Microbial compositions for fowl health and performance

Abstract

The disclosure relates to isolated microorganisms—including novel strains of the microorganisms—microbial ensembles, and compositions comprising the same. Furthermore, the disclosure teaches methods of utilizing the described microorganisms, microbial ensembles, and compositions comprising the same, in methods for modulating the production of poultry, disease resistance, and egg yield. In particular aspects, the disclosure provides methods of increasing feed efficiency, and methods of preventing colonization of pathogenic microbes.

1 . A method for improving one or more desirable traits in fowl, the method comprising:
 (a) administering to a fowl an effective amount of a microbial composition comprising:
 (i) a purified microbial population that comprises one or more bacteria with a 16S nucleic acid sequence that shares at least 97% sequence identity with a nucleic acid sequence selected from SEQ ID NOs: 1-50 and 59-387 and/or one or more fungi with an ITS nucleic acid sequence that shares at least 97% sequence identity with a nucleic acid sequence selected from SEQ ID NOs: 51-58, and 
 (ii) a carrier suitable for fowl administration; 
   
       wherein the purified microbial population is present in the microbial composition in an amount effective to improve the one or more desirable traits as compared to a fowl not having been administered the microbial composition; and wherein the improvement of the one or more desirable traits is an improvement in the innate immune response, an improvement in incidence of normal gastrointestinal morphology, an improvement in growth rate, an improvement in total body mass, an improvement in feed conversion ratio, an improvement in pathogen exclusion, an improvement in competitive exclusion against pathogens, a reduction in mortality, a reduction in flock variability, an improvement in antimicrobial production, an improvement in stimulating the production of B cells, an improvement in stimulating the production of lymphocytes, an improvement in length of villi, and/or an improvement in expression of inflammatory cytokines. 
     
     
         2 . The method of  claim 1 , wherein the fowl is a broiler. 
     
     
         3 . The method of  claim 1 , wherein the one or more bacteria and/or the one or more fungi have a MIC score of at least about 0.1. 
     
     
         4 . The method of  claim 1 , wherein the purified microbial population comprises a bacterium with a 16S nucleic acid sequence sharing at least 97% identity with SEQ ID NO:386. 
     
     
         5 . The method of  claim 1 , wherein the purified microbial population comprises a bacterium with a 16S nucleic acid sequence sharing at least 97% identity with SEQ ID NO:387. 
     
     
         6 . The method of  claim 4 , wherein the purified microbial population further comprises one or more bacteria with a 16S nucleic acid sequence sharing at least 97% sequence identity with nucleic acid sequences selected from the group consisting of SEQ ID NO:13, SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:31, SEQ ID NO:369, SEQ ID NO:374, and SEQ ID NO:348. 
     
     
         7 . The method of  claim 6 , wherein the purified microbial population comprises one or more bacteria with a 16S nucleic acid sequence sharing at least 97% sequence identity with SEQ ID NO:386 and SEQ ID NO:387. 
     
     
         8 . The method of  claim 7 , wherein the purified microbial population comprises one or more bacteria with a 16S nucleic acid sequence comprising SEQ ID NO:386 and SEQ ID NO:387. 
     
     
         9 . The method of  claim 6 , wherein the purified microbial population comprises one or more bacteria with a 16S nucleic acid sequence selected from the group consisting of SEQ ID NO:13, SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:31, SEQ ID NO:369, SEQ ID NO:374, and SEQ ID NO:348. 
     
     
         10 . The method of  claim 4 , wherein the purified microbial population further comprises one or more bacteria with a 16S nucleic acid sequence sharing at least 97% sequence identity with nucleic acid sequences selected from the group consisting of SEQ ID NO:1 and SEQ ID NO:3. 
     
     
         11 . The method of  claim 10 , wherein the purified microbial population comprises one or more bacteria with a 16S nucleic acid sequence sharing at least 97% sequence identity with SEQ ID NO:386 and SEQ ID NO:387. 
     
