**3. Results**

The diversity of bacterial populations detected in distinct intestinal segments was highlighted by data acquired by molecular detection and bioinformatics analysis. The 16S rDNA study produced a large amount of data that is beyond the scope of this article. As a result, the current study's findings have been confined to the most quantitatively significant Classes/Orders of bacteria.

#### **3.1 Sequencing overview**

A total of 128 samples were obtained from a combination of four intestinal segments—(duodenum, jejunum, ileum, and caecum) and four age periods—(day 5, day 15, day 25, and day 35) with n = 8 per group and subsequently sequenced to generate V3-V4 of the 16S rDNA gene profiles A total of 1179,68 sequences were obtained with the number of sequences ranging from 58,498 to 112,785 and clustered into 14 to 133 OTUs for each sample, resulting in a total of 253 OTUs for all samples at the 97% sequence similarity value. The microbial complexity and microbial community composition and abundance of water are summarized in their respective sections below.

#### *3.1.1 The microbial complexity*

The alpha-diversity indices were used to evaluate the microbial complexity in the duodenum, jejunum, ileum, and cecum (ACE index, Chao1 index, Simpson index, and Shannon index) **Table 2** The Chao1 was used to quantify species diversity, while Simpson's and Shannon's indexes were used to evaluate species richness. When comparing the means of the indices, there was a substantial difference across intestinal regions throughout age periods.

#### **3.2 Microbial composition of the duodenum**

Bacteria classified according to their respective Class and Order, found in the duodenum of broiler chickens at different ages, are presented in **Table 3**. Sixteen bacterial microbiota at the Order level were found in the duodenum. Of the 30,173 reads, Lactobacillales were the most abundant Order, from the Class Bacilli, at 78.73% of the total number of sequences. Clostridiales, a representative Order


**Table 2.**

*The average alpha-diversity indices (ACE, Chao1, Simpson, and Shannon indices) of the data distribution.*


*These results emanate from our own experiment.*

#### **Table 3.**

*The abundance of bacterial 16S rDNA sequences (n =* **30,173***) identified from the* **duodenum** *microflora of cobb 500 broiler chicken.*

from the Class Clostridia, was the second most common Order accounting for 17.32% of the total number of sequences. At the Class level, Actinobacteria, and Chloroplast accounted for 0.93% and 1.15%, of the total number of sequences, respectively, at the Class level. Lactobacillales were the most dominant group across all age groups, accounting for 93.37% at day 5, 98.80% at day 15, and 89.77% at day 25 to 5.77% at day 35 of the sequences. Clostridiales were the second most

*Microbial Diversity and Community Dynamics in the Intestines of Broiler Chicken Raised… DOI: http://dx.doi.org/10.5772/intechopen.103815*

abundant, sequences fluctuated from 1.78% at day 5, 0.06% at day 15, 4.61% at day25, and 88.71% at day 35. Comparatively, Coriobacteriales, (member from Class Coriobacteriia), Bacteroidales, (Class, Bacteroidia), Bacillales, (member from Class Bacilli), Erysipelotrichales (Class, Erysipelotrichi), Rhizobiales (Class, Alphaproteobacteria), Rhodocyclales (Class, Betaproteobacteria), Enterobacteriales (Class, Gammaproteobacteria), and RF39 (member from Class Mollicutes) grouprelated sequences were detected at smaller percentages through all age periods.

#### **3.3 Microbial composition of the jejunum**

Bacteria classified according to their respective Class and Order, found in the jejunum of broiler chickens at different ages, are presented in **Table 4**. Sixteen bacterial microbiota at the Order level were found in the jejunum. Of the 28,646 reads, Lactobacillales were the most abundant Order, from the Class Bacilli, at 75.95% of the total sequences. Clostridiales, a representative Order from the Class Clostridia, was the most second Order accounted for 11.21% of the total sequences. At the Class level, only a few 4.46% Actinobacteria-related sequences were detected; these were related to Actinomycetales and Bifidobacteriales. Chloroplast, Erysipelotrichi, and Gammaproteobacteria at the Class level represented a small percentage of 2.32%, 1.55%, and 4.06%, respectively, of the total sequences. Across different age periods,


#### **Table 4.**

*The abundance of bacterial 16S rDNA sequences (n =* **28,646***) identified from the* **jejunum** *microflora of cobb 500 broiler chicken.*

#### *Animal Husbandry*

Lactobacillales were the most dominant group, representing 93.09% at day 5, 86.01% at day15, 91.45% at day 25 to 23.46% at day 35 of the sequences. Clostridiales were the second most abundant, sequences fluctuated from 4.33% at day 5, 4.02% at day 15, 0.86% at day 25, and 40.07% at day 35. Relatively, Bifidobacteriales, (Class, Actinobacteria), Streptophyta (Class, Chloroplast), Bacillales (Class, Bacilli), Erysipelotrichales (Class, Erysipelotrichia), Rhizobiales (member from Class, Alphaproteobacteria), Rhodocylales (Class, Betaproteobacteria) and Enterobacteriales (member from Class, Gammaproteobacteria) group-related sequences were detected at lower levels across age periods.
