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Ortiz Sanjuán JM, Argüello H, Cabrera-Rubio R, Crispie F, Cotter PD, Garrido JJ, Ekhlas D, Burgess CM, Manzanilla EG. Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs. Anim Microbiome 2024; 6:18. [PMID: 38627869 PMCID: PMC11022352 DOI: 10.1186/s42523-024-00306-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 03/31/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Post weaning diarrhoea (PWD) causes piglet morbidity and mortality at weaning and is a major driver for antimicrobial use worldwide. New regulations in the EU limit the use of in-feed antibiotics (Ab) and therapeutic zinc oxide (ZnO) to prevent PWD. New approaches to control PWD are needed, and understanding the role of the microbiota in this context is key. In this study, shotgun metagenome sequencing was used to describe the taxonomic and functional evolution of the faecal microbiota of the piglet during the first two weeks post weaning within three experimental groups, Ab, ZnO and no medication, on commercial farms using antimicrobials regularly in the post weaning period. RESULTS Diversity was affected by day post weaning (dpw), treatment used and diarrhoea but not by the farm. Microbiota composition evolved towards the dominance of groups of species such as Prevotella spp. at day 14dpw. ZnO inhibited E. coli overgrowth, promoted higher abundance of the family Bacteroidaceae and decreased Megasphaera spp. Animals treated with Ab exhibited inconsistent taxonomic changes across time points, with an overall increase of Limosilactobacillus reuteri and Megasphaera elsdenii. Samples from non-medicated pigs showed virulence-related functions at 7dpw, and specific ETEC-related virulence factors were detected in all samples presenting diarrhoea. Differential microbiota functions of pigs treated with ZnO were related to sulphur and DNA metabolism, as well as mechanisms of antimicrobial and heavy metal resistance, whereas Ab treated animals exhibited functions related to antimicrobial resistance and virulence. CONCLUSION Ab and particularly ZnO maintained a stable microbiota composition and functionality during the two weeks post weaning, by limiting E. coli overgrowth, and ultimately preventing microbiota dysbiosis. Future approaches to support piglet health should be able to reproduce this stable gut microbiota transition during the post weaning period, in order to maintain optimal gut physiological and productive conditions.
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Affiliation(s)
- Juan M Ortiz Sanjuán
- Pig Development Department, Teagasc Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland.
- Grupo de Genómica y Mejora Animal, Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain.
| | - Héctor Argüello
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, León, Spain
| | - Raúl Cabrera-Rubio
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Institute, University College Cork, Co. Cork, Ireland
| | - Fiona Crispie
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Institute, University College Cork, Co. Cork, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
- APC Microbiome Institute, University College Cork, Co. Cork, Ireland
- VistaMilk SFI Research Centre, Fermoy, Co. Cork, Ireland
| | - Juan J Garrido
- Grupo de Genómica y Mejora Animal, Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain
| | - Daniel Ekhlas
- Pig Development Department, Teagasc Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland
- Department of Food Safety, Teagasc Food Research Centre, Ashtown, Dublin, Ireland
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Catherine M Burgess
- Department of Food Safety, Teagasc Food Research Centre, Ashtown, Dublin, Ireland
| | - Edgar G Manzanilla
- Pig Development Department, Teagasc Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
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Ortiz Sanjuán JM, Manzanilla EG, Cabrera-Rubio R, Crispie F, Cotter PD, Garrido JJ, Argüello H. Using Shotgun Sequencing to Describe the Changes Induced by In-Feed Zinc Oxide and Apramycin in the Microbiomes of Pigs One Week Postweaning. Microbiol Spectr 2022; 10:e0159722. [PMID: 35950862 PMCID: PMC9431492 DOI: 10.1128/spectrum.01597-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 07/18/2022] [Indexed: 11/20/2022] Open
Abstract