     
         12 . The method of  claim 11 , wherein the purified microbial population comprises one or more bacteria with a 16S nucleic acid sequence comprising SEQ ID NO:386 and SEQ ID NO:387. 
     
     
         13 . The method of  claim 10 , wherein the purified microbial population comprises one or more bacteria with a 16S nucleic acid sequence selected from the group consisting of SEQ ID NO:1 and SEQ ID NO:3. 
     
     
         14 . The method of  claim 1 , wherein the microbial composition is formulated as an encapsulation, tablet, capsule, pill, feed additive, food ingredient, food preparation, food supplement, water additive, water-mixed additive, heat-stabilized additive, moisture-stabilized additive, pre-pelleted feed additive, pelleted feed additive, post-pelleting-applied feed additive, consumable solution, consumable spray additive, consumable solid, consumable gel, injection, suppository, drench, bolus, or combination thereof. 
     
     
         15 . The method of  claim 1 , wherein the improvement of the one or more desirable traits is an improvement in antimicrobial production. 
     
     
         16 . The method of  claim 15 , wherein the improvement of antimicrobial production is an improvement of antimicrobial production in the gastrointestinal tract. 
     
     
         17 . The method of  claim 1 , wherein the administering a purified microbial population comprises administering a first microbial composition and a second microbial composition. 
     
     
         18 . The method of  claim 1 , wherein the microbial composition elicits a decrease in the variability of the number of unique species in the gastrointestinal tract. 
     
     
         19 . The method of  claim 18 , wherein the decrease in the variability of the number of unique species is a reduction of the total number of unique species of microbes to between about 50 and 400 species. 
     
     
         20 . A microbial composition comprising:
 (i) a purified microbial population that comprises one or more bacteria with a 16S nucleic acid sequence that shares at least 97% sequence identity with a nucleic acid sequence selected from SEQ ID NOs: 1-50 and 59-387 and/or one or more fungi with an ITS nucleic acid sequence that shares at least 97% sequence identity with a nucleic acid sequence selected from SEQ ID NOs: 51-58, and   (ii) a carrier suitable for fowl administration;   
       wherein the purified microbial population is present in the microbial composition in an amount effective to improve the one or more desirable traits as compared to a fowl not having been administered the microbial composition; and wherein the improvement of the one or more desirable traits is an improvement in the innate immune response, an improvement in incidence of normal gastrointestinal morphology, an improvement in growth rate, an improvement in total body mass, an improvement in feed conversion ratio, an improvement in pathogen exclusion, an improvement in competitive exclusion against pathogens, a reduction in mortality, a reduction in flock variability, an improvement in antimicrobial production, an improvement in stimulating the production of B cells, an improvement in stimulating the production of lymphocytes, an improvement in length of villi, and an improvement in expression of inflammatory cytokines; and/or wherein at least one of the one or more bacteria and/or at least one of the one or more fungi is desiccated. 
     
     
         21 . The composition of  claim 20 , wherein the fowl is a broiler. 
     
     
         22 . The composition of  claim 20 , wherein the one or more bacteria and/or the one or more fungi have a MIC score of at least about 0.1. 
     
     
         23 . The composition of  claim 20  wherein the purified microbial population comprises a bacterium with a 16S nucleic acid sequence sharing at least 97% identity with SEQ ID NO:386. 
     
     
         24 . The composition of  claim 20 , wherein the purified microbial population comprises a bacterium with a 16S nucleic acid sequence sharing at least 97% identity with SEQ ID NO:387. 
     
     
         25 . The composition of  claim 23 , wherein the purified microbial population further comprises one or more bacteria with a 16S nucleic acid sequence sharing at least 97% sequence identity with nucleic acid sequences selected from the group consisting of SEQ ID NO:13, SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:31, SEQ ID NO:369, SEQ ID NO:374, and SEQ ID NO:348. 
     
