What's Hot in the Microbial Sciences

What's Hot in the Microbial Sciences

Synthetic Biology and Ocean Health

From shoring up the ailing oceans, to engineering synthetic gene circuits and programmable cells to produce new diagnostics and therapeutics, synthetic biology provides scientists with innovative tools to address key issues.

The world’s oceans are threatened by human activities. In a recent review published in Trends in Biotechnology, researchers discussed ways to leverage synthetic biology to address issues, such as plastics pollution, that relate to ocean health.

Plastics pour into the seas from landfills and river systems. Weathering and churning seas grind the large plastic into smaller components, including tiny bits called microplastics. The tissues of marine organisms become home for the smallest microplastics, which exert toxic effects. Bigger plastics choke large areas of open ocean, where some sea life ingest or become entangled by them. Preventing land-based plastics from entering waterways represents one upstream way of safeguarding oceans. However, much plastic already resides there. Scientists envision the selective isolation of microorganisms that degrade plastics naturally (biotransformation) to inform strategies for engineering more robust plastic-degrading strains.

Stages of marine plastic biodegradation.Stages of marine plastic biodegradation.
Source: Wikimedia
For example, one study, published in Archives of Microbiology, examined the natural potential of communities of bacteria living in sediment found in Manila Bay, Philippines (an area that suffers from severe plastic pollution) to degrade low-density polyethylene (LDPE)—a soft, flexible, lightweight plastic material. First, scientists quantified plastic composition in selected sites of the bay. Then they collected sediment samples for further experimentation from sites that registered the highest and lowest concentrations of plastic. In the laboratory, sediment samples were incubated for 91 days with LDPE then examined by fourier transform infrared spectroscopy (FTIR). Researchers observed structural modifications (i.e., carbonyl and vinyl products) that were considered signs of polymer degradation on the surface of the LPDE. High-throughput sequencing further revealed that the dominant phylum in the microbial sediment consortium was Proteobacteria.

Other bacterial taxa that are associated with hydrocarbon degradation were also identified and thought to be playing active roles in partial biodegradation of the plastic. Researchers hypothesized the remaining microbial taxa were consuming byproducts, or providing nourishment for other groups in the consortia, and collectively creating a synergistic biofilm-associated microenvironment, which utilized plastic as its main carbon source.

In pursuit of scalable bioremediation techniques to address plastic pollution, researchers associated with the Trends in Biotechnology review proposed a multi-step synthetic approach to leverage knowledge gleaned from microenvironments within plastic biofilms, like those in Manila Bay. First, scientists called for a compilation of datasets pertaining to microbial communities that naturally degrade plastic. From there, genetic toolkits and engineering strategies could be developed to augment the pool of microorganisms that degrade plastics. Protein engineering could be explored to improve the effectiveness of plastic-degrading enzymes, with the downstream goal of constructing synthetic microbial consortia that degrade, and perhaps even biosynthesize value-added products from, the degraded plastic (e.g., carbon sources as added nutritional fodder for the engineered microorganisms themselves).

James J. Collins, Ph.D., one of the authors of the Trends in Biotechnology study, presented at ASM Microbe 2023 about harnessing synthetic biology and deep learning to fight pathogens in a session titled “Synthetic Biology Tools and Emerging Environmental Organisms for Antibiotic and Natural Product Discovery and Synthesis."

Novel Antibiotic Mounts a 2-Pronged Attack on Cell Envelope

Bacteria that are resistant to multiple antibiotics continue to be a grave threat to human health. Equally concerning is the dearth of new antibiotic development to combat them. Teixobactin, a novel antibiotic that came to light in 2015, fared well in animal models of infection, providing evidence of its potential as a human antibiotic agent. Recently, a paper published in Nature explored 2 modes by which teixobactin exerts activity against multidrug-resistant (MDR) gram-positive pathogens, including methicillin-resistant Staphylococcus aureus (MRSA), Streptococcus pneumoniae and drug-resistant enterococci.

Chemical structure of texiobactin.Chemical structure of texiobactin.
Source: PubChem (ID: 86341926)
One mode of action involved teixobactin targeting lipid II, a peptidoglycan precursor, which led to interference with peptidoglycan biosynthesis and contributed to defects in the bacterial cell membrane. Finding antibiotics that act on prokaryotic membranes, but leave human cells unharmed, has been challenging. However, teixobactin damages only membranes that contain lipid II—which human cells do not possess. This microbial-specific targeting eliminates the threat of toxicity for human applications.

In addition to lipid II targeting, teixobactin was shown to possess a supramolecular structure that sequesters lipid II into supramolecular fibrils (multi-protein complexes that polymerize into fiber-shaped structures) and displaces phospholipids. The result? Thinning and disruption of the bacterial cell membrane. Teixobactin’s 2 modes of action, (i.e., inhibition of cell wall synthesis and weakening of cytoplasmic membrane), produce an effective compound for targeting the bacterial cell envelope. Very few new classes of antibiotics have been created in the past 30 years, yet teixobactin shows promise for targeting bacterial pathogens while sparing mammalian cells.

Kim Lewis, Ph.D., one of the authors of the Nature study referenced above, presented about antibiotics from unusual microorganisms and "undruggable" targets at the ASM Microbe 2023 session “Synthetic Biology Tools and Emerging Environmental Organisms for Antibiotic and Natural Product Discovery and Synthesis."

