Most of our greatest weapons for fighting bacterial infections come from bacteria themselves. Bacteria produce antibiotics to fight other bacteria and establish homes for themselves in ecological niches from the hulls of boats to implanted catheters.
Soil bacteria from the actinomycetes phylum in particular are plentiful antibiotics producers. They have given the world most of the frontline antibiotics in use today, such as erythromycin, tetracycline, and vancomycin (1).
“These bacteria are very prolific, but they are a bit exhausted,” said Philippe Villain-Guillot, the leader and cofounder of Nosopharm, a biotechnology company focused on anti-infective drug discovery. “It's more and more difficult to discover novel microbes from these very prolific resources.”
As the incidence of antibiotic resistant bacterial infections rises, the need for new antibiotics is urgent. In 2016, researchers estimated that by the year 2050, 10 million people will die every year from drug resistant infections (2).
Two groups of bacteria with a unique lifecycle may be just the source the world is looking for. Photorhabdus and Xenorhabdus bacteria make their homes inside the guts of parasitic worms and insect larvae. These bacteria produce compounds that ward off other microbes from encroaching on their territories but do not harm their parasite hosts. These underappreciated bacteria have untapped antibiotic potential.
The larva, the worm, and the bacteria
The hunt for Photorhabdus and Xenorhabdus bacteria begins in the dirt. While the bacteria don’t live in the soil themselves, the parasitic worms they live inside do. When Aunchalee Thanwisai, a microbiologist at Naresuan University, looks for these worms, she literally leaves no stone unturned.
“We collect the soil in many areas of Thailand. We collect near the roads, near the pond, in the forest, and in the fields,” said Thanwisai.
These particular parasitic worms — Heterorhabditis bacteriophora and Steinernema carpocapsae — infect insect larvae. H. bacteriophora house Photorhabdus bacteria in their guts, and S. carpocapsae have Xenorhabdus. While there are multiple different species of both Xenorhabdus and Photorhabdus bacteria in nature, each insect parasitic worm only hosts one species at a time in its gut. Thanwisai searches through different soil environments hoping to identify a diverse array of Xenorhabdus and Photorhabdus bacteria.
While inside the worm’s gut, these bacteria live a pretty comfortable life. But when their worm hosts find an insect larva to infect, the bacteria jump into action. Once the parasitic worm burrows into an unsuspecting larva, the worm spits out its Photorhabdus or Xenorhabdus into the larva’s hemolymph — the insect’s bloodstream. There, the bacteria release toxins to kill the larva, allowing the parasitic worms to consume the dead insect larva. But a dead larva sitting in the soil doesn’t stay unnoticed for long.
“All the other soil bacteria, soil nematodes, soil fungi, soil insects [arrive] because the insect is dead; that's an easy-to-use food source,” said Helge Bode, a microbiologist at the Max Planck Institute for Terrestrial Microbiology. “Therefore, the bacteria produce a toxic cocktail of all kinds of toxic molecules including antibiotics, antifungal compounds, and so on to protect the insect cadaver against other competitors.”
Photorhabdus and Xenorhabdus encode many different families of these molecules, which are called natural products. Most of these natural product families contain multiple different compounds to ward off other microbes from colonizing the larva cadaver. Bode and his team recently identified more than 1000 natural product encoding gene clusters from more than 45 different strains of Photorhabdus and Xenorhabdus bacteria (3).
“The antibiotics produced in this ecological context, they kill some soil bacteria. Because soil bacteria might be similar to human pathogenic bacteria, there might also be some that kill human pathogenic bacteria, and indeed that’s the case,” said Bode.
Thanwisai and her team often collaborate with Bode, and together they reported that extracts from two different Photorhabdus species inhibited multiple multidrug resistant Acinetobacter baumannii bacterial strains, which cause a common hospital derived infection (4). These extracts also inhibited growth of two methicillin-resistant strains of Staphylococcus aureus. One of Thanwisai’s students is working with Bode’s group to isolate and identify the specific compounds with these antibiotic effects from the Photorhabdus extracts.
Thanwisai wants to know how this compound kills these drug-resistant bacteria so that one day she and her team can develop it into a new antibiotic for humans. “It is my dream in my research,” she said.
