Whole metagenome sequencing of cecum microbiomes in Ethiopian indigenous chickens from two different altitudes reveals antibiotic resistance genes

Kumar, Himansu; Park, Woncheoul; Lim, Dajeong; Srikanth, Krishnamoorthy; Kim, Junmo; Jia, Xin-Zheng; Han, Jin‐Hee; Hanotte, Olivier; Oyola, Samuel O.

doi:10.1016/j.ygeno.2019.11.011

Cited by 25 publications

(26 citation statements)

References 75 publications

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“…AMR patterns observed in chickens and pigs dominated with above mentioned classes of antimicrobials were consistent with results of the EFFORT project [20]. These results were also compliant with data from other metagenomics studies on chicken and pig microbiomes that indicated specified antimicrobial classes as the frequently abundant [20,[27][28][29][30][31].…”

Section: Plos Onesupporting

confidence: 89%

A metagenomic glimpse into the gut of wild and domestic animals: Quantification of antimicrobial resistance and more

et al. 2020

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Antimicrobial resistance (AMR) in bacteria is a complex subject, why one need to look at this phenomenon from a wider and holistic perspective. The extensive use of the same antimicrobial classes in human and veterinary medicine as well as horticulture is one of the main drivers for the AMR selection. Here, we applied shotgun metagenomics to investigate the AMR epidemiology in several animal species including farm animals, which are often exposed to antimicrobial treatment opposed to an unique set of wild animals that seems not to be subjected to antimicrobial pressure. The comparison of the domestic and wild animals allowed to investigate the possible anthropogenic impact on AMR spread. Inclusion of animals with different feeding behaviors (carnivores, omnivores) enabled to further assess which AMR genes that thrives within the food chain. We tested fecal samples not only of intensively produced chickens, turkeys, and pigs, but also of wild animals such as wild boars, red foxes, and rodents. A multi-directional approach mapping obtained sequences to several databases provided insight into the occurrence of the different AMR genes. The method applied enabled also analysis of other factors that may influence AMR of intestinal microbiome such as diet. Our findings confirmed higher levels of AMR in farm animals than in wildlife. The results also revealed the potential of wildlife in the AMR dissemination. Particularly in red foxes, we found evidence of several AMR genes conferring resistance to critically important antimicrobials like quinolones and cephalosporins. In contrast, the lowest abundance of AMR was observed in rodents originating from natural environment with presumed limited exposure to antimicrobials. Shotgun metagenomics enabled us to demonstrate that discrepancies between AMR profiles found in the intestinal microbiome of various animals probably resulted from the different antimicrobial exposure, habitats, and behavior of the tested animal species.

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Section: Plos Onesupporting

confidence: 89%

A metagenomic glimpse into the gut of wild and domestic animals: Quantification of antimicrobial resistance and more

et al. 2020

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“…The KEGG pathways, such as membrane transport, carbohydrate, and amino acid metabolism were significantly enriched in across the sample. There is evidence that the microbes present in the sample such as fecal matter, cecum content, sludge, slurry, and GIT microbes are greatly involved in multiple pathways of the host organism [ 52 , 53 ]. Cai, Mingwei, et al [ 54 ] reported that metagenomic sequences of municipal sludge are involved in carbohydrate and protein metabolism during wastewater biogas-producing systems.…”

Section: Discussionmentioning

confidence: 99%

Compositional and Functional Characteristics of Swine Slurry Microbes through 16S rRNA Metagenomic Sequencing Approach