Postweaning diarrhea (PWD) is a relevant problem associated with early weaning on pig farms. For decades, in-feed antibiotics and therapeutic zinc oxide (ZnO) have been widely used to prevent PWD in piglets. The European Union is banning both strategies in 2022 due to antimicrobial resistance and environmental contamination concerns, respectively. Understanding the effects of these products on the pig microbiome is crucial for correcting potential microbial disbalances that would prompt PWD. Using shotgun sequencing, three trials were carried out to explore the impact of in-feed apramycin and ZnO, combined with different farm hygiene protocols, on the fecal microbiomes of piglets 7 days postweaning. In trial 1, 28-day-old piglets were allocated to one of three groups: control diet (Ct), Ct + ZnO (Zn), and Ct + apramycin (Ab). In trials 2 and 3, piglets were allocated to the same treatments, but the trials also included different cleaning protocols, achieving different hygiene levels. In-feed treatments impacted the richness, diversity, and relative abundance of the piglets' microbiome more than hygiene. Pigs in the Ct group showed higher species richness than pigs in the Ab and Zn groups. A clustering analysis evidenced a link between Enterobacteriaceae in the Ct group; Lactobacillaceae and Veillonellaceae mainly in the Ct group; and Bacteroidaceae, Ruminococcaceae, Oscillospiraceae, Acidaminococcaceae, and Lactobacillaceae in the Ab and Zn groups. Functional data analysis revealed a higher abundance of virulence genes in the Ct group microbiomes and heavy metal and antimicrobial resistance-related functions in the Zn treatment group. The results demonstrate that alternatives to Ab and ZnO should balance the microbial abundance and stimulate the growth of commensals to outcompete potential pathogens. IMPORTANCE Weaning is a critical period for piglets, during which potentially harmful bacteria such as Escherichia coli can increase in abundance in the intestine, creating digestive problems and diarrhea. In-feed antibiotics, the most frequent administration route for antibiotics in livestock, and therapeutic doses of zinc oxide (ZnO) help to control diarrhea but prompt secondary problems such as antimicrobial resistance and soil pollution from heavy metals. Understanding how these strategies impact the gut microbiota is crucial for establishing health biomarkers and designing successful replacement strategies. Using shotgun sequencing, this study compares the microbiota of pigs after early weaning when treated with in-feed antibiotics, ZnO, or treatment-free diets to describe differences that could define the susceptibility to infections, providing the basis for future research on improving intestinal resilience through microbiota-based strategies.
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Affiliation(s)
- Juan M. Ortiz Sanjuán
- Pig Development Department, Teagasc Grassland Research and Innovation Centre, Moorepark, Fermoy, County Cork, Ireland
- Grupo de Genómica y Mejora Animal, Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain
| | - Edgar G. Manzanilla
- Pig Development Department, Teagasc Grassland Research and Innovation Centre, Moorepark, Fermoy, County Cork, Ireland
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Raúl Cabrera-Rubio
- Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, County Cork, Ireland
| | - Fiona Crispie
- Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, County Cork, Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, County Cork, Ireland
- VistaMilk SFI Research Centre, Fermoy, County Cork, Ireland
| | - Juan J. Garrido
- Grupo de Genómica y Mejora Animal, Departamento de Genética, Facultad de Veterinaria, Universidad de Córdoba, Córdoba, Spain
| | - Héctor Argüello
- Animal Health Department, Veterinary Faculty, Universidad de León, León, Spain
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Manoharan RK, Ishaque F, Ahn YH. Fate of antibiotic resistant genes in wastewater environments and treatment strategies - A review. CHEMOSPHERE 2022; 298:134671. [PMID: 35460672 DOI: 10.1016/j.chemosphere.2022.134671] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 03/29/2022] [Accepted: 04/18/2022] [Indexed: 06/14/2023]
Abstract
Antibiotic-resistant bacteria (ARB) and antibiotic-resistant genes (ARGs) have emerged in aquatic environments through the discharge of large amounts of antibiotics into wastewater. Well-designed wastewater treatment plants (WWTPs) with effective treatment processes are essential to prevent the release of ARGs directly into the environment. Although some systematic sequential treatment methods are used to remove ARGs, considerable gaps in removal mechanisms will be discussed. Therefore, deep analysis and discussion of various treatment methods are required to understand the ARGs removal mechanisms. In this manuscript, the role of antibiotics and the resistance mechanism of ARB are discussed in depth. In addition, the fate of ARGs in an aquatic environment and detection methods are compared comprehensively and discussed. In particular, the advantages and disadvantages of various methods are summarized and reviewed critically. Finally, combined technologies, such as advanced oxidation process (AOP) with biochemical systems, membrane separation with electrochemical AOP, ultrafiltration (UF) membrane coupled with photocatalytic treatment, and UF membrane separation coupled with sonication, are introduced. Overall, low-energy anaerobic treatment reactors with any of the above combined treatments might reduce the discharge of large quantities of ARGs into the environment. Finally, this review provides valuable insights for better ARG removal technologies by introducing combined effective treatment strategies used in real WWTPs.
