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Li Y, Fu S, Klein MS, Wang H. High Prevalence of Antibiotic Resistance in Traditionally Fermented Foods as a Critical Risk Factor for Host Gut Antibiotic Resistome. Microorganisms 2024; 12:1433. [PMID: 39065201 PMCID: PMC11279133 DOI: 10.3390/microorganisms12071433] [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: 06/13/2024] [Revised: 06/30/2024] [Accepted: 07/08/2024] [Indexed: 07/28/2024] Open
Abstract
This study aimed to assess the suitability of fermented food interventions to replenish damaged gut microbiota. Metagenomic assessment of published sequencing data found that fermented food interventions led to a significant increase in the gut antibiotic resistome in healthy human subjects. Antibiotic resistome and viable antibiotic-resistant (AR) bacteria were further highly prevalent in retail kimchi and artisan cheeses by metagenomic and culture analyses. Representative AR pathogens of importance in nosocomial infections, such as Klebsiella pneumoniae, Serratia marcescens, and vancomycin-resistant Enterococcus (VRE), as well as commensals and lactic acid bacteria, were characterized; some exhibited an extremely high minimum inhibitory concentration (MIC) against antibiotics of clinical significance. Exposing fermented food microbiota to representative antibiotics further led to a boost of the corresponding antibiotic and multidrug-resistance gene pools, as well as disturbed microbiota, including the rise of previously undetectable pathogens. These results revealed an underestimated public health risk associated with fermented food intervention at the current stage, particularly for susceptible populations with compromised gut integrity and immune functions seeking gut microbiota rescue. The findings call for productive intervention of foodborne AR via technology innovation and strategic movements to mitigate unnecessary, massive damages to the host gut microbiota due to orally administered or biliary excreted antibiotics.
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Affiliation(s)
| | | | | | - Hua Wang
- Department of Food Science and Technology, The Ohio State University, 2015 Fyffe Court, Columbus, OH 43210, USA (M.S.K.)
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Qi Q, Wang L, Zhu Y, Li S, Gebremedhin MA, Wang B, Zhu Z, Zeng L. Unraveling the Microbial Symphony: Impact of Antibiotics and Probiotics on Infant Gut Ecology and Antibiotic Resistance in the First Six Months of Life. Antibiotics (Basel) 2024; 13:602. [PMID: 39061284 PMCID: PMC11274100 DOI: 10.3390/antibiotics13070602] [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: 04/16/2024] [Revised: 05/24/2024] [Accepted: 06/05/2024] [Indexed: 07/28/2024] Open
Abstract
We aimed to examine the effects of antibiotic and probiotic usage on the gut microbiota structure and the presence of antibiotic-resistance genes (ARGs) in infants during the first six months of life. Questionnaires and fecal samples were collected within three days of birth, two months, and six months to assess antibiotic and probiotic exposure. Gut microbiotas were sequenced via 16S rRNA, and ARGs were conducted by qPCR, including beta-lactam (mecA, blaTEM), tetracycline (tetM), fluoroquinolone (qnrS), aminoglycoside (aac(6')-Ib), and macrolide (ermB). Infants were categorized by antibiotic and probiotic usage and stratified by delivery mode, microbial composition, and ARG abundances were compared, and potential correlations were explored. A total of 189 fecal samples were analyzed in this study. The gut microbiota diversity (Chao1 index) was significantly lower in the "only probiotics" (PRO) group compared to the "neither antibiotics nor probiotics" (CON) group at six months for the CS stratification (p = 0.029). Compositionally, the abundance of core genus Bifidobacterium_pseudocatenulatum was less abundant for the antibiotic during delivery (IAP) group than that in the CON group within the first three days (p = 0.009), while core genus Enterococcus_faecium was more abundant in the PRO than that in the CON group (p = 0.021) at two months. ARGs were highly detected, with Enterococcus hosting tetM and Escherichia associated with blaTEM within three days of birth, though no correlation was found between Bifidobacterium and ARGs. These findings emphasized the critical importance of carefully managing antibiotic and probiotic exposures in early life, with implications for promoting lifelong health through preserving a healthy infant gut ecosystem.
