Microbiome Science’s Potential Unveiled

At the World AMR Congress, Britton Strickland, PhD, field application scientist for CosmosID, presented the transformative potential of microbiome science in addressing antimicrobial resistance and developing new anti-infectives. Strickland, an expert in microbiome research, detailed how advancements in this field shape strategies to combat AMR.

Strickland discusses how advancements in microbiome science can enhance our strategies for managing antimicrobial resistance, with specific methods such as examining bacterial communities through omics technologies and identifying protective or harmful bacterial mechanisms being actively explored.

Strickland emphasized that the human microbiome, including the gut and other areas, plays a crucial role in defending against pathogens. He explained, “The human microbiome, including the gut and beyond, is one of the most critical defense systems against pathogens. Traditional microbiologists have identified mechanisms like nutrient competition, microbe inhibition, antimicrobial peptides, and catabolism that help with protection.

He noted that many bacteria are not culturable in the lab and are only detectable through advanced omics technologies. “NGS and metabolomics allow us to examine the entire bacterial community within the human gut or skin and identify bacterial taxa through DNA sequencing. Metabolomics also helps profile the chemicals involved in protective or harmful mechanisms of these bacteria.”

Addressing the challenges and opportunities in developing novel anti-infectives, Strickland pointed out that while probiotics have traditionally been used to inhibit pathogens, their effectiveness is not always well-supported. “Typically, microbiome therapies have focused on probiotics, known for their effectiveness in inhibiting pathogens and preventing colonization. This concept has been recognized for thousands of years, even before bacteria were understood.”

He noted that recent interest in probiotics has led to exaggerated claims and that many probiotics struggle to establish themselves in the host. Strickland highlighted how advances in molecular techniques and reduced sequencing costs are improving our understanding of bacterial metabolites and their effects. “New therapies, such as fecal transplants and live biotherapeutic products recently approved by the FDA, are emerging.”

Strickland also discussed recent breakthroughs and projects at CosmosID, explaining how they integrate microbiome science to develop new therapies. “CosmosID uses microbiome science in several applications. Traditional diagnostic methods, which took over a week, can now identify bacteria and their antibiotic resistance within days using DNA sequencing. We apply these technologies in preclinical models to optimize products and operate in a CLIA and GXP-compliant environment with clinical samples. This allows us to analyze large-scale human data to identify bacterial taxa, track changes before and after treatment with new therapeutics, and monitor AMR genes in various environments.”

Strickland concluded by noting the broader implications of these advancements for AMR, including studying probiotic engraftment, phage therapy, and the effects of antibiotics on the microbiome. “We also study probiotic engraftment to find the best candidates for the human environment. Other applications include phage therapy, studying the effects of antibiotics on the microbiome, and understanding how local antibiotics impact the entire microbiome.”