Comparison of media for isolation of poultry intestinal bacteria

Pioneer colonizers: Bacteria that alter the chicken intestinal morphology and development of the microbiota

Microbes commonly administered to chickens facilitate development of a beneficial microbiome that improves gut function, feed conversion and reduces pathogen colonization. Competitive exclusion products, derived from the cecal contents of hens and shown to reduce Salmonella colonization in chicks, possess important pioneer-colonizing bacteria needed for proper intestinal development and animal growth. We hypothesized that inoculation of these pioneer-colonizing bacteria to day of hatch chicks would enhance the development of their intestinal anatomy and microbiome. A competitive exclusion product was administered to broiler chickens, in their drinking water, at day of hatch, and its impact on intestinal morphometrics, intestinal microbiome, and production parameters, was assessed relative to a control, no treatment group. 16S rRNA gene, terminal restriction fragment length polymorphism (T-RFLP) was used to assess ileal community composition. The competitive exclusion product, administered on day of hatch, increased villus height, villus height/width ratio and goblet cell production ∼1.25-fold and expression of enterocyte sugar transporters 1.25 to 1.5-fold in chickens at 3 days of age, compared to the control group. As a next step, chicks were inoculated with a defined formulation, containing Bacteroidia and Clostridia representing pioneer-colonizing bacteria of the two major bacterial phyla present in the competitive exclusion product. The defined formulation, containing both groups of bacteria, were shown, dependent on age, to improve villus height (jejunum: 1.14 to 1.46-fold; ileum: 1.17-fold), goblet cell numbers (ileum 1.32 to 2.51-fold), and feed efficiency (1.18-fold, day 1) while decreasing Lactobacillus ileal abundance by one-third to half in birds at 16 and 42 days of age, respectively; compared to the phosphate buffered saline treatment group. Therefore, specific probiotic formulations containing pioneer colonizing species can provide benefits in intestinal development, feed efficiency and body weight gain.

Comparison of DNA extraction methods for analysis of turkey cecal microbiota

AIM

As a prelude to long-term studies to characterize the microbiota of the turkey ceca, 14 DNA isolation protocols were evaluated for their ability to reproducibly characterize microbial diversity.

METHODS AND RESULTS

Eight commercially available DNA extraction kits were assessed. DNA quantity and quality were assessed and competitive PCR was used to quantify the 16S bacterial rRNA genes. The Invitrogen Easy-DNA Kit extraction method for large samples yielded over eight times more DNA than any other method (3144 +/- 873 microg g(-1) of sample, P < 0.05). Bacterial and fungal species richness was estimated by Automated Ribosomal Intergenic Spacer Analysis. The Invitrogen Easy-DNA Kit generated the greatest bacterial species richness (46 +/- 7 peaks) while Bio-Rad Aquapure yielded the highest fungal species richness (71 +/- 9.5 peaks).

CONCLUSION

Cluster analysis indicated different DNA extraction methods generated different microbial community compositions using the same cecal matrix from a single donor bird.

SIGNIFICANCE AND IMPACT OF THE STUDY

Optimized DNA extraction protocols Invitrogen Easy-DNA Kit extraction method for large samples and Bio-Rad Aquapure outperform other methods for extraction of DNA from poultry fecal samples, although these methods do not necessarily recover all available DNA. They will be used in future studies to monitor the dynamics of microbial communities of the avian ceca.

Isolation and identification of mixed linkedβ -glucan degrading bacteria in the intestine of broiler chickens and partial characterization of respective 1,3-1,4-β -glucanase activities

Media with 1,3-1,4-beta -glucans as selective markers were used for isolation of non-starch-polysaccharide (NSP) degrading bacteria from the intestinal tract of broiler chicken. Formerly unknown 1,3-1,4-beta endoglucanase activities in various bacterial species were identified in this study. E. faecium , Streptococcus , Bacteroides and Clostridium strains seem to be responsible for degradation of mixed linked beta -glucans in the small intestine and in the hind gut of chickens. Strict anaerobic bacteria (Bacteroides ovatus , B. uniformis , presumably B. capillosus and Clostridium perfringens ) as well as an unidentified bacterium with 98% 16S rDNA homology to an uncultered chicken cecum bacterium were isolated. Additionally, Streptococcus bovis with 1,3-1,4-beta -endoglucanase activity was also detected. Different 1,3-1,4-beta -endoglucanase activity profiles were observed in SDS/PAGE zymograms.