Novel large-scale chromosomal transfer in Bacteroides fragilis contributes to its pan-genome and rapid environmental adaptation

Abstract

Bacteroides fragilis, an important component of the human gastrointestinal microbiota, can cause lethal extra-intestinal infection upon escape from the gastrointestinal tract. We demonstrated transfer and recombination of large chromosomal segments from B. fragilis HMW615, a multidrug resistant clinical isolate, to B. fragilis 638R. In one example, the transfer of a segment of ~435 Kb/356 genes replaced ~413 Kb/326 genes of the B. fragilis 638R chromosome. In addition to transfer of antibiotic resistance genes, these transfers (1) replaced complete divergent polysaccharide biosynthesis loci; (2) replaced DNA inversion-controlled intergenic shufflons (that control expression of genes encoding starch utilization system outer membrane proteins) with more complex, divergent shufflons; and (3) introduced additional intergenic shufflons encoding divergent Type 1 restriction/modification systems. Conjugative transposon-like genes within a transferred segment and within a putative integrative conjugative element (ICE5) ~45 kb downstream from the transferred segment both encode proteins that may be involved in the observed transfer. These data indicate that chromosomal transfer is a driver of antigenic diversity and nutrient adaptation in Bacteroides that (1) contributes to the dissemination of the extensive B. fragilis pan-genome, (2) allows rapid adaptation to a changing environment and (3) can confer pathogenic characteristics to host symbionts.

CRISPR-Cas Systems in Bacteroides fragilis, an Important Pathobiont in the Human Gut Microbiome

“…These included: pBF9343, CTnHybL, pHAG88, p610 88, BOB_25 PAO, CTn86, CTn341, CTnDot, and CTnPg1-a (note: many of the conjugative transposons in B. fragilis were only partially sequenced). Additionally, no CRISPRs were detected in the large horizontally transferred chromosomal fragments recently described (Husain et al, 2017 ). We also examined available sequences for 14 B. fragilis plasmids and did not find any CRISPR elements contained within their sequences.…”

“…This ability of B. fragilis to easily incorporate foreign genes is intriguing since B. fragilis also possesses strong DNA restriction modification (DNA/RM) systems to degrade “non-self” DNA. We previously demonstrated horizontal transfer of mobile elements bearing alternate variants of these genes from a multidrug resistant B. fragilis isolate (HMW 615) to B. fragilis 638R (Husain et al, 2017 ). These systems are located in shufflons with invertible promoters that can be turned off or on, so that the bacterium can control whether the incoming DNA will be degraded (Patrick et al, 2010 ).…”

“…Now we have shown that in addition to the DNA/RM systems, there are abundant CRISPR elements in B. fragilis with adjacent cas genes, suggesting that these CRISPRs are indeed active as a bacterial defense system. We had previously suggested that predation by bacteriophages is an evolutionary driving force for generation of variable polysaccharide and R-M systems in B. fragilis (Patrick et al, 2010 ) and that this system can be diversified by HGT (Husain et al, 2017 ). In an interesting twist, B. fragilis also has a Type IIC CRISPR system with a high proportion of crRNAs with homology to B. fragilis phages; it is likely that this CRISPR system is largely directed to protect against invading bacteriophage (but these systems are lacking in the most virulent B. fragilis strains).…”

Antigenic mimicry of ubiquitin by the gut bacteriumBacteroides fragilis: a potential link with autoimmune disease

“…The BFT gene is located within a potentially mobile genetic element of approximately 6‐kbp in size with 12 bp direct repeats at either end . This BFT element is variably present in large genomic islands, including integrative and conjugative genetic elements, that are transferred horizontally within the B. fragilis pan‐genome . There is the potential for more than one copy of the BFT gene to be present at different chromosomal locations.…”

Overview of the rules of the microbial engagement in the gut microbiome: a step towards microbiome therapeutics

“…The presence of the antibiotic resistance genes is relevant for the tolerance of antibiotics within the human body. Separate studies have proven that the genes for antibiotic tolerance may be exchanged horizontally among Bacteroides or between Bacteroides and Gram-positive bacteria (Husain et al 2017) and inherited as well (Vaishampayan et al 2010). The gut microbiota contains a set of antibiotic resistance genes especially against b-lactam, glycopeptides, tetracycline and aminoglycosides (Bag et al 2019).…”