Kumar

Jang

Kim³

et al. 2020

Animals

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Traditionally slurry is used as source of nitrogen, phosphorous, and potassium in bio fertilizers to improve crop production. However, poorly managed slurry causes a hazardous effect to the environment by producing greenhouse gases, causing the eutrophication of water bodies, and polluting the groundwater. It has been largely reported that the microbial presence in slurry causing a diverse effect on its storage and disposal system. However, the diversity of bacterial populations in pig slurries remains largely unexplored. Here we report the bacterial diversity present in the slurry from slurry pits, and the effect of storage time on bacterial population. We collected 42 samples from three different pig slurry pits, as three replicates from each one until the 14th week. We used the 16S rRNA, Quantitative Insights Into Microbial Ecology (QIIME) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) protocols for the metagenomic downstream analysis. Taxonomic annotation using the Greengenes metagenomic database indicated that on an average 76.2% Firmicutes, 14.4% Bacteroidetes, 4.9% Proteobacteria, etc. microbial populations were present. Comparative microbial analysis showed that the population of Firmicutes decreased from the first to the 14th week, whereas the population of Bacteroidetes increased from the first to the 14th week. Through principal coordinate analysis (PCoA), (linear discriminant analysis effect size (LEfSe), and Pearson’s correlation analysis, we found microbial biomarkers according to the storage time point. All bacterial populations were well clustered according to the early, middle, and last weeks of storage. LEfSe showed that Actinobacteria, Lachnospiraceae, Ruminococcaceae, and Bacteroidia are dominantly present in first, seventh, ninth, and 14th week, respectively. Lachnospiraceae and Ruminococcaceae are ubiquitous gastrointestinal non-pathogenic bacteria. KEGG pathways, such as membrane transport, carbohydrate and amino acid metabolism, genetic replication and repair, were significant among all samples. Such a KEGG pathway may indicate the association between the host organism’s metabolic activity and the microbes present in the gastro intestinal tract (GIT).

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“…Goodrich et al have found evidence that the host genome in uence on the composition of microbiome in humans [31]. KEGG, eggNOG, and CAZy are the most frequently used databases to study functional properties of the microbial population [32]. Generally, three level classi cation approaches against all three databases have been used for functional pro ling.…”

Section: Discussionmentioning

confidence: 99%

Metagenomic Analysis Reveals the Microbiome and Antibiotic Resistance Genes in Guangdong Yellow-feathered Indigenous Chicken

Guo

Huang

et al. 2021

Preprint

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Background: The yellow-feathered broiler has great nutritional value and a huge industrial scale as a traditional broiler in China. The intestinal microbes have been shown to correlate with poult performance, and serve as an essential reservoir of antibiotic resistance gene (ARG), and antimicrobial resistance is a major public health concern. We investigated the functional characteristics of the six different breeds of yellow-feathered broiler’s (Huiyang Bearded chicken, Xinghua chicken, Huaixiang chicken, Zhongshan Shalan chicken, Qingyuan Patridge chicken, Yangshan chicken) gut microbiome through metagenomics sequencing, to investigate the functions and ARGs in the intestinal microbial communities.Results: The results found that microbial populations of yellow-feathered broilers were mainly dominated by Bacteroidetes and Firmicutes at phylum level and Bacteroides at genus level, and the qingyuanPatridge chicken had a significantly higher level of Prevotella genus than the other five breeds of chicken. PCoA analysis indicated significant differences in the structures of the microbial communities and ARGs based on binary-jaccard distance (analysis of similarities ANOSIM R=0.747, P=0.001 and R=0.525, P=0.001, respectively) among the six breeds of chicken. Analyses using KEGG, eggNOG, and CAZy databases indicated that the pathways of metabolism, genetic information processing and glucoside hydrolase were significantly enriched in the yellow-feathered broilers. We also identified 989 ARGs and mainly composed of ARGs that confer tetracycline, multidrug and aminoglycoside represented more than 80% of the fecal resistomes, and then the tet(Q) gene is the most abundant in yellow-feathered chickens. In addition, we found a greater abundance of resistance genes detected in the Xinghua chicken.Conclusions: Our study presents a metagenomic resource of indigenous chicken cecum microbiomes from six breeds of yellow-feathered broiler. It demonstrates the measure of metagenomic method for annotating microbial taxonomy and functional abundance. With the help of metagenomic, we have shown the difference in the gut microbial community structure of indigenous broiler breeds, and their potential to ARGs and antibiotic resistance. Xinghua chicken has great resistance to antibiotics. Overall, the current data provides a significant improvement to our knowledge and study of the gut microbiome and antibiotic resistance, especially in the indigenous yellow-feathered Chinese chicken.

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Whole metagenome sequencing of cecum microbiomes in Ethiopian indigenous chickens from two different altitudes reveals antibiotic resistance genes

Cited by 25 publications

References 75 publications

A metagenomic glimpse into the gut of wild and domestic animals: Quantification of antimicrobial resistance and more

A metagenomic glimpse into the gut of wild and domestic animals: Quantification of antimicrobial resistance and more

Compositional and Functional Characteristics of Swine Slurry Microbes through 16S rRNA Metagenomic Sequencing Approach

Metagenomic Analysis Reveals the Microbiome and Antibiotic Resistance Genes in Guangdong Yellow-feathered Indigenous Chicken

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