Metagenomics analysis of the morphological aspects and bacterial composition of broiler feces.

In this descriptive study, we used metagenomics to analyze the relationship between the morphological aspects of chicken feces and its respective bacterial compositions. The microbiota composition was determined by sequencing the V4 region of the 16S rRNA genes collected from fresh broiler feces at 19 d old. In total, 48 samples were collected and divided into 8 groups of 6 samples each. The morphological changes studied were feed passage (FP) and reddish mucus (RM). Each was classified into 3 levels of intensity: 1 (slight), 2 (moderate), or 3 (intense). Thus, the 8 groups studied were feed passage (FP-1; FP-2; FP-3), reddish mucus (RM-1; RM-2; RM-3), normal ileal feces (NIF), and cecal discharge (CD). The alpha diversity (Shannon's index) revealed that the CD group showed greater diversity, and was significantly different from FP-2, FP-3, and RM-1. The beta diversity showed that the CD group samples were more homogeneous than the ileal feces groups. The relative abundance analysis revealed that Firmicutes and Proteobacteria were the most abundant phyla in the ileal feces groups. In CD, Firmicutes and Bacteroidetes were the most abundant. The relative abundance at the genus level revealed 136 different bacterial genera. In the ileal feces groups, the two most abundant genera were Lactobacillus and Escherichia/Shigella, except in the FP-1 and RM-2 groups, which had the opposite order. Unlike the others, the CD group had a higher abundance of Bacteroides and Faecalibacterium. When comparing the NIF group with the others, significant changes were found in the fecal microbiota, with nine genera for the FP groups, 19 for the RM groups, and 61 when compared to CD. The results of the present study suggest that evaluation of fecal morphology is a fundamental task that makes it possible to act quickly and assertively, as the morphological aspects of the feces may be related to the composition and structure of fecal microbiota.

Proper Immune Response Depends on Early Exposure to Gut Microbiota in Broiler Chicks.

The successional changes in the early intestinal microbiota occur concomitantly with the development, expansion, and education of the mucosal immune system. Although great attention of researchers has been focused on understanding the linkage between microbiota and immune functions, many essential details of the symbiotic relationship between the intestinal pioneer microbiota and the avian immune system remain to be discovered. This study was conducted to understand the impact of different early life intestinal colonizers on innate and adaptive immune processes in chicks and further identify immune-associated proteins expressed in the intestinal tissue. To accomplish it, we performed an in ovo application of two apathogenic Enterobacteriaceae isolates and lactic acid bacteria (L) to determine their influences on the intestinal proteome profile of broilers at the day of hatch (DOH) and at 10 days old. The results indicated that there were predicted biological functions of L-treated chicks associated with the activation and balanced function of the innate and adaptive immune systems. At the same time, the Enterobacteriaceae-exposed birds presented dysregulated immunological mechanisms or downregulated processes related to immune development. Those findings suggested that a proper immune function was dependent on specific gut microbiota exposure, in which the prenatal probiotic application may have favored the fitting programming of immune functions in chicks.

Cecal microbiome composition and metabolic function in probiotic treated broilers.

Probiotics have become increasingly popular in the poultry industry as a promising nutritional intervention to promote the modulation of intestinal microbial communities and their metabolic activities as a means of improving health and performance. This study aimed to determine the influence of different probiotic formulations on the taxonomic and metabolic profiling of cecal microbial communities, as well as to define associations between cecal microbiota and growth parameters in 21 and 42-day-old broilers. Probiotics investigated included a synbiotic (SYNBIO), a yeast-based probiotic (YEAST), and three single-strain formulations of spore-forming Bacillus amyloliquefaciens (SINGLE1), B. subtilis (SINGLE2) and B. licheniformis (SINGLE3). Dietary inclusion of SYNBIO, YEAST, SINGLE2, and SINGLE3 into the diets supported a significant stimulation of BW and BWG by 7 days of age. Besides, SYNBIO reduced the overall mortality rate by 42d (p<0.05). No significant variation was observed among different probiotic-based formulations for cecal microbiota composition. However, there was a treatment-specific effect on the metabolic profiles, with a particular beneficial metabolic adaptation by the microbiota when supplemented by SYNBIO and SINGLE2. Furthermore, the population of Lactobacillales was identified to be strongly associated with lower Enterobacteriales colonization, higher BW means, and lower mortality rate of growing broilers. Overall, the results emphasize that probiotic supplementation may enhance the microbial energy metabolism in the ceca of young broilers.

Comparative effectiveness of probiotic-based formulations on cecal microbiota modulation in broilers.

The potential of probiotics to manipulate the intestinal microbial ecosystem toward commensal bacteria growth offers great opportunity for enhancing health and performance in poultry. This study aimed to evaluate the efficacy of five probiotic-based formulations in modulating cecal microbiota in broilers at 21 and 42 days of age. Probiotics investigated included a synbiotic (SYNBIO), a yeast (YEAST), and three single-strain formulations of Bacillus amyloliquefaciens (SINGLE1), B. subtilis (SINGLE2) and B. licheniformis (SINGLE3). Alpha-diversity analyses showed that cecal microbiota of SINGLE1, SINGLE2, and YEAST had low diversity compared to the control diet with no feed additive (CON) at 21d. At the same age, weighted Unifrac distance measure showed significant differences between samples from SYNBIO and CON (P = 0.02). However, by analyzing principal coordinates analysis (PCoA) with unweighted Unifrac, there was no evidence of clustering between CON and probiotic treatments. By 42d, there were no differences in alpha or beta-diversity in the microbiota of probiotic treatments compared to CON. Similarly, taxonomic microbial profiling did not show major changes in cecal microbial taxa. In conclusion, not all probiotic-based formulations tested had a core benefit on the modulation of microbiota. However, based on the quantitative beta diversity results, SYNBIO greatly influenced the cecal microbial community structure attributable to transient variations in relative taxon abundance.

Intestinal Pioneer Colonizers as Drivers of Ileal Microbial Composition and Diversity of Broiler Chickens.

Given that recent advances in metagenomics have highlighted the importance of intestinal microbes for poultry health, there has been a corresponding search for early manipulation strategies of intestinal microbiota in order to advance immune system development and optimize functional properties of growth. In this study, we used the in ovo technique as an experimental model to address how early bacterial intestinal colonization could affect the development and establishment of the mature ileal microbiota. Inoculations containing one of the following: 0.2 mL of 0.9% sterile saline (S), approximately 102 cells of Citrobacter freundii (CF), Citrobacter species (C2) or lactic acid bacteria mixture (L) were administered via in ovo into the amnion. Results showed that Enterobacteriaceae abundance was negatively correlated with aging, although its high population at day of hatch affected the microbiota composition, delaying mature microbiota establishment. L treatment increased colonization of butyrate-producing bacteria by 3 and 10 days, and segmented filamentous bacteria in the lower ileum by 10 days. On the other hand, L-probiotic decreased the population of Enterococcaceae. In addition, L and C2 microbial communities were less diverse at 10 than 3 days of age in the upper ileum. Importantly, these findings provide a valuable resource for a potential study model for interactions between microbial colonization and associated immune responses. In conclusion, our analysis demonstrates that intestinal pioneer colonizers play a critical role in driving the course of microbial community composition and diversity over time, in which early life exposure to L-based probiotic supported selection alongside greater colonization of symbiotic populations in the ileum of young broilers.