RESUMO
BACKGROUND: Gut dysbiosis has been associated with colorectal cancer (CRC), the third most prevalent cancer in the world. This study compares microbiota taxonomic and abundance results obtained by 16S rRNA gene sequencing (16S) and whole shotgun metagenomic sequencing to investigate their reliability for bacteria profiling. The experimental design included 156 human stool samples from healthy controls, advanced (high-risk) colorectal lesion patients (HRL), and CRC cases, with each sample sequenced using both 16S and shotgun methods. We thoroughly compared both sequencing technologies at the species, genus, and family annotation levels, the abundance differences in these taxa, sparsity, alpha and beta diversities, ability to train prediction models, and the similarity of the microbial signature derived from these models. RESULTS: As expected, the results showed that 16S detects only part of the gut microbiota community revealed by shotgun, although some genera were only profiled by 16S. The 16S abundance data was sparser and exhibited lower alpha diversity. In lower taxonomic ranks, shotgun and 16S highly differed, partially due to a disagreement in reference databases. When considering only shared taxa, the abundance was positively correlated between the two strategies. We also found a moderate correlation between the shotgun and 16S alpha-diversity measures, as well as their PCoAs. Regarding the machine learning models, only some of the shotgun models showed some degree of predictive power in an independent test set, but we could not demonstrate a clear superiority of one technology over the other. Microbial signatures from both sequencing techniques revealed taxa previously associated with CRC development, e.g., Parvimonas micra. CONCLUSIONS: Shotgun and 16S sequencing provide two different lenses to examine microbial communities. While we have demonstrated that they can unravel common patterns (including microbial signatures), shotgun often gives a more detailed snapshot than 16S, both in depth and breadth. Instead, 16S will tend to show only part of the picture, giving greater weight to dominant bacteria in a sample. Therefore, we recommend choosing one or another sequencing technique before launching a study. Specifically, shotgun sequencing is preferred for stool microbiome samples and in-depth analyses, while 16S is more suitable for tissue samples and studies with targeted aims.
Assuntos
Neoplasias Colorretais , Microbioma Gastrointestinal , RNA Ribossômico 16S , Humanos , Neoplasias Colorretais/microbiologia , Neoplasias Colorretais/genética , RNA Ribossômico 16S/genética , Microbioma Gastrointestinal/genética , Fezes/microbiologia , Metagenômica/métodos , Bactérias/genética , Bactérias/classificação , Análise de Sequência de DNA/métodos , Masculino , Metagenoma , FemininoRESUMO
Colorectal cancer (CRC), the third most common cancer globally, has shown links to disturbed gut microbiota. While significant efforts have been made to establish a microbial signature indicative of CRC using shotgun metagenomic sequencing, the challenge lies in validating this signature with 16S ribosomal RNA (16S) gene sequencing. The primary obstacle is reconciling the differing outputs of these two methodologies, which often lead to divergent statistical models and conclusions. In this study, we introduce an algorithm designed to bridge this gap by mapping shotgun-derived taxa to their 16S counterparts. This mapping enables us to assess the predictive performance of a shotgun-based microbiome signature using 16S data. Our results demonstrate a reduction in performance when applying the 16S-mapped taxa in the shotgun prediction model, though it retains statistical significance. This suggests that while an exact match between shotgun and 16S data may not yet be feasible, our approach provides a viable method for comparative analysis and validation in the context of CRC-associated microbiome research.
Assuntos
Neoplasias Colorretais , Microbioma Gastrointestinal , Humanos , RNA Ribossômico 16S/genética , Algoritmos , Microbioma Gastrointestinal/genética , Pessoal de Saúde , Neoplasias Colorretais/genéticaRESUMO
BACKGROUND: Mobile phone-based SMS text message reminders have the potential to improve colorectal cancer screening participation rates. OBJECTIVE: This study assessed the effectiveness and acceptability of adding targeted SMS text message reminders to the standard procedure for those who picked up but did not return their screening kit at the pharmacy within 14 days in a colorectal cancer screening program in Catalonia, Spain. METHODS: We performed a randomized control trial among individuals who picked up a fecal immunochemical test (FIT) kit for colorectal cancer screening at the pharmacy but did not return it within 14 days. The intervention group (n=4563) received an SMS text message reminder on the 14th day of kit pick up and the control group (n=4806) received no reminder. A 30-day reminder letter was sent to both groups if necessary. The main primary outcome was the FIT completion rate within 30, 60, and 126 days from FIT kit pick up (intention-to-treat analysis). A telephone survey assessed the acceptability and appropriateness of the intervention. The cost-effectiveness of adding an SMS text message reminder to FIT completion was also performed. RESULTS: The intervention group had higher FIT completion rates than the control group at 30 (64.2% vs 53.7%; P<.001), 60 (78.6% vs 72.0%; P<.001), and 126 (82.6% vs 77.7%; P<.001) days. Participation rates were higher in the intervention arm independent of sex, age, socioeconomic level, and previous screening behavior. A total of 339 (89.2%) interviewees considered it important and useful to receive SMS text message reminders for FIT completion and 355 (93.4%) preferred SMS text messages to postal letters. We observed a reduction of US $2.4 per participant gained in the intervention arm for invitation costs compared to the control arm. CONCLUSIONS: Adding an SMS text message reminder to the standard procedure significantly increased FIT kit return rates and was a cost-effective strategy. SMS text messages also proved to be an acceptable and appropriate communication channel for cancer screening programs. TRIAL REGISTRATION: ClinicalTrials.gov NCT04343950; https://www.clinicaltrials.gov/study/NCT04343950. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): RR2-10.1371/journal.pone.0245806.