Planning and Analyzing a Low-Biomass Microbiome Study: A Data Analysis Perspective DOI
George I. Austin, Tal Korem

The Journal of Infectious Diseases, Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 27, 2024

Abstract As investigations of low-biomass microbial communities have become more common, so too has the recognition major challenges affecting these analyses. These been shown to compromise biological conclusions and contributed several controversies. Here, we review some most common influential in microbiome research. We highlight key approaches alleviate potential pitfalls, combining experimental planning strategies data analysis methods.

Language: Английский

The relationship between the gastric cancer microbiome and clinicopathological factors: a metagenomic investigation from the 100,000 genomes project and The Cancer Genome Atlas DOI Creative Commons
Mary E. Booth, Henry M. Wood, Mark A. Travis

et al.

Gastric Cancer, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 17, 2025

Abstract Background Findings from previous gastric cancer microbiome studies have been conflicting, potentially due to patient and/or tumor heterogeneity. The intratumoral and its relationship with clinicopathological variables not yet characterized in detail. We hypothesized that variation microbial abundance, alpha diversity, composition is related characteristics. Methods Metagenomic analysis of 529 GC samples was performed, including whole exome sequencing data Cancer Genome Atlas (TCGA) genome the 100,000 Genomes Project. Microbial were compared across age, sex, location, geographic origin, pathological depth invasion, lymph node status, histological phenotype, microsatellite instability TCGA molecular subtype. Results Gastric microbiomes resembled results, Prevotella , Selenomonas Stomatobaculum Streptococcus Lactobacillus Lachnospiraceae commonly seen both cohorts. Within cohort, abundance diversity greater cancers instability, lower intestinal-type histology, those originating Asia. Microsatellite status associated Sex invasion cohort. Conclusion appears differ according factors. Certain factors favourable outcomes observed be diversity. This highlights need for further work understand underlying biological mechanisms behind differences their potential clinical therapeutic impact.

Language: Английский

Citations

0
Exploring the prognostic and predictive potential of bacterial biomarkers in non-gastrointestinal solid tumors DOI Creative Commons

Caoimbhe Burke,

Thomas J. Glynn, Chowdhury Arif Jahangir

et al.

Expert Review of Molecular Diagnostics, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 20, 2025

Standard clinical parameters like tumorsize, age, lymph node status, and molecular markers are used to predictprogression risk treatment response. However, exploring additional markersthat reflect underlying biology could offer a more comprehensive understandingof the tumor microenvironment (TME). The TME influences development,progression, disease severity, survival, with tumor-associated bacteriaposited play significant roles. Studies on microbiota havefocused high bacterial-load sites such as gut, oral cavity, stomach,but interest is growing in non-gastrointestinal (GI) solid tumors, asbreast, lung, pancreas. Microbe-based biomarkers, including Helicobacter pylori, humanpapillomavirus (HPV), hepatitis B C viruses, have proven valuable inpredicting gastric, cervical, renal cancers. Potential of prognostic andpredictive bacterial biomarkers non-GI tumors methodologiesused. Advances techniques 16SrRNA gene sequencing, qPCR, immunostaining, situ hybridization enabled detailed analysis ofdifficult-to-culture microbes tumors. ensure reliableresults, it critical standardize protocols, accurately align reads,address contamination, maintain proper sample handling. This will pave theway for developing reliable that enhance prognosis,prediction, personalized planning.

Language: Английский

Citations

0
Diet-microbiome interactions in cancer DOI
Suhaib K. Abdeen, Ignacio Mastandrea,

Nina Stinchcombe

et al.

Cancer Cell, Journal Year: 2025, Volume and Issue: unknown

Published: April 1, 2025

Language: Английский

Citations

0
Bioinformatic approaches to blood and tissue microbiome analyses: challenges and perspectives DOI Creative Commons

Jammi Prasanthi Sirasani,

Cory Gardner,

G. Jung

et al.

Briefings in Bioinformatics, Journal Year: 2025, Volume and Issue: 26(2)

Published: March 1, 2025

Abstract Advances in next-generation sequencing have resulted a growing understanding of the microbiome and its role human health. Unlike traditional analysis, blood tissue analyses focus on detection characterization microbial DNA tissue, previously considered sterile environment. In this review, we discuss challenges methodologies associated with analyzing these samples, particularly emphasizing research. Key preprocessing steps—including removal ribosomal RNA, host DNA, other contaminants—are critical to reducing noise accurately capturing evidence. We also explore how taxonomic profiling tools, machine learning, advanced normalization techniques address contamination low biomass, thereby improving reliability. While it offers potential for identifying involvement systemic diseases undetectable by methods, methodology carries risks lacks universal acceptance due concerns over reliability interpretation errors. This paper critically reviews factors, highlighting both promise pitfalls using as tool biomarker discovery.

Language: Английский

Citations

0
Comprehensive analysis of microbial content in whole-genome sequencing samples from The Cancer Genome Atlas project DOI Creative Commons
Yuchen Ge, Jennifer Lu, Daniela Puiu

et al.

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

Published: May 29, 2024

In recent years, a growing number of publications have reported the presence microbial species in human tumors and mixtures microbes that appear to be highly specific different cancer types. Our re-analysis data from three types revealed technical errors caused erroneous reports numerous found sequencing The Cancer Genome Atlas (TCGA) project. Here we expanded our analysis cover all 5,734 whole-genome (WGS) sets currently available TCGA, covering 25 distinct cancer. We analyzed content using updated computational methods databases, compared results those two major studies focused on bacteria, viruses, fungi expand upon reinforce findings, which showed is far smaller than had been previously reported, many identified TCGA are either not present at all, or known contaminants rather residing within tumors. As part this analysis, help others avoid being misled by flawed data, released dataset contains detailed read counts for archaea, detected samples, can serve as public reference future investigations.

Language: Английский

Citations

3
Planning and Analyzing a Low-Biomass Microbiome Study: A Data Analysis Perspective DOI
George I. Austin, Tal Korem

The Journal of Infectious Diseases, Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 27, 2024

Abstract As investigations of low-biomass microbial communities have become more common, so too has the recognition major challenges affecting these analyses. These been shown to compromise biological conclusions and contributed several controversies. Here, we review some most common influential in microbiome research. We highlight key approaches alleviate potential pitfalls, combining experimental planning strategies data analysis methods.

Language: Английский

Citations

1