Bacterial meta-analysis of chicken cecal microbiota

Abstract

Poultry production is an industry that generates 90,000 metric tons of chicken meat worldwide. Thus, optimizing chicken growth and sustainable production is of great importance. A central factor determining not only production parameters, but also stability of the immune system and chicken health, is the diversity and variability of the microbiota present throughout the gastrointestinal tract. To date, several studies have investigated the relationship between bacterial communities and the gut microbiome, with limited data to compare. This study aims to create a bacterial meta-analysis based on studies using amplicon sequencing with Illumina sequencing technologies in order to build a baseline for comparison in future analyses of the cecal bacterial composition in chicken. A systematic literature review was performed (SYRF ID: e84f0468-e418-4eec-9da4-b517f1b4809d. Full project URL: https://app.syrf.org.uk/projects/e84f0468-e418-4eec-9da4-b517f1b4809d/detail). From all the available and analyzed manuscripts only nine contained full raw-sequence data available and the corresponding metadata. A total of 324 samples, comprising three different regions within the 16S rRNA gene, were analyzed. Due to the heterogeneity of the data, each region was analyzed independently and an effort for a joint analysis was performed as well. Taxonomic profiling revealed 11 phyla, with Firmicutes as the most prevalent phylum, followed by Bacteroidetes and Proteobacteria. At genus level, 109 genera were found. Shannon metric for alpha diversity showed that factors like type of chickens (Commercial or experimental) and 16S rRNA gene subregion have negligible effect on diversity. Despite the large number of parameters that were taken into account, the identification of common bacteria showed five genera to be common for all sets in at least 50% of the samples. These genera are highly associated to cellulose degradation and short chain fatty acids synthesis. In general, it was possible to identify some commonalities in the bacterial cecal microbial community despite the extensive variability and factors differing from one study to another.

Purified Plant-Derived Phenolic Acids Inhibit Salmonella Typhimurium without Alteration of Microbiota in a Simulated Chicken Cecum Condition

“…Results from the 16S-rRNA gene sequencing and subsequent microbiome analysis revealed that Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria were the most abundant phyla, which is consistent with the pre-established literature regarding the composition of chicken microbiomes in the cecum [42,43]. These phyla persisted as the most abundant across timepoints and treatments, though they did experience changes in the percentages of the abundance ratios within each group that were time and treatment dependent.…”

Protected Organic Acid and Essential Oils for Broilers Raised Under Field Conditions: Intestinal Health Biomarkers and Cecal Microbiota

“…The samples of the present study were collected from 25- to 28-days old birds, which falls within the former range, and shows beneficial effects of the P(OA + EO) supplementation for antibiotic-free chickens. According to a bacterial meta-analysis of the cecal microbiota of chickens, Coprobacillus , even though in a small abundance, has been found in most of the analyzed studies ( Chica Cardenas et al, 2021 ).…”

A Probabilistic Structural Equation Model to Evaluate Links between Gut Microbiota and Body Weights of Chicken Fed or Not Fed Insect Larvae

“…Although bacterial relative abundances are known to vary across studies [48], Firmicutes was found to be the most abundant phylum and Lactobacillus the most abundant genus, as was reported in a recent meta-analysis [49], although in different percentages. The composition of fecal microbiota samples obtained via cloacal swabs or directly from the caecum were different, as observed by others [50][51][52].…”