New findings reveal that a significant and widespread mobile genetic element alters the defensive capabilities of Bacteroides fragilis, a prevalent bacterium found in the human gut.
Bacteria in the human gut have the ability to quickly adapt by exchanging genetic material among themselves. The order Bacteroidales, which consists of numerous gut bacterial species, shares hundreds of genetic elements. However, the consequences of these DNA exchanges—both for bacterial survival and the health of the host—are not well understood.
Recent research from the University of Chicago indicates that a prominent, mobile genetic element modifies the antagonistic capabilities of Bacteroides fragilis, a commonly occurring gut bacterium. The acquisition of this element disables a powerful weapon of B. fragilis, while simultaneously equipping it with a new defense strategy that protects the strain from which the DNA was acquired. These defensive tools enable the bacteria to establish their presence in the densely populated regions of the gut.
Dr. Laurie Comstock, a Professor of Microbiology and a member of the Duchossois Family Institute at UChicago, has been investigating various antagonistic strategies of Bacteroidales and their DNA transfer processes for over a decade. “These organisms undergo rapid evolution through DNA transfers. It’s truly fascinating,” she stated. “We were aware that certain B. fragilis strains lacked the ability to deploy their weapons, but when we discovered it was because they acquired a large mobile genetic element, we realized we had stumbled upon something significant.”
The study, titled “A ubiquitous mobile genetic element changes the antagonistic weaponry of a human gut symbiont,” was published on October 24 in Science.
A spring-loaded, poison-tipped spear
Many species within Bacteroidales possess the ability to eliminate neighboring bacteria by producing harmful toxins. Some toxins diffuse from the cell into the surrounding area, killing nearby sensitive strains. Another form of defense is the type VI secretion system (T6SS), which functions as a nanomachine containing a pointed, spring-loaded tube filled with toxins. Once activated, it injects toxins directly into neighboring bacterial cells like a spear with poison.
There are three distinct variations of the T6SS among Bacteroidales. One of these, known as genetic architecture 3 (GA3), is unique to B. fragilis and shows remarkable effectiveness against other Bacteroidales species. The other two variations, GA1 and GA2, are associated with large mobile genetic elements called integrative and conjugative elements (ICEs). These GA1 and GA2 ICEs are in rapid flux, transferring between Bacteroidales species in various human populations globally. However, researchers have not yet observed the same lethal effectiveness in the GA1 and GA2 T6SSs that is seen with the GA3 T6SS.
Comstock noted, “The ICE containing the GA1 T6SS is swiftly spreading through human demographics and rapidly transferring to various Bacteroidales species in individuals’ guts.”
Comstock’s team examined natural isolates of B. fragilis possessing either a GA3 T6SS or a combination of GA3 and GA1 ICE. Those with both ICE variants had lost the ability to utilize the GA3 weapon, rendering them ineffective against other Bacteroidales. To confirm that this change was due to the GA1 ICE acquisition, they introduced the GA1 ICE into B. fragilis strains only possessing GA3 T6SS and observed that the new strains, referred to as “transconjugants,” were similarly incapable of attacking other strains with their GA3 T6SS.
The team subsequently removed components of the GA1 ICE to identify which part of the 116 kilobase ICE was responsible for disabling the GA3 weapon. They discovered that a section of the GA1 T6SS region, which codes for the membrane complex of the GA1 nanomachine, inhibited the functioning of the GA3 T6SS.
Next, researchers aimed to observe how these strains would compete in a mammalian gut setting. They orally inoculated germ-free (gnotobiotic) mice with equal amounts of isogenic, wild-type B. fragilis (which only had GA3 T6SS) and the GA3/GA1 ICE transconjugant. The transconjugant quickly surpassed the wild-type strain in competition within the mice. Further analysis demonstrated that this competitive success was due to the antagonism mediated by the GA1 T6SS, marking the first evidence of effective antagonism associated with the GA1 T6SS.
Comstock remarked, “We were uncertain whether the GA1 strain would be competitive, and initially thought that the ancestral GA3 strain would prevail in the gut. However, that did not occur.”
Switching sides and going on defense
An unexpected revelation from the experiment was that in the mice’s gut, the GA3 T6SS was completely absent. Subsequent investigation revealed that a gene located on the GA1 ICE codes for a transcriptional repressor that halts the transcription of the GA3 T6SS. This enables enhanced production of the GA1 T6SS.
The implications of this DNA element transfer impact the overall gut microbial community. The Bacteroidales strains that harbor the GA1 ICE can be eliminated by the B. fragilis GA3 T6SS; however, if a strain can transfer its GA1 ICE into the attacking B. fragilis strain, it results in a new strain that can outcompete the original B. fragilis strain. This newly formed strain does not target the strain that donated the GA1 ICE and can leverage the GA1 T6SS to protect the community from other invading Bacteroidales strains.
Comstock aims to delve deeper into this diverse group of transcriptional repressors that frequently appear on mobile genetic elements of Bacteroidales and their impacts on recipient strains.
“This family of transcriptional repressors can be deactivated upon binding with specific ligands. We are eager to identify the ligands found in the gut that could relieve their suppression,” she stated.
The study also demonstrated that GA1 ICE transfer occurs swiftly within the mouse gut, allowing the transconjugant to become a significant part of the resident population. This insight suggests that researchers working on synthetic bacterial communities for therapeutic purposes need to consider the potential effects of genetic transfer.
“As scientists select bacteria for inclusion in therapeutic consortia, it’s crucial to guard against introducing any components that might transfer to or from these strains and potentially have negative impacts,” Comstock concluded.
