 2, 2024

Abstract Archival DNA samples collected and analysed for a range of research applied questions have accumulated in the laboratories universities, government agencies commercial service providers decades. These archives represent valuable, yet largely un‐tapped repository genomic information. With lowering costs of, increasing access to, high‐throughput sequencing, we predict an increase retrospective to explore wealth information that resides these archival samples. However, this occur, need confidence integrity samples, often stored under suboptimal conditions their fitness purpose downstream analysis. Here, borrow from well‐established concept ancient evaluate sample integrity, defined as loss content recovered amplicons, frozen based on ratio ⍺‐diversity short‐ long‐read 16S rRNA gene sequences. The variable region 87 extracted soil, western southern agricultural regions Australia between 2001 2021 were sequenced using both PacBio full length reads (V1–V9, 1.5 kbp) Illumina short‐reads (V3–V4, 200–450 bp). When ratios calculated long short assess degradation, did not decrease older versus younger We suggest novel method confirm before embarking large‐scale diversity profiling projects DNA.

Language: Английский

Citations

0