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Affiliation(s)
| | - Fahmida Ishaque
- Department of Civil Engineering, Yeungnam University, Gyeongsan, 38541, Republic of Korea
| | - Young-Ho Ahn
- Department of Civil Engineering, Yeungnam University, Gyeongsan, 38541, Republic of Korea.
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Dioletis E, Paiva RS, Kaffe E, Secor ER, Weiss TR, Fields MR, Ouyang X, Ali A. The fermented soy beverage Q-CAN® plus induces beneficial changes in the oral and intestinal microbiome. BMC Nutr 2021; 7:6. [PMID: 33658080 PMCID: PMC7931600 DOI: 10.1186/s40795-021-00408-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 01/27/2021] [Indexed: 11/30/2022] Open
Abstract
Background Soy products are associated with many beneficial health consequences, but their effects on the human intestinal microbiome are poorly characterized. Objectives To identify the changes in the oral and fecal microbiome in lean and obese participants due to consumption of Q-CAN®, and to assess the expected consequences of these changes based on the published literature. Methods Prospective study of lean (10) and obese (9) participants consuming Q-CAN® twice daily for 4 weeks with 8 weeks follow-up. Microbial DNA was extracted from saliva and stool samples, amplified against the V4 region of the 16S ribosomal RNA gene and data analyzed using QIIME 1.9.1 bioinformatics. Four hundred forty-four samples were collected in total, 424 of which were productive and yielded good quality data. Results STOOL. In the lean population Bifidobacteria and Blautia show a significant increase while taking Q-CAN®, and there was a trend for this in the obese population. ORAL. There were relatively fewer major changes in the oral microbiome with an increase in the family Veillonellaceae in the lean population while on Q-CAN®. Conclusion Q-CAN® consumption induced a number of significant changes in the fecal and oral microbiome. Most notably an increase in the stool microbiome of Bifidobacteria and Blautia, both of which are associated with positive health benefits, and in the saliva an increase in Veillonellaceae. Trial registration This trial was registered with Clinicaltrials.gov on January 14th 2016. ClinicalTrials.gov Identifier: NCT02656056 Supplementary Information The online version contains supplementary material available at 10.1186/s40795-021-00408-4.
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Affiliation(s)
- Evangelos Dioletis
- Internal Medicine (Digestive Diseases), Yale University School of Medicine, One Gilbert Street, TAC Bldg, Room #S241, New Haven, CT, 06519, USA
| | - Ricardo S Paiva
- Internal Medicine (Digestive Diseases), Yale University School of Medicine, One Gilbert Street, TAC Bldg, Room #S241, New Haven, CT, 06519, USA
| | - Eleanna Kaffe
- Internal Medicine (Digestive Diseases), Yale University School of Medicine, One Gilbert Street, TAC Bldg, Room #S241, New Haven, CT, 06519, USA
| | - Eric R Secor
- Hartford Hospital and University of Connecticut, Hartford, CT, USA
| | - Theresa R Weiss
- Department of Pediatrics (General Pediatrics), Yale University School of Medicine, New Haven, USA
| | - Maxine R Fields
- Department of Pediatrics (General Pediatrics), Yale University School of Medicine, New Haven, USA
| | - Xinshou Ouyang
- Internal Medicine (Digestive Diseases), Yale University School of Medicine, One Gilbert Street, TAC Bldg, Room #S241, New Haven, CT, 06519, USA.
