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.

Three novel, anaerobic, Gram-positive bacteria were isolated from the eggshell of two separate white leghorn chicken flocks and the ileum of a healthy pig, and designated MMM721^T, ISU324 and PIG517 respectively. Cells were pleomorphic and capable of forming long chains of rods or coccoid clusters. Phylogenetic analysis of the 16S rRNA gene sequences identified these strains to be within the genus Turicibacter , of which only one species, Turicibacter sanguinis , has been formally described. However, whole genome sequencing of novel isolates returned a digital DNA–DNA hybridization value of 22.5 % and average nucleotide identity (ANI) values of 76.4 % (ANIb) and 86.0 % (ANIm), indicating divergence between the type strain MMM721^T and T. sanguinis , suggesting the strains represented a novel species. The major fatty acid methyl esters of strain MMM721^T were C_16 : 0, C_18 : 1 ω7c and C_18 : 0. The strains mainly produced the volatile fatty acid lactate, along with smaller amounts of acetate and butyrate. Together, these data indicate that MMM721^T, along with ISU324 and PIG517, represent a novel species within the genus Turicibacter . We propose the name Turicibacter bilis sp. nov. for the species. The type strain is MMM721^T (=ATCC TSD-238^T=CCUG 74757^T).

Turicibacter sanguinis MOL361 (DSM 14220) is the reference and type strain for the Turicibacter genus, commonly found in the intestinal tract of animal species. Long-read sequencing was performed on this strain to complement publicly available Illumina HiSeq-based data, producing a complete annotated genome sequence.

A novel bacterium, Megasphaera stantonii (strain AJH120 ^T ), was isolated from the cecum of a chicken during a screen for microorganisms using a brain heart infusion (BHI) medium. PacBio and Illumina MiSeq sequencing technologies were used to produce a single contiguous chromosome.

Here, we describe the complete genome sequence of Romboutsia sp. strain CE17, which was isolated during a screen for spore-forming anaerobic microorganisms that colonized the surface of chicken eggs.

The genus Turicibacter is a common inhabitant of the small intestine of numerous animal species, including chickens. However, little is known about the phenotypic and genetic diversity of the genus. Within the chicken small intestine, bile and its primary components, bile acids, are involved in nutrient absorption and modulating microbial community structure. Here, we compare T. sanguinis MOL361 (type strain of the genus), with three strains of the recently described species T. bilis, two from chicken and one from swine. Multiple bile salt hydrolase (BSH) genes, responsible for modification of host-derived bile acids, were identified in each strain and were compared to other Turicibacter BSH with known activities. The bile acid deconjugation ability of individual strains were assessed using chicken bile, as well as the primary bile acids taurochenodeoxycholic acid and taurocholic acid. Both chicken isolates, T. bilis MMM721 and T. bilis ISU324, as well as T. sanguinis MOL361, significantly reduced the concentrations of the tauro-conjugated bile acids. Overall, this work identifies the context-dependent nature of Turicibacter BSH activity.