Characterization of the Pig Gut Microbiome and Antibiotic Resistome in Industrialized Feedlots in China

Wang, Chunlai; Li, Peng; Yan, Qiulong; Chen, Liping; Li, Tiantian; Zhang, Wanjiang; Li, He; Chen, Changming; Han, Xiaoying; Zhang, Siyi; Xu, Meijuan; Li, Bo; Zhang, Xiaoxuan; Ni, Hong-Bo; Ma, Yufang; Dong, Bo; Li, Shenghui; Liu, Siguo

doi:10.1128/msystems.00206-19

Cited by 48 publications

(29 citation statements)

References 36 publications

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“…The resulting distance matrix was used to perform a principal coordinate analysis (PCoA). heatmaps were generated using Calour version 2018.10.1 with default parameters 21 . Differentially expressed ASVs between positive and negative results were detected using one sample per subject, with a non-parametric rank mean test as implemented in Calour 21 with dsFDR multiple hypothesis correction 13 (FDR < 0.25).…”

Section: Methodsmentioning

confidence: 99%

“…heatmaps were generated using Calour version 2018.10.1 with default parameters 21 . Differentially expressed ASVs between positive and negative results were detected using one sample per subject, with a non-parametric rank mean test as implemented in Calour 21 with dsFDR multiple hypothesis correction 13 (FDR < 0.25). As a second approach to test for ASVs significantly associated with COVID-19 positive test, we used MaAsLin2 (Multivariate Association with Linear Models) R package version 1.0.0.…”

Section: Methodsmentioning

confidence: 99%

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SARS-CoV-2 does not have a strong effect on the nasopharyngeal microbial composition

Braun

Halevi

Hadar

et al. 2021

Sci Rep

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The coronavirus disease 2019 (COVID-19) has rapidly spread around the world, impacting the lives of many individuals. Growing evidence suggests that the nasopharyngeal and respiratory tract microbiome are influenced by various health and disease conditions, including the presence and the severity of different viral disease. To evaluate the potential interactions between Severe Acute Respiratory Syndrome Corona 2 (SARS-CoV-2) and the nasopharyngeal microbiome. Microbial composition of nasopharyngeal swab samples submitted to the clinical microbiology lab for suspected SARS-CoV-2 infections was assessed using 16S amplicon sequencing. The study included a total of 55 nasopharyngeal samples from 33 subjects, with longitudinal sampling available for 12 out of the 33 subjects. 21 of the 33 subjects had at least one positive COVID-19 PCR results as determined by the clinical microbiology lab. Inter-personal variation was the strongest factor explaining > 75% of the microbial variation, irrespective of the SARS-CoV-2 status. No significant effect of SARS-CoV-2 on the nasopharyngeal microbial community was observed using multiple analysis methods. These results indicate that unlike some other viruses, for which an effect on the microbial composition was noted, SARS-CoV-2 does not have a strong effect on the nasopharynx microbial habitants.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

SARS-CoV-2 does not have a strong effect on the nasopharyngeal microbial composition

Braun

Halevi

Hadar

et al. 2021

Sci Rep

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“…Associations between animal genetics, age or diet with microbiome composition and, therefore, with its resistome, have also been uncovered [16]. So far, pig resistome studies have been performed in industrialized intensive swine herds [18,19]. The traditional extensive system, mainly associated with the Iberian pig breed (Sus scrofa domesticus) in Spain, is defined by eco-friendly and sustainable husbandry practices, including the constrained use of antimicrobials [20], which has been maintained for decades.…”