| | - Ather Ali
- Department of Pediatrics (General Pediatrics), Yale University School of Medicine, New Haven, USA
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Achard CS, Dupouy V, Cauquil L, Arpaillange N, Bousquet-Melou A, Floc’h NL, Zemb O. Early Inoculation of Microbial Suspension in Suckling Piglets Affects the Transmission of Maternal Microbiota and the Associated Antibiotic Resistance Genes. Microorganisms 2020; 8:microorganisms8101576. [PMID: 33066283 PMCID: PMC7602062 DOI: 10.3390/microorganisms8101576] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/29/2020] [Accepted: 10/07/2020] [Indexed: 12/18/2022] Open
Abstract
Antibiotic resistance of microbes thriving in the animal gut is a growing concern for public health as it may serve as a hidden reservoir for antibiotic resistance genes (ARGs). We compared 16 control piglets to 24 piglets fed for 3 weeks with S1 or S2 fecal suspensions from two sows that were not exposed to antibiotics for at least 6 months: the first suspension decreased the erythromycin resistance gene ermB and the aminoglycoside phosphotransferase gene conferring resistance to kanamycine (aphA3), while the second decreased the tetracycline resistance gene tetL, with an unexpected increase in ARGs. Using 16S RNA sequencing, we identified microbial species that are likely to carry ARGs, such as the lincosamide nucleotidyltransferase lnuB, the cephalosporinase cepA, and the tetracycline resistance genes tetG and tetM, as well as microbes that never co-exist with the tetracycline resistance gene tetQ, the erythromycin resistance gene ermG and aphA3. Since 73% of the microbes detected in the sows were not detected in the piglets at weaning, a neutral model was applied to estimate whether a microbial species is more important than chance would predict. This model confirmed that force-feeding modifies the dynamics of gut colonization. In conclusion, early inoculation of gut microbes is an interesting possibility to stimulate gut microbiota towards a desirable state in pig production, but more work is needed to be able to predict which communities should be used.
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Affiliation(s)
- Caroline S. Achard
- Génétique Physiologie et Systèmes d’Elevage (GenPhySE), Université de Toulouse, Institut National De Recherche Pour L’agriculture, L’alimentation Et L’environnement (INRAE), Institut National Polytechnique de Toulouse (INPT), École nationale vétérinaire de Toulouse (ENVT), F-31320 Castanet Tolosan, France; (C.S.A.); (L.C.)
- Lallemand SAS, 19 rue des Briquetiers, BP 59, 31702 Blagnac CEDEX, France
| | - Veronique Dupouy
- Innovations thérapeutiques et résistances (INTHERES), Université de Toulouse, INRAE, ENVT, F-31300 Toulouse, France; (V.D.); (N.A.); (A.B.-M.)
| | - Laurent Cauquil
- Génétique Physiologie et Systèmes d’Elevage (GenPhySE), Université de Toulouse, Institut National De Recherche Pour L’agriculture, L’alimentation Et L’environnement (INRAE), Institut National Polytechnique de Toulouse (INPT), École nationale vétérinaire de Toulouse (ENVT), F-31320 Castanet Tolosan, France; (C.S.A.); (L.C.)
| | - Nathalie Arpaillange
- Innovations thérapeutiques et résistances (INTHERES), Université de Toulouse, INRAE, ENVT, F-31300 Toulouse, France; (V.D.); (N.A.); (A.B.-M.)
| | - Alain Bousquet-Melou
- Innovations thérapeutiques et résistances (INTHERES), Université de Toulouse, INRAE, ENVT, F-31300 Toulouse, France; (V.D.); (N.A.); (A.B.-M.)
| | - Nathalie Le Floc’h
- Physiologie, Environnement et Génétique pour l’Animal et les Systèmes d’Élevage (PEGASE), Institut national de recherche pour l’agriculture, l’alimentation et l’environnement (INRAE), Institut Agro, 35590 Saint-Gilles, France;
| | - Olivier Zemb
- Génétique Physiologie et Systèmes d’Elevage (GenPhySE), Université de Toulouse, Institut National De Recherche Pour L’agriculture, L’alimentation Et L’environnement (INRAE), Institut National Polytechnique de Toulouse (INPT), École nationale vétérinaire de Toulouse (ENVT), F-31320 Castanet Tolosan, France; (C.S.A.); (L.C.)