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Affiliation(s)
- Qi Qi
- Department of Epidemiology and Biostatistics, School of Public Health, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China; (Q.Q.); (L.W.); (Y.Z.); (M.A.G.); (B.W.)
| | - Liang Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China; (Q.Q.); (L.W.); (Y.Z.); (M.A.G.); (B.W.)
| | - Yingze Zhu
- Department of Epidemiology and Biostatistics, School of Public Health, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China; (Q.Q.); (L.W.); (Y.Z.); (M.A.G.); (B.W.)
| | - Shaoru Li
- Experimental Teaching Center, School of Public Health, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China;
| | - Mitslal Abrha Gebremedhin
- Department of Epidemiology and Biostatistics, School of Public Health, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China; (Q.Q.); (L.W.); (Y.Z.); (M.A.G.); (B.W.)
| | - Baozhu Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China; (Q.Q.); (L.W.); (Y.Z.); (M.A.G.); (B.W.)
- Department of Health, Northwest Women’s and Children’s Hospital, Xi’an 710003, China
| | - Zhonghai Zhu
- Department of Epidemiology and Biostatistics, School of Public Health, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China; (Q.Q.); (L.W.); (Y.Z.); (M.A.G.); (B.W.)
| | - Lingxia Zeng
- Department of Epidemiology and Biostatistics, School of Public Health, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China; (Q.Q.); (L.W.); (Y.Z.); (M.A.G.); (B.W.)
- Center for Chronic Disease Control and Prevention, Global Health Institution, Xi’an Jiaotong University, Xi’an 710061, China
- Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, Xi’an 710061, China
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Double-edged sword: impact of fecal microbiome transplants on the gut resistome. Curr Opin Gastroenterol 2023; 39:16-22. [PMID: 36504032 DOI: 10.1097/mog.0000000000000894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
PURPOSE OF REVIEW Fecal microbiome transplants (FMT) show promise in treating various diseases, such as Clostridioides difficile infections. FMT have also demonstrated the capacity to modulate the collection of antibiotic resistance genes (ARGs), termed the resistome, within the gut. The purpose of this review was to critically evaluate the literature regarding the interaction between FMT and the gut resistome and determine whether FMT could be used specifically to reduce ARG carriage in the gut. RECENT FINDINGS Several studies have demonstrated a decrease in ARG carriage post-FMT administration in various disease states, including recurrent C. difficile infection and after antibiotic usage. However, other studies have reported an expansion of the resistome following FMT. Most studies contained small patient cohorts regardless of the outcome and showed heterogeneity in responses. SUMMARY Research on resistome modulation by FMT is preliminary, and human studies currently lack consensus regarding benefits and risks. From a safety perspective, screening donor samples for ARGs in addition to antibiotic-resistant organisms may be advisable. Additional studies on the mechanisms underlying heterogeneity between studies and individuals are required before FMT is considered an efficient approach for resistome amelioration.
