Quantitative Genetic Background of the Host Influences Gut Microbiomes in Chickens

Zhao, Lele; Wang, Gang; Siegel, P. B.; He, Chuan; Wang, Hezhong; Zhao, Wenjing; Zhai, Zhengxiao; Tian, Fengwei; Zhao, Jianxin; Zhang, Hao; Sun, Zikui; Chen, Wei; Zhang, Yan; Meng, He

doi:10.1038/srep01163

Cited by 286 publications

(249 citation statements)

References 30 publications

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“…The present study and previous studies 55,67 noticed that the development and dissemination of ARGs in feedlot environments could be influenced by production conditions such as feed, henhouse environment, chicken breed and age in the broiler feedlots as those factors can affect the evolution of the intestinal microbiome. The abundance and distribution of bacteria and antibiotic resistance may vary according to different rearing systems.…”

Section: Dissemination Of Args In the Broiler Feedlotsmentioning

confidence: 98%

Dissemination of Antibiotic Resistance Genes in Representative Broiler Feedlots Environments: Identification of Indicator ARGs and Correlations with Environmental Variables

Liu

et al. 2014

Environ. Sci. Technol.

213

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Livestock operations are known to harbor elevated levels of antibiotic resistance genes (ARGs) that may pose a threat to public health. Broiler feedlots may represent an important source of ARGs in the environment. However, the prevalence and dissemination mechanisms of various types of ARGs in the environment of broiler feedlots have not previously been identified. We examined the occurrence, abundance and variation of ARGs conferring resistance to chloramphenicols, sulfonamides and tetracyclines in the environments of two representative types of broiler feedlots (free range and indoor) by quantitative PCR, and assessed their dissemination mechanisms. The results showed the prevalence of various types of ARGs in the environmental samples of the broiler feedlots including manure/litter, soil, sediment, and water samples, with the first report of five chloramphenicol resistance genes (cmlA, floR, fexA, cf r, and fexB) in broiler feedlots. Overall, chloramphenicol resistance genes and sulfonamides sul genes were more abundant than tetracyclines tet genes. The ARG abundances in the samples from indoor boiler feedlots were generally different to the free range feedlots, suggesting the importance of feeding operations in ARG dissemination. Pearson correlation analysis showed significant correlations between ARGs and mobile genetic element genes (int1 and int2), and between the different classes of ARGs themselves, revealing the roles of horizontal gene transfer and coselection for ARG dissemination in the environment. Further regression analysis revealed that fexA, sul1 and tetW could be reliable indicator genes to surrogate anthropogenic sources of ARGs in boiler feedlots (correlations of fexA, sul1 and tetW to all ARGs: R = 0.95, 0.96 and 0.86, p < 0.01). Meanwhile, significant correlations were also identified between indicator ARGs and their corresponding antibiotics. In addition, some ARGs were significantly correlated with typical metals (e.g., Cu, Zn, and As with fexA, fexB, cf r, sul1, tetW, tetO, tetS: R = 0.52−0.71) and some environmental parameters (e.g., TOC, TN, TP, NH 3 −N with fexA, fexB, cf r, sul1, tetW, tetO, tetQ, tetS: R = 0.53−0.87) (p < 0.01). Further redundancy analysis demonstrated that the distribution and transportation of ARGs from the boiler feedlots to the receiving environments were correlated with environmental variables. The findings highlight the contribution of some chemicals such as antibiotics and metals to the development of ARGs in broiler feedlots environments; and the observed ARG dissemination mechanism in the broiler feedlots facilitates the development of effective mitigation measures.

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Section: Dissemination Of Args In the Broiler Feedlotsmentioning

confidence: 98%

Dissemination of Antibiotic Resistance Genes in Representative Broiler Feedlots Environments: Identification of Indicator ARGs and Correlations with Environmental Variables

Liu

et al. 2014

Environ. Sci. Technol.

213

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“…Microbial genome DNA was extracted from the duodenal, cecal and fecal samples using a QIAamp DNA stool mini kit (QIAGEN, cat#51504) 58 following the manufacturer's instructions. The V4 hypervariable region of the 16S rRNA genes was PCR amplified from the microbial genomic DNA using primers 515F -806R (515F: GTGCCAGCMGCCGCGGTAA, 806R: GGACTACHVGGGTWTCTAAT).…”

Section: Methodsmentioning

confidence: 99%

Gut metagenomic analysis reveals prominent roles of Lactobacillus and cecal microbiota in chicken feed efficiency