- Correspondence:
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Achard CS, Dupouy V, Siviglia S, Arpaillange N, Cauquil L, Bousquet-Mélou A, Zemb O. Variability of the Ability of Complex Microbial Communities to Exclude Microbes Carrying Antibiotic Resistance Genes in Rabbits. Front Microbiol 2019; 10:1503. [PMID: 31333614 PMCID: PMC6615258 DOI: 10.3389/fmicb.2019.01503] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 06/14/2019] [Indexed: 01/16/2023] Open
Abstract
Reducing antibiotic use is a necessary step toward less antibiotic resistance in livestock, but many antibiotic resistance genes can persist for years, even in an antibiotic-free environment. In this study, we investigated the potential of three fecal complex microbial communities from antibiotic-naive does to drive the microbiota of kits from antibiotic-exposed dams and outcompete bacteria-carrying antibiotic-resistant genes. The fecal complex microbial communities were either orally delivered or simply added as fresh fecal pellets in four to five nests that were kept clean from maternal feces. Additionally, four nests were cleaned for the maternal feces and five nests were handled according to the common farm practice (i.e., cleaning once a week) as controls. At weaning, we measured the relative abundance of 26 antibiotic resistance genes, the proportion of Enterobacteriaceae resistant to tetracycline and sulfonamide antibiotics, and the taxonomic composition of the microbiota by sequencing the 16S rRNA genes of one kit per nest. Changing the surrounding microbes of the kits can hinder the transmission of antibiotic resistance genes from one generation to the next, but the three communities widely differed in their ability to orient gut microbes and in their impact on antibiotic resistance genes. The most efficient delivery of the microbial community reduced the proportion of resistant Enterobacteria from 93 to 9%, decreased the relative abundance of eight antibiotic resistance genes, and changed the gut microbes of the kits at weaning. The least efficient did not reduce any ARG or modify the bacterial community. In addition, adding fecal pellets was more efficient than the oral inoculation of the anaerobic suspension derived from these fecal pellets. However, we were unable to predict the outcome of the exclusion from the data of the donor does (species composition and abundance of antibiotic resistance genes). In conclusion, we revealed major differences between microbial communities regarding their ability to exclude antibiotic resistance genes, but more work is needed to understand the components leading to the successful exclusion of antibiotic resistance genes from the gut. As a consequence, studies about the impact of competitive exclusion should use several microbial communities in order to draw general conclusions.
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Affiliation(s)
| | | | - Suzanne Siviglia
- GenPhySE, INRA, ENVT, Université de Toulouse, Toulouse, France.,InTheRes, INRA, ENVT, Université de Toulouse, Toulouse, France
| | | | - Laurent Cauquil
- GenPhySE, INRA, ENVT, Université de Toulouse, Toulouse, France
| | | | - Olivier Zemb
- GenPhySE, INRA, ENVT, Université de Toulouse, Toulouse, France
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Prospective Influence of Phytotherapy on Resistant Bacterial Tonsillitis. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2019. [DOI: 10.22207/jpam.13.1.17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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Effect of Tetracycline Dose and Treatment Mode on Selection of Resistant Coliform Bacteria in Nursery Pigs. Appl Environ Microbiol 2017; 83:AEM.00538-17. [PMID: 28389548 DOI: 10.1128/aem.00538-17] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 04/03/2017] [Indexed: 01/13/2023] Open
Abstract
This study describes the results of a randomized clinical trial investigating the effect of oxytetracycline treatment dose and mode of administration on the selection of antibiotic-resistant coliform bacteria in fecal samples from nursery pigs. Nursery pigs (pigs of 4 to 7 weeks of age) in five pig herds were treated with oxytetracycline for Lawsonia intracellularis-induced diarrhea. Each group was randomly allocated to one of five treatment groups: oral flock treatment with a (i) high (20 mg/kg of body weight), (ii) medium (10 mg/kg), or (iii) low (5 mg/kg) dose, (iv) oral pen-wise (small-group) treatment (10 mg/kg), and (v) individual intramuscular injection treatment (10 mg/kg). All groups were treated once a day for 5 days. In all groups, treatment caused a rise in the numbers and proportions of tetracycline-resistant coliform bacteria right after treatment, followed by a significant drop by the time that the pigs left the nursery unit. The counts and proportions of tetracycline-resistant coliforms did not vary significantly between treatment groups, except immediately after treatment, when the highest treatment dose resulted in the highest number of resistant coliforms. A control group treated with tiamulin did not show significant changes in the numbers or proportions of tetracycline-resistant coliforms. Selection for tetracycline-resistant coliforms was significantly correlated to selection for ampicillin- and sulfonamide-resistant strains but not to selection for cefotaxime-resistant strains. In conclusion, the difference in the dose of oxytetracycline and the way in which the drug was applied did not cause significantly different levels of selection of tetracycline-resistant coliform bacteria under the conditions tested.IMPORTANCE Antimicrobial resistance is a global threat to human health. Treatment of livestock with antimicrobials has a direct impact on this problem, and there is a need to improve the ways that we use antimicrobials in livestock production. We hypothesized that antibiotic resistance development following treatment of diarrhea in nursery pigs could be reduced either by lowering the dose of oxytetracycline or by replacing the commonly used practice of flock treatment with individual or small-group treatments, since this would reduce the number of pigs treated. However, the study showed no significant difference between treatment groups with respect to the number or proportion of tetracycline-resistant coliforms selected. The most important conclusion is that under practical field conditions, there will be no added value, in terms of lowering resistance development, by exchanging flock treatment for individual or small-group treatment of nursery pigs. The reason for the lack of an effect of single-animal treatment is probably that such animals share the environment with treated animals and take up resistant bacteria from the environment.