     
         26 . The composition of  claim 25 , wherein the purified microbial population comprises one or more bacteria with a 16S nucleic acid sequence sharing at least 97% sequence identity with SEQ ID NO:386 and SEQ ID NO:387. 
     
     
         27 . The composition of  claim 26 , wherein the purified microbial population comprises one or more bacteria with a 16S nucleic acid sequence comprising SEQ ID NO:386 and SEQ ID NO:387. 
     
     
         28 . The composition of  claim 25 , wherein the purified microbial population comprises one or more bacteria with a 16S nucleic acid sequence selected from the group consisting of SEQ ID NO:13, SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:31, SEQ ID NO:369, SEQ ID NO:374, and SEQ ID NO:348. 
     
     
         29 . The composition of  claim 23 , wherein the purified microbial population further comprises one or more bacteria with a 16S nucleic acid sequence sharing at least 97% sequence identity with nucleic acid sequences selected from the group consisting of SEQ ID NO:1 and SEQ ID NO:3. 
     
     
         30 . The composition of  claim 29 , wherein the purified microbial population comprises one or more bacteria with a 16S nucleic acid sequence sharing at least 97% sequence identity with SEQ ID NO:386 and SEQ ID NO:387. 
     
     
         31 . The composition of  claim 30 , wherein the purified microbial population comprises one or more bacteria with a 16S nucleic acid sequence comprising SEQ ID NO:386 and SEQ ID NO:387. 
     
     
         32 . The composition of  claim 29 , wherein the purified microbial population comprises one or more bacteria with a 16S nucleic acid sequence selected from the group consisting of SEQ ID NO:1 and SEQ ID NO:3. 
     
     
         33 . The composition of  claim 20 , wherein the microbial composition is formulated as an encapsulation, tablet, capsule, pill, feed additive, food ingredient, food preparation, food supplement, water additive, water-mixed additive, heat-stabilized additive, moisture-stabilized additive, pre-pelleted feed additive, pelleted feed additive, post-pelleting-applied feed additive, consumable solution, consumable spray additive, consumable solid, consumable gel, injection, suppository, drench, bolus, or combination thereof. 
     
     
         34 . The composition of  claim 20 , wherein the improvement of the one or more desirable traits is an improvement in antimicrobial production in the gastrointestinal tract. 
     
     
         35 . The composition of  claim 20 , wherein the microbial composition elicits a decrease in the variability of the number of unique species in the gastrointestinal tract. 
     
     
         36 . The composition of  claim 35 , wherein the decrease in the variability of the number of unique species is a reduction of the total number of unique species of microbes to between about 50 and 400 species. 
     
     
         37 . The method of  claim 5 , wherein the purified microbial population further comprises one or more bacteria with a 16S nucleic acid sequence sharing at least 97% sequence identity with nucleic acid sequences selected from the group consisting of SEQ ID NO:13, SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:31, SEQ ID NO:369, SEQ ID NO:374, and SEQ ID NO:348. 
     
     
         38 . The method of  claim 5 , wherein the purified microbial population further comprises one or more bacteria with a 16S nucleic acid sequence sharing at least 97% sequence identity with nucleic acid sequences selected from the group consisting of SEQ ID NO:1 and SEQ ID NO:3. 
     
     
         39 . The composition of  claim 24 , wherein the purified microbial population further comprises one or more bacteria with a 16S nucleic acid sequence sharing at least 97% sequence identity with nucleic acid sequences selected from the group consisting of SEQ ID NO:13, SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:31, SEQ ID NO:369, SEQ ID NO:374, and SEQ ID NO:348. 
     
     
         40 . The composition of  claim 24 , wherein the purified microbial population further comprises one or more bacteria with a 16S nucleic acid sequence sharing at least 97% sequence identity with nucleic acid sequences selected from the group consisting of SEQ ID NO:1 and SEQ ID NO:3.