Dynamics of the fecal microbiome and antimicrobial resistome in commercial piglets during the weaning period

Abstract This study aimed to characterize the alteration of the fecal microbiome and antimicrobial resistance (AMR) determinants in 24 piglets at day 3 pre-weaning (D. − 3), weaning day (D.0), days 3 (D.3) and 8 post-weaning (D.8), using whole-genome shotgun sequencing. Distinct clusters of microbio...

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Autores principales:	Prapat Suriyaphol, Jimmy Ka Ho Chiu, Nathamon Yimpring, Paiboon Tunsagool, Wuttichai Mhuantong, Rungtip Chuanchuen, Irina Bessarab, Rohan B. H. Williams, Rick Twee-Hee Ong, Gunnaporn Suriyaphol
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/f0d2b3888b4c4246bab5e15e24dd8833
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spelling	oai:doaj.org-article:f0d2b3888b4c4246bab5e15e24dd88332021-12-02T17:19:15ZDynamics of the fecal microbiome and antimicrobial resistome in commercial piglets during the weaning period10.1038/s41598-021-97586-92045-2322https://doaj.org/article/f0d2b3888b4c4246bab5e15e24dd88332021-09-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-97586-9https://doaj.org/toc/2045-2322Abstract This study aimed to characterize the alteration of the fecal microbiome and antimicrobial resistance (AMR) determinants in 24 piglets at day 3 pre-weaning (D. − 3), weaning day (D.0), days 3 (D.3) and 8 post-weaning (D.8), using whole-genome shotgun sequencing. Distinct clusters of microbiomes and AMR determinants were observed at D.8 when Prevotella (20.9%) was the major genus, whereas at D. − 3–D.3, Alistipes (6.9–12.7%) and Bacteroides (5.2–8.5%) were the major genera. Lactobacillus and Escherichia were notably observed at D. − 3 (1.2%) and D. − 3–D.3 (0.2–0.4%), respectively. For AMR, a distinct cluster of AMR determinants was observed at D.8, mainly conferring resistance to macrolide–lincosamide–streptogramin (mefA), β-lactam (cfxA6 and aci1) and phenicol (rlmN). In contrast, at D. − 3–D.3, a high abundance of determinants with aminoglycoside (AMG) (sat, aac(6')-aph(2''), aadA and acrF), β-lactam (fus-1, cepA and mrdA), multidrug resistance (MDR) (gadW, mdtE, emrA, evgS, tolC and mdtB), phenicol (catB4 and cmlA4), and sulfonamide patterns (sul3) was observed. Canonical correlation analysis (CCA) plot associated Escherichia coli with aac(6')-aph(2''), emrA, mdtB, catB4 and cmlA4 at D. − 3, D.0 and/or D.3 whereas at D.8 associations between Prevotella and mefA, cfxA6 and aci1 were identified. The weaning age and diet factor played an important role in the microbial community composition.Prapat SuriyapholJimmy Ka Ho ChiuNathamon YimpringPaiboon TunsagoolWuttichai MhuantongRungtip ChuanchuenIrina BessarabRohan B. H. WilliamsRick Twee-Hee OngGunnaporn SuriyapholNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Prapat Suriyaphol Jimmy Ka Ho Chiu Nathamon Yimpring Paiboon Tunsagool Wuttichai Mhuantong Rungtip Chuanchuen Irina Bessarab Rohan B. H. Williams Rick Twee-Hee Ong Gunnaporn Suriyaphol Dynamics of the fecal microbiome and antimicrobial resistome in commercial piglets during the weaning period
description	Abstract This study aimed to characterize the alteration of the fecal microbiome and antimicrobial resistance (AMR) determinants in 24 piglets at day 3 pre-weaning (D. − 3), weaning day (D.0), days 3 (D.3) and 8 post-weaning (D.8), using whole-genome shotgun sequencing. Distinct clusters of microbiomes and AMR determinants were observed at D.8 when Prevotella (20.9%) was the major genus, whereas at D. − 3–D.3, Alistipes (6.9–12.7%) and Bacteroides (5.2–8.5%) were the major genera. Lactobacillus and Escherichia were notably observed at D. − 3 (1.2%) and D. − 3–D.3 (0.2–0.4%), respectively. For AMR, a distinct cluster of AMR determinants was observed at D.8, mainly conferring resistance to macrolide–lincosamide–streptogramin (mefA), β-lactam (cfxA6 and aci1) and phenicol (rlmN). In contrast, at D. − 3–D.3, a high abundance of determinants with aminoglycoside (AMG) (sat, aac(6')-aph(2''), aadA and acrF), β-lactam (fus-1, cepA and mrdA), multidrug resistance (MDR) (gadW, mdtE, emrA, evgS, tolC and mdtB), phenicol (catB4 and cmlA4), and sulfonamide patterns (sul3) was observed. Canonical correlation analysis (CCA) plot associated Escherichia coli with aac(6')-aph(2''), emrA, mdtB, catB4 and cmlA4 at D. − 3, D.0 and/or D.3 whereas at D.8 associations between Prevotella and mefA, cfxA6 and aci1 were identified. The weaning age and diet factor played an important role in the microbial community composition.
format	article
author	Prapat Suriyaphol Jimmy Ka Ho Chiu Nathamon Yimpring Paiboon Tunsagool Wuttichai Mhuantong Rungtip Chuanchuen Irina Bessarab Rohan B. H. Williams Rick Twee-Hee Ong Gunnaporn Suriyaphol
author_facet	Prapat Suriyaphol Jimmy Ka Ho Chiu Nathamon Yimpring Paiboon Tunsagool Wuttichai Mhuantong Rungtip Chuanchuen Irina Bessarab Rohan B. H. Williams Rick Twee-Hee Ong Gunnaporn Suriyaphol
author_sort	Prapat Suriyaphol
title	Dynamics of the fecal microbiome and antimicrobial resistome in commercial piglets during the weaning period
title_short	Dynamics of the fecal microbiome and antimicrobial resistome in commercial piglets during the weaning period
title_full	Dynamics of the fecal microbiome and antimicrobial resistome in commercial piglets during the weaning period
title_fullStr	Dynamics of the fecal microbiome and antimicrobial resistome in commercial piglets during the weaning period
title_full_unstemmed	Dynamics of the fecal microbiome and antimicrobial resistome in commercial piglets during the weaning period
title_sort	dynamics of the fecal microbiome and antimicrobial resistome in commercial piglets during the weaning period
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/f0d2b3888b4c4246bab5e15e24dd8833
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Dynamics of the fecal microbiome and antimicrobial resistome in commercial piglets during the weaning period

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