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Qin H, Sun Q, Pan X, Qiao Z, Yang H. Microbial Diversity and Biochemical Analysis of Suanzhou: A Traditional Chinese Fermented Cereal Gruel. Front Microbiol 2016; 7:1311. [PMID: 27610102 PMCID: PMC4997791 DOI: 10.3389/fmicb.2016.01311] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 08/08/2016] [Indexed: 11/27/2022] Open
Abstract
Suanzhou as a traditional Chinese gruel is fermented from proso millet and millet. The biochemical analysis showed Suanzhou had relatively high concentrations of lactic acid, acetic acid, and free amino acids. The metagenomics of Suanzhou were studied, with the analysis of the V4 region of 16S rRNA gene, the genera Lactobacillus and Acetobacter were found dominant with the average abundance of 58.2 and 24.4%, respectively; and with the analysis of the ITS1 region between 18S and 5.8S rRNA genes, 97.3% of the fungal community was found belonging to the genus Pichia and 2.7% belonging to five other genera. Moreover, the isolates recovered from 59 Suanzhou samples with various media were identified with the 16S rRNA or 18S rRNA gene analyses. Lactobacillus fermentum (26.9%), L. pentosus (19.4%), L. casei (17.9%), and L. brevis (16.4%) were the four dominant Lactobacillus species; Acetobacter lovaniensis (38.1%), A. syzygii (16.7%), A. okinawensis (16.7%), and A. indonesiensis (11.9%) were the four dominant Acetobacter species; and Pichia kudriavzevii (55.8%) and Galactomyces geotrichum (23.1%) were the two dominant fungal species. Additionally, L. pentosus p28-c and L. casei h28-c1 were selected for the fermentations mimicking the natural process. Collectively, our data demonstrate that Suanzhou is a nutritional food high in free amino acids and organic acids. Diverse Lactobacillus, Acetobacter, and yeast species are identified as the dominant microorganisms in Suanzhou. The isolated strains can be further characterized and used as starters for the industrial production of Suanzhou safely.
