Comparative Metagenomic Analysis of Chicken Gut Microbial Community, Function, and Resistome to Evaluate Noninvasive and Cecal Sampling Resources

Abstract

When conducting metagenomic analysis on gut microbiomes, there is no general consensus concerning the mode of sampling: non-contact (feces), noninvasive (rectal swabs), or cecal. This study aimed to determine the feasibility and comparative merits and disadvantages of using fecal samples or rectal swabs as a proxy for the cecal microbiome. Using broiler as a model, gut microbiomes were obtained from cecal, cloacal, and fecal samples and were characterized according to an analysis of the microbial community, function, and resistome. Cecal samples had higher microbial diversity than feces, while the cecum and cloaca exhibited higher levels of microbial community structure similarity compared with fecal samples. Cecal microbiota possessed higher levels of DNA replicative viability than feces, while fecal microbiota were correlated with increased metabolic activity. When feces were excreted, the abundance of antibiotic resistance genes like tet and ErmG decreased, but some antibiotic genes became more prevalent, such as fexA, tetL, and vatE. Interestingly, Lactobacillus was a dominant bacterial genus in feces that led to differences in microbial community structure, metabolism, and resistome. In conclusion, fecal microbiota have limited potential as a proxy in chicken gut microbial community studies. Thus, feces should be used with caution for characterizing gut microbiomes by metagenomic analysis.

Interaction Between Cecal Metabolites and Liver Lipid Metabolism Pathways During Induced Molting in Laying Hens

“…They play a very important role in maintaining the relative stability of the poultry gastrointestinal tract and nutrient digestion and absorption ( Jiangrang, 2003 ; Ilina, 2016 ). The cecum is the most developed site of intestinal microorganisms in poultry ( Jianhua, 2010 ; Kang et al, 2021 ; Pedroso et al, 2021 ). However, studies have found that gut microbes form a mutualistic symbiosis with their hosts during a long process of coevolution.…”

Plant-Derived Polysaccharides Regulated Immune Status, Gut Health and Microbiota of Broilers: A Review

“…Through 12 phyla of bacteria, represented analysis by highquality 16S rRNA gene sequences of chicken bacteria, the predominant bacteria were Firmicutes (almost 70% of sequences) and Bacteroidetes (12.3% of sequences) phyla, with cell densities exceeding 10 11 per g of digesta (58,59). Within the phylum Firmicutes, Clostridium, Ruminococcus, Lactobacillus, Eubacterium, and Fecalibacterium are the domain bacteria (60), while genera Bacteroides, Prevotella, Parabacteroides, and Alistipes are the domain bacteria in phylum Bacteroidetes (58). However, the composition of the intestinal microbiota can be altered by dietary manipulations and pathological environment (61).…”

Role of diet-microbiota interactions in precision nutrition of the chicken: facts, gaps, and new concepts

“…However, as described by Sklan and colleagues (1978) , these communities are connected, able to sow microbes and influence the microbiota throughout in the gastrointestinal tract. However, the functional activities of the sections of the intestine are quite different ( Huang et al, 2018 ; Rychlik, 2020 ; Yuan et al, 2020 ; Kang et al, 2021 ). The microbial functions in the hindgut have been well-documented, but in the foregut, to date, these functions of the microbiota and their relationship with gut function have received scant attention in the research literature which limits the understanding of the interplay between the gut microbiome and cellular functions.…”

“…Existing investigations in poultry have afforded a basic understanding of the impact of diet and feed supplements on the composition and activity of the gut microbiota in the hindgut, but not in the foregut, with a few exceptions ( Wen et al, 2019 ; Kang et al, 2021 ; Schekkers et al, 2021 ). However, currently, a detailed translational approach in applying diet as a tool to improve bird performance and health remains limited.…”

“…New investigations should include the identification of specific microbiota signatures (specific species, genes or enterotypes [Kang et al, 2021] ) and their associated metabolic properties and will generate large and comprehensive data sets that will require the development and use of new computational tools and analytical technologies including big data, multiomics, and machine learning in which information on feed composition or feed additive components, microbiota signature(s), and the bird physiological responses can be used to predict the impact of each factor on any desired outcomes.…”