Odilorhabdins and beyond
While Photorhabdus and Xenorhabdus normally release their antibiotic compounds in the belly of dead larvae, scientists can easily grow these bacteria under ordinary laboratory conditions, and with specific nutrients, they can trigger these bacteria to produce and release their antibiotic products.
Researchers at Nosopharm developed a drug discovery platform to isolate and screen Xenorhabdus and Photorhabdus for natural products with cell killing, antifungal, and antibiotic effects. They identified a family of compounds from a Xenorhabdus nematophila strain that had strong antibacterial activity called odilorhabdins (5). By making small chemical modifications to the most effective odilorhabdin molecules, the Nosopharm scientists ended up with the compound NOSO-502 as their most promising new antibiotic.
“It actually targets a well known structure for antibiotics, which is the bacterial ribosome,” said Villain-Guillot, but it latches onto “a new binding site on the ribosome and with a different mode of action compared to other ribosome targeting antibiotics.” While other ribosome targeting antibiotics act by binding to either the small ribosomal subunit or the transfer RNA (tRNA) binding site on the large ribosomal subunit, NOSO-502 and other odilorhabdins interact with both the small ribosomal subunit and the tRNA molecule, which leads to improper bacterial translation.
NOSO-502 has broad spectrum activity against both Gram negative and Gram positive pathogens, and it significantly reduced the levels of drug resistant bacteria in mouse models of sepsis, urinary tract infections, and respiratory infections (6). With some recent positive toxicology studies, the Nosopharm team plans to begin clinical trials of NOSO-502 in humans in 2023.
“We are very pleased with this,” said Villain-Guillot. “We can do something useful for patients, to treat and cure patients more rapidly, more efficiently.”
In addition to NOSO-502, the team at Nosopharm is exploring the antifungal and antiparasitic effects of Photorhabdus and Xenorhabdus natural products. Thanwisai investigates these bacterial compounds for their abilities to kill the larvae of the virus transmitting mosquitoAedes aegypti and Aedes albopictus (7).
Bode is taking his search for new Photorhabdus and Xenorhabdus antibacterial natural products one step further by engineering the bacteria’s biosynthetic pathways to design hybrid natural products.
“You can take those pathways, put them apart, [and] put them together in different ways so they can make natural products that nature has not invented yet,” said Bode. “It might be possible to make hybrids of those natural products in such a way that we can address targets that nature has not had a need for.”
Bode hopes that using Photorhabdus and Xenorhabdus natural products as a starting point will quickly lead to the development of new antibiotics, but even while he’s designing new natural products, he’s excited by the potential of bacterial natural products that haven’t been discovered yet.
“There are so many bacteria out there. I think if we sequence everything, we will find so many prolific natural product producers. I would say we have cures for almost all diseases already somewhere. We just have to find it,” said Bode. “The ‘just’ makes it complicated.”
- Racine, E. & Gualtieri, M. From Worms to Drug Candidate: The Story of Odilorhabdins, a New Class of Antimicrobial Agents. Front Microbiol 10, 2893 (2019).
- O’Neill, J. Tackling drug-resistant infections globally: Final report and recommendations. Review on Antimicrobial Resistance (2016). https://amr-review.org/sites/default/files/160518_Final%20paper_with%20cover.pdf
- Shi, Y.M. et al. Global analysis of biosynthetic gene clusters reveals conserved and unique natural products in entomopathogenic nematode-symbiotic bacteria. Nat Chem 14, 701-712 (2022).
- Muangpat, P. et al. Genome analysis of secondary metabolite?biosynthetic gene clusters of Photorhabdus akhurstii subsp. akhurstii and its antibacterial activity against antibiotic-resistant bacteria. PLoS ONE 17, e0274956 (2022).
- Pantel, L. et al. Odilorhabdins, antibacterial agents that cause miscoding by binding at a new ribosomal site. Mol Cell 70, 83-94 (2018).
- Racine, E. et al. In Vitro and In Vivo Characterization of NOSO-502, a Novel Inhibitor of Bacterial Translation. Antimicrob Agents Chemother 62, e01016-18 (2018).
- Subkrasae, C. et al. Larvicidal activity of Photorhabdus and Xenorhabdus bacteria isolated from insect parasitic nematodes against Aedes aegypti and Aedes albopictus. Acta Tropica 235, 106668 (2022).