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Affiliation(s)
- Huibin Qin
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and TechnologyTianjin, China
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture, Shanxi Key Laboratory of Genetic Resources and Genetic Improvement of Minor Crops, Institute of Crop Germplasm Resources of Shanxi Academy of Agricultural SciencesTaiyuan, China
| | - Qinghui Sun
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and TechnologyTianjin, China
| | - Xuewei Pan
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and TechnologyTianjin, China
| | - Zhijun Qiao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture, Shanxi Key Laboratory of Genetic Resources and Genetic Improvement of Minor Crops, Institute of Crop Germplasm Resources of Shanxi Academy of Agricultural SciencesTaiyuan, China
| | - Hongjiang Yang
- Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and TechnologyTianjin, China
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Xing Y, Wang S, Fan J, Oso AO, Kim SW, Xiao D, Yang T, Liu G, Jiang G, Li Z, Li L, Zhang B. Effects of dietary supplementation with lysine-yielding Bacillus subtilis on gut morphology, cecal microflora, and intestinal immune response of Linwu ducks1. J Anim Sci 2015; 93:3449-57. [DOI: 10.2527/jas.2014-8090] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Y. Xing
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128, China
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - S. Wang
- Hunan Microbiology Institute, Changsha, 410009, China
| | - J. Fan
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128, China
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - A. O. Oso
- Department of Animal Nutrition, College of Animal Science and Livestock Production, Federal University of Agriculture, Abeokuta, PMB 2240, Nigeria
| | - S. W. Kim
- Department of Animal Science, North Carolina State University, Raleigh, NC 27695
| | - D. Xiao
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128, China
| | - T. Yang
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - G. Liu
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - G. Jiang
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - Z. Li
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128, China
| | - L. Li
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - B. Zhang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128, China
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11
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Wang FH, Qiao M, Su JQ, Chen Z, Zhou X, Zhu YG. High throughput profiling of antibiotic resistance genes in urban park soils with reclaimed water irrigation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:9079-85. [PMID: 25057898 DOI: 10.1021/es502615e] [Citation(s) in RCA: 296] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Reclaimed water irrigation (RWI) in urban environments is becoming popular, due to rapid urbanization and water shortage. The continuous release of residual antibiotics and antibiotic resistance genes (ARGs) from reclaimed water could result in the dissemination of ARGs in the downstream environment. This study provides a comprehensive profile of ARGs in park soils exposed to RWI through a high-throughput quantitative PCR approach. 147 ARGs encoding for resistance to a broad-spectrum of antibiotics were detected among all park soil samples. Aminoglycoside and beta-lactam were the two most dominant types of ARGs, and antibiotic deactivation and efflux pump were the two most dominant mechanisms in these RWI samples. The total enrichment of ARGs varied from 99.3-fold to 8655.3-fold compared to respective controls. Six to 60 ARGs were statistically enriched among these RWI samples. Four transposase genes were detected in RWI samples. TnpA-04 was the most enriched transposase gene with an enrichment was up to 2501.3-fold in Urumqi RWI samples compared with control soil samples. Furthermore, significantly positive correlation was found between ARGs and transposase abundances, indicating that transposase might be involved in the propagation of ARGs. This study demonstrated that RWI resulted in the enrichment of ARGs in urban park soils.
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Affiliation(s)
- Feng-Hua Wang
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, People's Republic of China
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12
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Abstract
The human food chain begins with upwards of 1,000 species of bacteria that inhabit the intestinal tracts of poultry and livestock. These intestinal denizens are responsible for the health and safety of a major protein source for humans. The use of antibiotics to treat animal diseases was followed by the surprising discovery that antibiotics enhanced food animal growth, and both led to six decades of antibiotic use that has shaped food animal management practices. Perhaps the greatest impact of antibiotic feeding in food animals has been as a selective force in the evolution of their intestinal bacteria, particularly by increasing the prevalence and diversity of antibiotic resistance genes. Future antibiotic use will likely be limited to prudent applications in both human and veterinary medicine. Improved knowledge of antibiotic effects, particularly of growth-promoting antibiotics, will help overcome the challenges of managing animal health and food safety.
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Affiliation(s)
- Heather K Allen
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, Iowa 50010; ,
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13
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Liu HY, Dicksved J, Lundh T, Lindberg JE. Expression of heat shock proteins 27 and 72 correlates with specific commensal microbes in different regions of porcine gastrointestinal tract. Am J Physiol Gastrointest Liver Physiol 2014; 306:G1033-41. [PMID: 24763551 DOI: 10.1152/ajpgi.00299.2013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The gastrointestinal (GI) tract of mammals is inhabited by trillions of microorganisms, resulting in exceedingly complex networking. The interaction between distinct bacterial species and the host immune system is essential in maintaining homeostasis in the gut ecosystem. For instance, the gut commensal microbiota dictates intestinal mucosa maturation and its abundant immune components, such as cytoprotective heat shock proteins (HSP). Here we examined physiological expression of HSP in the normal porcine GI tract and found it to be gut region- and cell type-specific in response to dietary components, microbes, and microbial metabolites to which the mucosa surface is exposed. Correlations between HSP72 expression and ileal Lactobacillus spp. and colonic clostridia species, and between HSP27 expression and uronic acid ingestion, were important interplays identified here. Thus this study provides novel insights into host-microbe interactions shaping the immune system that are modifiable by dietary regime.