Yan

Sun

Yuan

et al. 2017

Sci Rep

195

179

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Interactions between the host and gut microbiota can affect gut metabolism. In this study, the individual performances of 252 hens were recorded to evaluate feed efficiency. Hens with contrasting feed efficiencies (14 birds per group) were selected to investigate their duodenal, cecal and fecal microbial composition by sequencing the 16S rRNA gene V4 region. The results showed that the microbial community in the cecum was quite different from those in the duodenum and feces. The highest biodiversity and all differentially abundant taxa between the different efficiency groups were observed in the cecal microbial community with false discovery rate (FDR) <0.05. Of these differentially abundant cecal microbes, Lactobacillus accounted for a greater proportion than the others. The abundances of Lactobacillus and Akkermansia were significantly higher while that of Faecalibacterium was lower (FDR < 0.05) in the better feed efficiency (BFE) group. Phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis revealed that the functions relating to glycometabolism and amino acid metabolism were enriched in the cecal microbiota of the BFE group. These results indicated the prominent role of cecal microbiota in the feed efficiency of chickens and suggested plausible uses of Lactobacillus to improve the feed efficiency of host.The gastrointestinal tract is the major site of food digestion and nutrient absorption. Cecum is the chief functional section in the distal intestine, and its importance in birds' metabolism has received increasing attention 1,2 . The cecum, which is full of microbial fermentations, plays important roles in preventing pathogen colonization, detoxifying harmful substances, recycling nitrogen and absorbing additional nutrients 3 . The digestibility and the ability to metabolize crude fiber or other nutrients are lower in birds with a cecectomy than in normal birds 4 . In addition, significant absorption of glucose was observed in the cecum 5 , and a higher ability to actively absorb sugars at low concentrations was found in the cecum compared with the jejunum 6 . Located at the beginning of the intestine, the duodenum is crucial for feed digestion and absorption; it has a lower pH than the hindgut and is the region that absorbs most glucose 7 and other nutrients within the small intestine 8,9 . Although the cecum and the duodenum themselves are important, interactions between the gut and commensal microbes may exert a significant influence on the function of the intestine. Previous studies showed that the digestion of uric acid, cellulose, starch and other resistant carbohydrates in the cecum was associated with the cecal microbial members 3,10,11 . In a recent study, numerous oligosaccharide-and polysaccharide-degrading enzyme-encoding genes and several pathways involved in the production of short-chain fatty acids (SCFAs) were observed in the cecal metagenome of the chicken 12 . The SCFAs were produced mainly by microbial fermentation in the hindgut and could be a...

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“…In this study, the V4 region of bacterial 16S rRNA gene was amplified from the total extracted DNA, because this region, which is commonly used in microbial community analysis, provides sufficient phylogenetic richness (Zhao et al 2013;Caporaso et al 2011). PCR amplification was performed using the Takara Ex-taq polymerase (Takara Bio, Shiga, Japan) and universal primers (forward: 5′-GGACTACHVGGGTWTCTAAT-3′, reverse: 5′-GTGCCAGCMGCCGCGGTAA-3′).…”

Section: Dna Extraction and Sequencingmentioning

confidence: 99%

0991 Relationship between the microbiota in different sections of the gastrointestinal tract, and the body weight of broiler chickens

Lee

Kong

2016

Journal of Animal Science

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In the poultry industry, many efforts have been undertaken to further improve the growth performance of broilers and identification and modulation of body weight (BW)-related bacteria could be one of the strategies to improve productivity. However, studies regarding the relationship between microbiota and BW are scarce. The objective of the present study was to investigate the relationship between microbiota and BW in different sections of the gastrointestinal tract (GIT). A total of twenty 18-day-old birds were selected based on the BW, and samples were collected from the three different sections of the GIT, which included the crop, ileum and cecum. Bacterial genomic DNA was extracted from the samples, and the V4 region of 16S rRNA gene were amplified. Amplicons were sequenced on Illumina MiSeq, and microbial communities were analyzed by using QIIME. In principal coordinate analysis, bacterial communities were clustered into three groups, based on the sections of GIT. Several BW-related bacterial groups were identified from linear regression analysis. At the genus level, Streptococcus from the ileum as well as Akkermansia in both ileum and cecum, were negatively related to BW, whereas Bifidobacterium in the ileum and Lactococcus in the cecum showed a positive correlation. The results from the present study showed that particular bacterial communities in the GIT were related to BW, and the study has broadened the understanding of the intestinal microbial ecosystem in broiler chickens.

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Quantitative Genetic Background of the Host Influences Gut Microbiomes in Chickens

Cited by 286 publications

References 30 publications

Dissemination of Antibiotic Resistance Genes in Representative Broiler Feedlots Environments: Identification of Indicator ARGs and Correlations with Environmental Variables

Dissemination of Antibiotic Resistance Genes in Representative Broiler Feedlots Environments: Identification of Indicator ARGs and Correlations with Environmental Variables

Gut metagenomic analysis reveals prominent roles of Lactobacillus and cecal microbiota in chicken feed efficiency

0991 Relationship between the microbiota in different sections of the gastrointestinal tract, and the body weight of broiler chickens

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