Fowl production by administration of a synthetic bioensemble of microbes or purified strains thereof
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 a fowl, the method comprising
administering to the fowl an effective amount of a microbial composition comprising:
(a) a purified microbial population that comprises:
(i) a bacterium with a 16S nucleic acid sequence that shares at least 97% sequence identity with SEQ ID NO: 386, and/or
(ii) a bacterium with a 16S nucleic acid sequence that shares at least 97% sequence identity with SEQ ID NO: 387, and
(b) 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.
2. The method of claim 1 , wherein the fowl is a broiler.
3. The method of claim 1 , wherein the bacterium has a maximal information coefficient (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% sequence 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% sequence identity with SEQ ID NO:387.
6. The method of claim 1 , wherein the purified microbial population further comprises one or more bacteria with a 16S nucleic acid sequence sharing at least 97% sequence identity with a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1-50 and 59-385; and/or one or more fungi with an internal transcribed spacer (ITS) nucleic acid sequence that shares at least about 97% sequence identity with a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 51-58.
7. The method of claim 1 , wherein the purified microbial population comprises: a bacterium with a 16S nucleic acid sequence sharing at least 98% sequence identity with SEQ ID NO:386 and/or a bacterium with a 16S nucleic acid sequence sharing at least 98% sequence identity with SEQ ID NO:387.
8. The method of claim 1 , wherein the purified microbial population comprises: a bacterium with a 16S nucleic acid sequence sharing at least 99% sequence identity with SEQ ID NO:386 and/or a bacterium with a 16S nucleic acid sequence sharing at least 99% sequence identity with SEQ ID NO:387.
9. The method of claim 1 , wherein the purified microbial population further comprises one or more bacteria with a 16S nucleic acid sequence sharing at least 98% sequence identity with a nucleic acid sequence selected from the group consisting of: SEQ ID NOs: 1-50 and 59-385; and/or one or more fungi with an ITS nucleic acid sequence that shares at least 98% sequence identity with a nucleic acid sequence selected from the group consisting of: SEQ ID NOs: 51-58.
10. The method of claim 1 , wherein the purified microbial population further comprises one or more bacteria with a 16S nucleic acid sequence sharing at least 97% sequence identity with a nucleic acid sequence selected from the group consisting of: SEQ ID NO:3, SEQ ID NO: 13, SEQ ID NO: 369, SEQ ID NO: 370, and SEQ ID NO: 374.
11. The method of claim 1 , wherein the purified microbial population comprises: a bacterium with a 16S nucleic acid sequence of SEQ ID NO:386 and/or a bacterium with a 16S nucleic acid sequence of SEQ ID NO:387.
12. The method of claim 1 , wherein the purified microbial population comprises: a bacterium with a 16S nucleic acid sequence comprising SEQ ID NO:386 or a bacterium with a 16S nucleic acid sequence comprising SEQ ID NO:387.
13. The method of claim 1 , wherein the purified microbial population comprises one or more bacteria with a 16S nucleic acid sequence sharing at least 98% sequence identity with a nucleic acid sequence selected from the group consisting of: SEQ ID NO:3, SEQ ID NO: 13, SEQ ID NO: 369, SEQ ID NO: 370, and SEQ ID NO: 374.
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. The method of claim 1 , wherein the purified microbial population further comprises one or more bacteria with a 16S nucleic acid sequence sharing at least 99% sequence identity with a nucleic acid sequence selected from the group consisting of: SEQ ID NOs: 1-50 and 59-385; and/or one or more fungi with an ITS nucleic acid sequence that shares at least 99% sequence identity with a nucleic acid sequence selected from the group consisting of: SEQ ID NOs: 51-58.
21. The method of claim 1 , wherein the purified microbial population further comprises one or more bacteria with a 16S nucleic acid sequence sharing at least 99% sequence identity with a nucleic acid sequence selected from the group consisting of: SEQ ID NO:3, SEQ ID NO: 13, SEQ ID NO: 369, SEQ ID NO: 370, and SEQ ID NO: 374.
22. The method of claim 1 , 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.
23. The method of claim 1 , wherein the purified microbial population further comprises one or more bacteria with a 16S nucleic acid sequence selected from the group consisting of: SEQ ID NOs: 1-50 and 59-385; and/or one or more fungi with an ITS nucleic acid sequence selected from the group consisting of: SEQ ID NOs: 51-58.
24. The method of claim 1 , wherein the purified microbial population further comprises one or more bacteria with a 16S nucleic acid sequence selected from the group consisting of: SEQ ID NO:3, SEQ ID NO: 13, SEQ ID NO: 369, SEQ ID NO: 374, and SEQ ID NO: 370.
25. The method of claim 1 , wherein the purified microbial population comprises a bacterium with a 16S nucleic acid sequence sharing at least 98% sequence identity with SEQ ID NO:387.
26. The method of claim 1 , wherein the purified microbial population comprises a bacterium with a 16S nucleic acid sequence sharing at least 99% sequence identity with SEQ ID NO:387.
27. The method of claim 1 , wherein the purified microbial population comprises a bacterium with a 16S nucleic acid sequence of SEQ ID NO:387.
28. The method of claim 1 , wherein the purified microbial population comprises a bacterium as deposited as NRRL B-67691.
29. The method of claim 1 , wherein the carrier is calcium carbonate.
30. The method of claim 1 , wherein the microbial composition is formulated as a pelleted feed additive.
31. The method of claim 1 , wherein the purified microbial population comprises at least 10 2 cells.