Research Highlight: The Microbiome as a Source of Immune-Active Respiratory Therapeutics

The microbiome as a source of immune active respiratory therapeutics

Resilient Biotics is identifying strains that activate beneficial host immune responses for the development of new microbial products in production animal systems.

Interactions between commensal microbes and the host immune system

Human and animal hosts are home to trillions of bacteria, known as the microbiome, which play a vital role in keeping us healthy. These commensal bacteria aren’t harmful—in fact, they help protect us from infections. One way they do this is by interacting with the body’s first line of defense, the innate immune system, which is designed to quickly respond to potential threats like harmful bacteria or viruses. Commensal bacteria can activate special sensors that detect signs of infection. These sensors, called pattern recognition receptors (PRRs), trigger a series of immune responses, including the production of molecules that kill harmful bacteria, strengthen the body’s natural epithelial tissue barriers, and signal immune cells to come and defend the area.

In the respiratory tract, commensal bacteria help protect against infections by stimulating immune cells in the airway lining to produce antimicrobial substances that target harmful microbes. They also activate PRRs in the respiratory epithelium, such as Toll-like receptors (TLRs) and NOD-like receptors (NLRs). Activation of these receptors triggers signaling cascades that result in the production of antimicrobial peptides, cytokines, and chemokines, reinforcing the barrier function of epithelial cells and recruiting immune cells like neutrophils and macrophages to sites of potential infection.

The underlying mechanisms that activate innate immune responses and help defend against respiratory infection represent a new modality we can harness for combating respiratory diseases in human and animal populations. In humans, pulmonary and respiratory infections are significant because they are among the leading causes of illness and death worldwide, particularly in vulnerable populations like young children, the elderly, and those with weakened immune systems. In production animal systems, respiratory diseases are just as deadly, and perhaps an even greater concern due to the high risk of emerging, zoonotic viral pathogens.

Toll-like receptor (TLR) activation can protect against viral infection

The activation of TLR receptors can produce a strong protective effect against viral infection; a mechanism that is well supported by numerous scientific reports. Activation of toll-like receptor 2 (TLR2) within respiratory tract mucosal sites has resulted in TLR-dependent protection against a viral infection. Tan et al (2012) demonstrated that use of PEG-Pam2Cys, a small molecule TLR2 agonist and synthetic analog of a bacterial lipopeptide, could enhance pulmonary innate immunity against influenza A virus (IAV) infection. Intranasal administration of PEG-Pam2Cys significantly alters the lung’s cellular environment, improving resistance to IAV while allowing for the development of memory CD8+ T cell responses. CD8 T cell responses are one of the key mediators of viral clearance. Although PEG-Pam2Cys does not completely prevent infection, it reduces viral burden and mortality. Tan et al concluded that TLR agonists, such as PEG-Pam2Cys, could serve as a broad-spectrum treatment against various respiratory infections.

Additionally, commensal bacteria in the gut can activate protective TLR responses via interactions with the gut epithelium. As one example, seminal research from the Kasper laboratory at Harvard Medical School has demonstrated via experiments in germ-free mice that a gut commensal organism can activate an important antiviral innate immune response. Stefan et al (2020) demonstrated that Bacteroides fragilis glycolipids activate immune cells in the colon, specifically dendritic cells, through TLR4 receptors. This signaling triggers the release of IFNβ, which plays a key role in enhancing the host’s resistance to viral infections. IFNβ also induces interferon-stimulated genes (ISGs) systemically, helping to prepare the immune system for future infections. The study highlights the unique anti-inflammatory properties of B. fragilis molecules, suggesting therapeutic potential to enhance immune responses without causing harmful inflammation.

Microbiome TLR activation is a promising therapeutic modality 

Microbiome strains, as shown with the B. fragilis example above, represent a deep pool of possible TLR activators that could promote beneficial innate immunity, particularly against viral infection. A deeper understanding of the specific TLR activation profiles of commensal bacteria can open new therapeutic doors, and offers an opportunity to produce unique microbial cocktails with broad, low level inflammatory properties targeting specific antiviral responses. Delivery of these microbial cocktails at key points in animal development could help reduce the impact of long-standing respiratory disease challenges in production animal systems. Furthermore, promoting strong immune responses not only provides protection against a primary viral pathogen, but could also help prevent secondary bacterial infections from taking hold.

At Resilient Biotics, we have focused on microbiome driven innate immune signaling as a key therapeutic mechanism in microbial consortia developed for respiratory disease indications. To understand which commensal strains activate these responses, we have systematically tested respiratory mucosal-associated strains in cell culture assays to identify specific TLR responses (see figure).

Using this approach, we have constructed a database of commensal TLR activation profiles and revealed TLR response patterns for a wide range of different bacterial families. Importantly, we have identified significant strain variation for TLR activation profiles within a single genus. This implies even within a well-characterized genus, such as Bacillus, there exist species and strain variants in host-associated samples that have unique TLR activation properties. Resilient Biotics is utilizing this valuable strain-specific TLR activation profile data to formulate new microbial consortia for therapeutic and health promotion uses in food animal systems. Ultimately, our goal is to help reduce the burden of disease and limit over-use of antimicrobials in production animals in order to help create a safe and sustainable food supply.

Stefan KL, Kim MV, Iwasaki A, Kasper DL. Commensal Microbiota Modulation of Natural Resistance to Virus Infection. Cell. 2020 Nov 25;183(5):1312-1324.e10. doi: 10.1016/j.cell.2020.10.047. Epub 2020 Nov 18. PMID: 33212011; PMCID: PMC7799371.

Tan AC, Mifsud EJ, Zeng W, Edenborough K, McVernon J, Brown LE, Jackson DC. Intranasal administration of the TLR2 agonist Pam2Cys provides rapid protection against influenza in mice. Mol Pharm. 2012 Sep 4;9(9):2710-8. doi: 10.1021/mp300257x. Epub 2012 Aug 3. PMID: 22823162.