First published on: Springer Nature

The author, Youwen Qin, is a Research Scientist at BGI Genomics Shenzhen.

The rising incidence of young-onset sporadic colorectal cancer (CRC) is a global concern. Leveraging a substantial number of deep sequencing metagenomes, our study shows striking similarities in gut microbial patterns at both taxonomic and selected gene marker levels between yCRC and old-onset CRC.

This is my first research paper following my PhD training with Prof. Michael Inouye and Prof. Kathryn Holt in Melbourne and Cambridge.

My research journey with CRC microbiome traces back to 2012 when I collaborated with Prof. Jun Yu and found bacterial taxa and functional genes associated with CRC. Since then, the field has progressed fast, with well-established associations between CRC and gut microbiome. However, few studies have delved into the gut microbiome concerning yCRC (aged <50), partly due to its lower incidence rate compared to old-onset CRC (oCRC, aged ≥50).

The gut microbiome is known to vary with age. With phenotypic differences in disease stage and tumor location between yCRC and oCRC, one could hypothesize that the gut microbiome might also differ. Aiming to characterize the gut microbiome of yCRC, I collaborated with Prof. Pei-Rong Ding at Sun Yat-Sen University Cancer Center since 2021.

Negative findings

In our study we conducted deep metagenomic sequencing on stool samples collected from a sizable cohort of CRC patients, including 167 yCRC. By comparing microbiome compositions between yCRC and oCRC, we observed only a few bacterial taxa that met the statistically significant threshold. Notably, the associations between age and microbial features across all studied samples were weak. Despite our rigorous efforts involving various analytical strategies, such as comparing individuals aged <40 to those aged >60, our investigations failed to yield promising results.

The Fudan Study

While we were disappointed, a study by Yang et al. from Fudan University working on the same topic was published. They reported distinct signatures of yCRC relative to oCRC. We got even more disappointed.

After thoroughly reviewing the Fudan paper multiple times, I found that their findings on oCRC weren't corroborated by other studies. One possible explanation is that their results primarily relied on 16S rRNA sequencing, although they were validated by shotgun metagenomic sequencing. Fortunately, the Fudan team also made the shotgun metagenomic sequencing (raw) data publicly available for 200 individuals. I downloaded and analyzed this data using our pipeline. Surprisingly, my findings diverged from those reported in the original paper. Notably, I found several well-known CRC-associated bacteria (Clostridium symbiosum, Hungatella hathewyi, Peptostreptococcus stomatis and Parvimonas micra) that were enriched in both oCRC and yCRC. Encouraged by these promising findings, we integrated our data with the Fudan one, along with other published datasets, ultimately uncovering consistent signatures for both oCRC and yCRC.

Editor's Support

Then we found ourselves in a challenging position: eager to publish our results but needing more confidence in presenting contrasting findings to a previously published study. Despite our reservations, we decided to take a chance. I reached out to Dr. Javier Martinez-Vesga to discuss our intention to write a short paper detailing our contrasting results to a study published in Nature Communications. Interestingly, Javier suggested that we expand our scope and submit a full research article instead, highlighting the new data we had generated from numerous CRC patients.

Reviewers' Support

During the peer-review process, we received positive feedback from all reviewers, who recommended conducting a more in-depth analysis of the bacterial genomes and exploring bacterial toxin and virulence factors. Following their suggestions, we conducted a more focused analysis, leading us to uncover insights into well-known CRC-associated taxa with clear pathogenic pathways: Fusobacterium nucleatum, Bacteroides fragilis, and Escherichia coli.

Story of F. nucleatum

In our studied samples, we detected both F. nucleatum (Fn) and its close relative F. animalis (Fa; also known as Fn subspecies animalis, Fna). Strikingly, Fa had higher abundance and prevalence compared to Fn. This observation coincided with a very recent study published in Nature, which reported the enrichment of a distinct Fa clade in CRC niche, consistent with an earlier study. Moreover, in our Chinese cohort, we found no differentiation in the presence of the fadA gene (encoded adhesion protein A, which mediates Fn attachment to and invasion of host epithelial cells) between samples enriched with either Fn or Fa.

Story of B. fragilis

We identified two distinct clusters of B. fragilis in our data. In line with a previous study, each individual was dominated by one strain. Pathogenic B. fragilis strains can produce enterotoxin, which plays a role in cell cycle regulation. While the specific identities of these two strain clusters were unknown to us, we observed differential abundance and prevalence of the enterotoxin-encoding gene but between the two clusters.

Story of E. coli

Only one strain cluster of E. coli was identified in our samples. As a commensal bacterium in the gut, most E. coli strains are non-pathogenic. However, pathogenic strains often harbor the pks genomic island, which encodes colibactin, a compound implicated in DNA damage. Subsequently, we examined the relationship between the abundance of E. coli and pks. Interestingly, we observed a positive association in the Guangzhou cohort, but no correlation was evident in the Fudan cohort. This population heterogeneity implies a complex microbiome background of CRC across different geographic regions.

Potential impact

The shared microbiome signatures between yCRC and oCRC could serve as a foundation for developing microbiome-based diagnostic methods for CRC screening. Our study showed that microbiome-based classifiers trained for oCRC had similar prediction
performance for yCRC, and viceversa. The consistency in signatures across CRC cases of different ages suggests that the microbiota may play a pivotal role in CRC carcinogenesis.

Ongoing work

One of the most intriguing questions is whether these microbial signatures correlate with CRC clinical outcomes. To address this, we are actively collecting follow-up data for many of the patients included in our study and investigating the relationship between gut microbiome and CRC outcomes. Since many CRC-associated bacteria are commonly found in the oral cavity, we have also generated matched metagenomes from saliva/tongue samples for most of our patients. It's worth noting that our current study only focused on bacterial taxa. However, considering that fungal and viral signatures have also been reported to be associated with CRC, conducting further analyses on fungi and viruses will offer new biological insights into CRC pathogenesis.

Simultaneously, BGI Genomics is embarking on a mission to sequence 10 million microbiome samples as part of a large-scale cancer screening project for CRC. This endeavor will yield an unprecedented volume of microbiome data for humans. Science thrives on collaboration, and I extend a warm invitation to researchers worldwide to join us in deciphering this vast dataset and harnessing its potential for the greater good.

About BGI Genomics:

BGI Genomics, headquartered in Shenzhen, China, is the world's leading integrated solutions provider of precision medicine. Our services cover more than 100 countries and regions, involving more than 2,300 medical institutions. In July of 2017, as a subsidiary of BGI Group, BGI Genomics (300676.SZ) was officially listed on the Shenzhen Stock Exchange.