Phage Therapy to Treat Multidrug Resistant Infections

Not surprisingly, MDR bacterial pathogens are also emerging as a major threat in common infections like urinary tract infections (UTI)—one of the most frequent infections for which antibiotics are prescribed. As antimicrobial resistance (AMR) continues to increase in uropathogenic Escherichia coli (UPEC), a primary agent of UTIs, new antibiotics and therapies will be critical to maintain ability to control infections.

Bacteriophage coming in contact with cell surface.Bacteriophage coming in contact with cell surface.
Source: iStock
New developments in bacteriophage (phage) therapy are showing promise to combat AMR UTIs. However, bacteria also develop resistance to phages, which could impact the efficacy of this treatment. In a recent mSphere paper, researchers evaluated the costs of the development of phage resistance during UPEC infection.

To gauge phage activity in a simulation of the human urinary environment, scientists compared susceptibility of UPEC strains to 2 distinct phages (HP3 and ES17), using both in vitro and in vivo models. Researchers found that development of phage resistance in UPEC strains began within the first 6-8 hours post-phage introduction in both pooled human urine and bacterologic medium. Phage-resistant UPEC strains demonstrated some distinct genotypic and in vitro phenotyipc changes. Namely, these strains possessed mutations in genes involved in lipopolysaccharide (LPS) biosynthesis and demonstrated altered adherence to and invasion of human bladder epithelial HTB-9 cells. Furthermore, resistant strains demonstrated reduced growth in vitro and reduced ability to colonize the mouse urinary tract in vivo, compared to parental strains.

Overall, researchers observed that phage resistance is accompanied by fitness costs. They concluded that phage therapy for UTIs will succeed when the development of said resistance decreases UPEC fitness to the extent that it causes phage-resistant bacteria to become less virulent—promoting immune clearance and resolution of infection. Finally, researchers noted that phage-resistant bacteria may also become more sensitive to other antibacterial treatments, suggesting that phage resistance could bolster efficacy of antimicrobial agents against MDR pathogens.

Barbara Trautner, M.D., Ph.D., one of the authors of the mSphere study referenced here, convened a session about phage therapy at ASM Microbe 2023 titled, “New Perspectives on Phage Therapy to Treat Multidrug Resistant Infections."

Lessons From the Assembly and Transmission of Single-Seed Microbiota

Climate change is driving further adaptation in an already incalculably diverse microbial world, suggesting that when it comes to microbiome management of synthetic and natural communities, the principles of ecology and evolution are critical.

Young sprouts of mung bean seeds.Young sprouts of mung bean seeds.
Source: Flickr
The microbiota within seeds of agriculturally important plants exhibit roles in ending seed dormancy, improving seed germination and helping ward off certain plant pathogens, thus influencing a plant’s potential to grow and thrive. Evidence further indicates that the seed microbiota may also have an impact on soil microbiome establishment and, as a result, confer longer-term consequences on crop development. Characterizing seed microbiota may, therefore, permit improvement in plant phenotypes, which could have important ramifications on agricultural practices. With this in mind, scientists published an mBio paper in which they examined the diversity of bacteria associated with individual seeds during development and sought to understand how plant phenotype was influenced by variations in seed microbiome composition.

Using common bean and radish seeds, researchers estimated the microbiota structure and assembly of 1,000 individual seeds during seed development and maturation. To account for the low microbial biomass presented at the single-seed level, scientists employed a culture-based enrichment strategy prior to DNA extraction and sequencing.

Overall, researchers reported that individual seeds were associated with low bacterial richness. In fact, more than 75% of reads were associated with only 1 dominant taxon, the identity of which varied greatly between plants and even between individual seeds of the same plant. Fifteen bacterial orders were represented in these dominant taxa. Authors noted that these results aligned with previous reports that the plant microbiome might be bottlenecked at the individual seed level, as a result of plant defenses and microbial interactions, which supports the primary symbiont hypothesis.

Next, researchers sought to identify the origins and changes in community composition of seed-associated microbial taxa after colonization (succession). Scientists discovered that initial seed colonizers arrived by 1 of 2 primary methods: internally (through the vascular tissue) or externally (through the colonization of reproductive tissues via airborne organisms or pollinators). However, succession profiles differed amongst plants. In radish seeds, bacterial diversity and taxonomic composition remained stable, suggesting that the original bacterial settlers persisted during seed maturation. Whereas, in bean seeds, the original bacterial taxa were replaced with new microbial residents during seed development.

When it came to seed microbiota assembly, researchers reported that local processes were more impactful than seed dispersal, indicating that selection of microbial taxa is, at least partially, dependent upon host defenses. Authors therefore suggested that the differences in succession profiles might be driven by a variability in available resources amongst bean and radish plants but acknowledged that this hypothesis required further testing. Differences in fitness between taxa exerted the most influence on transmission of seed-borne microbes to seedlings for bean and radish seeds alike. Bacterial population size was not significantly impactful.

Overall, this study provided insight into the origin, composition, assembly and transmission of the seed-microbiota. Developing a more robust understanding of how these factors impact seed phenotype and vitality will inform possible avenues for seed microbiome manipulation to increase crop productivity and sustainability.

Marie Simonin, Ph.D., one of the authors of this mBio study, discussed plant microbiota engineering at ASM Microbe 2023 in the session titled “Microbiome Management in a Changing World."

Author: Ashley Hagen

Ashley Hagen
Ashley Hagen, M.S., joined the American Society for Microbiology as the Science Communications Specialist in 2020. Today, she is the Scientific and Digital Editor and host of ASM's Meet the Microbiologist and Microbial Minutes.

Author: John Bell

Ashley Hagen
John Bell moved to the ASM Science Communications team from ASM's Journals Department. He brings with him many years of experience in copyediting, proofreading and production.