Segmented filamentous bacteria (SFB) are a group of host-adapted, gut commensal organisms that attach to the ileal epithelium of vertebrate and invertebrate hosts. A genetic relative of the genus Clostridium, these morphologically unique bacteria display a replication and differentiation life cycle initiated by epithelial binding, making it difficult to culture these bacteria in vitro. SFB intimately bind to the surface of absorptive intestinal epithelium without inducing an inflammatory response. Rather, their presence impacts the generation of innate and acquired immunity and clearance of extracellular bacterial or fungal pathogens in the gastrointestinal and respiratory tracts. SFB have recently garnered attention due to their role in promoting adaptive and innate immunity in mice and rats through the differentiation and maturation of Th17 cells in the intestinal tract and production of immunoglobulin A (IgA) and stimulating the differentiation and maturation of Th17 cells. SFB are the first commensal bacteria identified that impact the maturation and development of Th17 cells in mice. Recently, microbiome studies have revealed the presence of Candidatus Arthromitus (occasionally designated as Candidatus Savagella), a proposed candidate species of SFB, in higher proportions in higher-performing flocks as compared to matched lower-performing flocks, suggesting that SFB may serve to establish a healthy gut and protect turkeys from pathogens resulting in morbidity and decreased performance. In this review we seek to describe the life cycle, host specificity, and genetic capabilities of SFB and how these factors influence the host immunity and microbiome. Although the role of SFB to induce antigen-specific Th17 cells in poultry is unknown, they may play an important role in modulating the immune response in the intestinal tract to promote resistance against some infectious diseases and promote food-safety. This review will serve to demonstrate the importance of studying and further characterizing commensal, host-specific bacteria, as many animal studies have demonstrated their importance to host health.

Mycobacterium aviumsubsp.paratuberculosisis an intracellular pathogen of macrophages that causes a chronic enteritis (Johne's disease) in ruminants. The purpose of this study was to determine whetherM. aviumsubsp.paratuberculosisinfection causes apoptosis in bovine monocytes. Using Hoechst 33342 staining, we observed increased numbers of apoptotic monocytes within 6 h of infection withM. aviumsubsp.paratuberculosis, and these numbers increased further at 24 and 48 h. This effect appeared to require viable bacilli, because monocytes infected with heat-killedM. aviumsubsp.paratuberculosisdid not exhibit a significant increase in apoptosis. Preincubation of monocytes with bovine growth hormone prior to infection withM. aviumsubsp.paratuberculosisdid not significantly alter the number of apoptotic cells.

The loss of antibiotics as a tool to improve feed efficiency in poultry production has increased the urgency to understand how the microbiota interacts with animals to impact productivity and health. Modulating and harnessing microbiota-host interactions is a promising way to promote poultry health and production efficiencies without antibiotics. In poultry, the microbiome is influenced by many host and external factors including host species, age, gut compartment, diet, and environmental exposure to microbes. Because so many factors contribute to the microbiota composition, specific knowledge is needed to predict how the microbiome will respond to interventions. The effects of antibiotics on microbiomes have been well documented, with different classes of antibiotics having distinctive, specific outcomes on bacterial functions and membership. Non-antibiotic interventions, such as probiotics and prebiotics, target specific bacterial taxa or function to enhance beneficial properties of microbes in the gut. Beneficial bacteria provide a benefit by displacing pathogens and/or producing metabolites (e.g., short chain fatty acids or tryptophan metabolites) that promote poultry health by improving mucosal barrier function or immune function. Microbiota modulation has been used as a tool to reduce pathogen carriage, improve growth, and modulate the immune system. An increased understanding of how the microbiota interacts with animal hosts will improve microbiome intervention strategies to mitigate production losses without the need for antibiotics.

Beginning in 2017, the subtherapeutic use of most antibiotic compounds for growth promotion in food producing animals in the US was prohibited, highlighting the need to discover alternative growth promotants. Identifying the mechanism of action of growth promoting antibiotics may aid in the discovery of antibiotic alternatives. We describe the effects of feeding a subtherapeutic (50 g/ton of feed) and therapeutic (200 g/ton) concentration of bacitracin methylene disalicylate (BMD) to commercial turkeys for 14 weeks, and its effect on turkey intestinal microbial communities and cecal metabolomes. Both BMD concentrations had an immediate and lasting impact on the microbiota structure, and reduced bacterial richness through the end of the study (12 weeks). Metabolomic analysis identified 712 biochemicals, and 69% of metabolites were differentially present in BMD treated turkeys for at least one time point (q < 0.1). Amino acids, carbohydrates, nucleotides, peptides, and lipids were decreased in the turkey ceca early after BMD administration. Long-term metabolome alterations continued even after withdrawal of BMD. The microbial composition, determined by 16S rRNA gene sequencing, was predictive of the metabolome, indicating a connection between the microbiome and metabolome. In-feed BMD may cause bacterial metabolic shifts, leading to beneficial traits that can be targeted to improve animal health and production.