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Affiliation(s)
- Hao-Yu Liu
- Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Johan Dicksved
- Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Torbjörn Lundh
- Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jan Erik Lindberg
- Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences, Uppsala, Sweden
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14
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Stanton TB. A call for antibiotic alternatives research. Trends Microbiol 2013; 21:111-3. [PMID: 23473628 DOI: 10.1016/j.tim.2012.11.002] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 10/29/2012] [Accepted: 11/02/2012] [Indexed: 11/26/2022]
Abstract
The persistence and spread of antibiotic resistance, in conjunction with decreased profitability of new antibiotics, have created the dangerous prospect of ineffective therapies against bacterial diseases. National strategies aimed at discovery, development, and definition of the mechanisms of effective antibiotic alternatives, especially for agricultural applications, should be encouraged.
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Affiliation(s)
- Thaddeus B Stanton
- Food Safety and Enteric Diseases Unit, National Animal Disease Center, USDA-ARS, Ames, IA 50010, USA.
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15
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Butyrate-producing bacteria, including mucin degraders, from the swine intestinal tract. Appl Environ Microbiol 2013; 79:3879-81. [PMID: 23584773 DOI: 10.1128/aem.00589-13] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
To identify bacteria with potential for influencing gut health, 980 anaerobes were cultured from the swine intestinal tract and analyzed for butyrate production. Fifteen isolates in the order Clostridiales produced butyrate and had butyryl coenzyme A (CoA):acetate CoA transferase activity. Three of the isolates grew on mucin, suggesting an intimate association with host intestinal mucosa.
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16
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In-feed antibiotic effects on the swine intestinal microbiome. Proc Natl Acad Sci U S A 2012; 109:1691-6. [PMID: 22307632 DOI: 10.1073/pnas.1120238109] [Citation(s) in RCA: 727] [Impact Index Per Article: 60.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Antibiotics have been administered to agricultural animals for disease treatment, disease prevention, and growth promotion for over 50 y. The impact of such antibiotic use on the treatment of human diseases is hotly debated. We raised pigs in a highly controlled environment, with one portion of the littermates receiving a diet containing performance-enhancing antibiotics [chlortetracycline, sulfamethazine, and penicillin (known as ASP250)] and the other portion receiving the same diet but without the antibiotics. We used phylogenetic, metagenomic, and quantitative PCR-based approaches to address the impact of antibiotics on the swine gut microbiota. Bacterial phylotypes shifted after 14 d of antibiotic treatment, with the medicated pigs showing an increase in Proteobacteria (1-11%) compared with nonmedicated pigs at the same time point. This shift was driven by an increase in Escherichia coli populations. Analysis of the metagenomes showed that microbial functional genes relating to energy production and conversion were increased in the antibiotic-fed pigs. The results also indicate that antibiotic resistance genes increased in abundance and diversity in the medicated swine microbiome despite a high background of resistance genes in nonmedicated swine. Some enriched genes, such as aminoglycoside O-phosphotransferases, confer resistance to antibiotics that were not administered in this study, demonstrating the potential for indirect selection of resistance to classes of antibiotics not fed. The collateral effects of feeding subtherapeutic doses of antibiotics to agricultural animals are apparent and must be considered in cost-benefit analyses.
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Antibiotic resistance: how much do we know and where do we go from here? Appl Environ Microbiol 2011; 77:7093-5. [PMID: 21908629 DOI: 10.1128/aem.06565-11] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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18
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Chlortetracycline-resistant intestinal bacteria in organically raised and feral Swine. Appl Environ Microbiol 2011; 77:7167-70. [PMID: 21821750 DOI: 10.1128/aem.00688-11] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Organically raised swine had high fecal populations of chlortetracycline (CTC)-resistant (growing at 64 μg CTC/ml) Escherichia coli, Megasphaera elsdenii, and anaerobic bacteria. By comparison, CTC-resistant bacteria in feral swine feces were over 1,000-fold fewer and exhibited lower taxonomic diversity.
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