Section: Introductionmentioning

confidence: 99%

Antimicrobial use and production system shape the fecal, environmental, and slurry resistomes of pig farms

et al. 2020

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Background The global threat of antimicrobial resistance (AMR) is a One Health problem impacted by antimicrobial use (AMU) for human and livestock applications. Extensive Iberian swine production is based on a more sustainable and eco-friendly management system, providing an excellent opportunity to evaluate how sustained differences in AMU impact the resistome, not only in the animals but also on the farm environment. Here, we evaluate the resistome footprint of an extensive pig farming system, maintained for decades, as compared to that of industrialized intensive pig farming by analyzing 105 fecal, environmental and slurry metagenomes from 38 farms. Results Our results evidence a significantly higher abundance of antimicrobial resistance genes (ARGs) on intensive farms and a link between AMU and AMR to certain antimicrobial classes. We observed differences in the resistome across sample types, with a higher richness and dispersion of ARGs within environmental samples than on those from feces or slurry. Indeed, a deeper analysis revealed that differences among the three sample types were defined by taxa-ARGs associations. Interestingly, mobilome analyses revealed that the observed AMR differences between intensive and extensive farms could be linked to differences in the abundance of mobile genetic elements (MGEs). Thus, while there were no differences in the abundance of chromosomal-associated ARGs between intensive and extensive herds, a significantly higher abundance of integrons in the environment and plasmids, regardless of the sample type, was detected on intensive farms. Conclusions Overall, this study shows how AMU, production system, and sample type influence, mainly through MGEs, the profile and dispersion of ARGs in pig production.

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“…Pediatric patients with end-stage liver diseases, such as due to biliary atresia or other cholestatic diseases, often have an altered microbial composition (Guo et al 2018 ; Wang et al 2020a ; Wang et al 2019 ). Such alteration in the microbiome would possibly lead to gut barrier disruption, to bacterial translocation and to triggering of the host’s immune and metabolic responses in the liver (De Minicis et al 2014 ; Fouts et al 2012 ).…”

Section: Introductionmentioning

confidence: 99%

“…For instance, infants with biliary atresia have lower microbial diversity and higher intestinal permeability than healthy infants (Wang et al 2020a ). In particular, patients showed a decrease in the relative abundance of genera which are considered beneficial, i.e., Bifidobacterium and Faecalibacterium (Guo et al 2018 ; Wang et al 2019 ), as well as an imbalance in the components of bile acids (Wang et al 2019 ). The surgical procedure of LT may temporarily increase the intestinal permeability and allow some pathogenic bacteria to enter the portal or systemic circulation and initiate the immune response (Okumura and Takeda 2018 ).…”

Section: Introductionmentioning

confidence: 99%

The role of the gut microbiome in graft fibrosis after pediatric liver transplantation

Qin

Verkade

2020

Hum Genet

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Liver transplantation (LT) is a life-saving option for children with end-stage liver disease. However, about 50% of patients develop graft fibrosis in 1 year after LT, with normal liver function. Graft fibrosis may progress to cirrhosis, resulting in graft dysfunction and ultimately the need for re-transplantation. Previous studies have identified various risk factors for the post-LT fibrogenesis, however, to date, neither of the factors seems to fully explain the cause of graft fibrosis. Recently, evidence has accumulated on the important role of the gut microbiome in outcomes after solid organ transplantation. As an altered microbiome is present in pediatric patients with end-stage liver diseases, we hypothesize that the persisting alterations in microbial composition or function contribute to the development of graft fibrosis, for example by bacteria translocation due to increased intestinal permeability, imbalanced bile acids metabolism, and/or decreased production of short-chain fatty acids (SCFAs). Subsequently, an immune response can be activated in the graft, together with the stimulation of fibrogenesis. Here we review current knowledge about the potential mechanisms by which alterations in microbial composition or function may lead to graft fibrosis in pediatric LT and we provide prospective views on the efficacy of gut microbiome manipulation as a therapeutic target to alleviate the graft fibrosis and to improve long-term survival after LT.

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Characterization of the Pig Gut Microbiome and Antibiotic Resistome in Industrialized Feedlots in China

Cited by 48 publications

References 36 publications

SARS-CoV-2 does not have a strong effect on the nasopharyngeal microbial composition

SARS-CoV-2 does not have a strong effect on the nasopharyngeal microbial composition

Antimicrobial use and production system shape the fecal, environmental, and slurry resistomes of pig farms

The role of the gut microbiome in graft fibrosis after pediatric liver transplantation

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