Genomic alterations in Bacteroides fragilis favor adaptation in colorectal cancer microenvironment

Abstract

Background: The occurrence and development of colorectal cancer (CRC) is an incredibly long process that involves continuous changes in the tumor microenvironment. These constant changes may ultimately result in genetic alterations and changes in the metabolic processes of some symbiotic bacteria as a way to adapt to the changing environment. Patients with CRC exhibit an altered abundance of Bacteroides fragilis (B. fragilis) as indicated by several studies. To better understand the genomic characteristics and virulence spectrum of B. fragilis strains in tumor tissues, B. fragilis strains were isolated from tumor and paracancerous tissues of CRC patients.

Methods: The isolates were identified using 16 S rRNA sequencing, morphological analysis, physiological and biochemical characterization and PCR, and they were then subjected to whole genome sequencing (WGS) analysis.

Results: A strain of B. fragilis enterotoxin (BFT) bft1-producing ZY0302 and a non-enterotoxin-producing B. fragilis ZY0804 were isolated from cancerous and paraneoplastic tissues, respectively. Analysis based on the core and nonessential genes showed that the genomic profiles of the isolates, ZY0302 and ZY0804, differed from those of B. fragilis from other tissue sources. This core and the co-evolution of non-essential genes may be the result of their adaptation to fluctuations in the tumor microenvironment and enhancing their survival. In addition, the ZY0302 and ZY0804 genomes underwent extensive horizontal gene transfer and varying degrees of genomic rearrangements, inversions, insertions, and deletion events, which may favor the enhancement of bacteria's ability to adapt to environmental changes. For instance, the virulence factors, such as the capsular biosynthesis gene clusters and components of the type IV secretion system, acquired through horizontal gene transfer, may facilitated B. fragilis in evading immune responses and managing oxidative stress. Moreover, our analysis revealed that multiple virulence factors identified in the isolates were mainly involved in bacterial adhesion and colonization, oxidative stress, iron acquisition, and immune evasion. This observation is worth noting given that enzymes such as neuraminidase, lipase, hemolysin, protease, and phosphatase, along with genes responsible for LPS biosynthesis, which are recognized for their association with the virulence of B. fragilis, were prevalent among the isolates.

Conclusions: In summary, it is our assertion that the alterations observed in both core and nonessential genes of B. fragilis, which have been isolated from tissues of colorectal cancer patients, along with significant instances of horizontal gene transfer to the genome, are likely intended to enhance adaptation to the evolving conditions of the tumor microenvironment. This study may provide new insights into the interaction between B. fragilis and the CRC microenvironment.

Keywords: Bacteroides fragilis; Colorectal cancer; Complete genome; Tumor microenvironment; Virulence factor.

Fig. 1

Morphological characteristics of strains ZY0302 and ZY0804. (A and D) After Gram staining, observe the morphology of strains ZY0302 and ZY0804 under an optical microscope (100x) The bar represents a unit length of 10 μm. (B and E) The growth of this strain after 48 h at 37 °C on CDC anaerobic blood agar medium. The bar represents a unit length of 1 cm. (C and F) The growth of this strain after 48 h at 37 °C on BBE blood agar medium. The bar represents a unit length of 1 cm

Fig. 2

Phylogenetic tree and typing identification of strains ZY0302 and ZY0804. (A) The evolutionary history was inferred by using the Maximum Likelihood method and Kimura 2-parameter model. Bootstrap values were based on 1,000 resamplings. Strain Porphyromonas gingivalis ATCC 33,277 was used as an outgrouping. Evolutionary analyses were conducted in MEGA11. (B) Gel electrophoresis images of PCR products amplified based on BFT and its typing primers. M: 2000 DL Marker; 1–3: BFT primer. 4–6: bft-1 primer. 7–9: bft-2 primer. 10–12: bft-3 primer. The products of 1,4,7,10 lanes were produced using DNA from strain ZY0302 as a template, 2,5,8,11 using DNA from strain ZY0804 as a template, and 3,6,9,12 using DEPC water as a template. Imaging was performed using a BIO-RAD gel imaging system

Fig. 3

Circular maps of the chromosome of B. fragilis strain ZY0302 and ZY0804. Each circle represents (From outer to inner): 1. Genome Size; 2–3. Forward strand gene and reverse strand gene, colored according to cluster of orthologous groups (COG) classification; 4–5. Forward and Reverse Strand ncRNA, including rRNA (Red), sRNA (Green), tRNA (Yellow); 6. Repeat; 7. G + C content; 8. GC skew (G-C/G + C)

Fig. 4

Common and unique genes of ZY0302 and ZY0804 with reference strains. (A) Venn diagram of the Pan gene set. (B) Phylogenetic trees were constructed based on core genes of the sample and reference strains. The NJ algorithm of TreeBeST was used to construct the phylogenetic tree. (C) Dispensable gene heatmap