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Qi Q, Wang L, Gebremedhin MA, Li S, Wang X, Shen J, Zhu Y, Andegiorgish AK, Cheng Y, Shi L, Zhou J, Yang Y, Kang Y, Yang W, Zhu Z, Zeng L. The impact of early-life antibiotics and probiotics on gut microbial ecology and infant health outcomes: a Pregnancy and Birth Cohort in Northwest China (PBCC) study protocol. BMC Pediatr 2022; 22:738. [PMID: 36577993 PMCID: PMC9795439 DOI: 10.1186/s12887-022-03811-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 12/18/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Unreasonable use of antibiotics and probiotics can alter the gut ecology, leading to antibiotic resistance and suboptimal health outcomes during early life. Our study aims are to clarify the association among antibiotic and probiotic exposure in early life, the microecology of the gut microbiota, and the development of antibiotic resistance; to investigate the long-term impact of antibiotics and probiotics on the health outcomes of infants and young children; and to provide a theoretical basis for the rational use of antibiotics and probiotics from a life course perspective. METHODS The study is a prospective, longitudinal birth cohort study conducted in Shaanxi Province, China from 2018 to 2024. A total of 3,000 eligible mother-child pairs will be enrolled from rural, suburban, and urban areas. The recruitment of the participants begins at pregnancy, and the newborns will be followed up for 2 years at successive timepoints: within 3 days after birth, 42 days after birth, and at 3, 6, 12, 18, and 24 months of age. Sociodemographic data, environmental exposures, dietary patterns, psychological conditions, and medical and drug histories are collected. Cognitive and behavioural development among infants and young children and questionnaires on antibiotic knowledge and behaviour among caregivers will be collected at 12 and 24 months of age. The faecal samples are collected and analysed by 16S rRNA high-throughput sequencing and quantitative PCR (qPCR) for antibiotic resistance genes. DISCUSSION The findings will inform antibiotic and probiotic use for pregnant women and infants and contribute to establishing rational use strategies of antibiotics and probiotics for paediatricians, health practitioners, and drug administration policy-makers. TRIAL REGISTRATION The study was registered on the Chinese Clinical Trial Registry (ChiCTR) platform, http://www.chictr.org.cn (Record ID: ChiCTR2100047531, June 20, 2021).
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Affiliation(s)
- Qi Qi
- grid.43169.390000 0001 0599 1243School of Public Health, Xi’an Jiaotong University Health Science Centre, Xi’an, Shaanxi People’s Republic of China
| | - Liang Wang
- grid.43169.390000 0001 0599 1243School of Public Health, Xi’an Jiaotong University Health Science Centre, Xi’an, Shaanxi People’s Republic of China
| | - Mitslal Abrha Gebremedhin
- grid.43169.390000 0001 0599 1243School of Public Health, Xi’an Jiaotong University Health Science Centre, Xi’an, Shaanxi People’s Republic of China
| | - Shaoru Li
- grid.43169.390000 0001 0599 1243School of Public Health, Xi’an Jiaotong University Health Science Centre, Xi’an, Shaanxi People’s Republic of China
| | - Xueyao Wang
- grid.43169.390000 0001 0599 1243School of Public Health, Xi’an Jiaotong University Health Science Centre, Xi’an, Shaanxi People’s Republic of China
| | - Jiali Shen
- grid.43169.390000 0001 0599 1243School of Public Health, Xi’an Jiaotong University Health Science Centre, Xi’an, Shaanxi People’s Republic of China
| | - Yingze Zhu
- grid.43169.390000 0001 0599 1243School of Public Health, Xi’an Jiaotong University Health Science Centre, Xi’an, Shaanxi People’s Republic of China
| | - Amanuel Kidane Andegiorgish
- grid.43169.390000 0001 0599 1243School of Public Health, Xi’an Jiaotong University Health Science Centre, Xi’an, Shaanxi People’s Republic of China
| | - Yue Cheng
- grid.43169.390000 0001 0599 1243School of Public Health, Xi’an Jiaotong University Health Science Centre, Xi’an, Shaanxi People’s Republic of China
| | - Lu Shi
- grid.43169.390000 0001 0599 1243School of Public Health, Xi’an Jiaotong University Health Science Centre, Xi’an, Shaanxi People’s Republic of China
| | - Jing Zhou
- grid.452672.00000 0004 1757 5804Department of Paediatrics, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi People’s Republic of China
| | - Ying Yang
- Xi’an Lintong District Maternal and Child Health Hospital, Xi’an, Shaanxi People’s Republic of China
| | - Yijun Kang
- grid.43169.390000 0001 0599 1243School of Public Health, Xi’an Jiaotong University Health Science Centre, Xi’an, Shaanxi People’s Republic of China
| | - Wenfang Yang
- grid.452438.c0000 0004 1760 8119Department of Obstetrics and Gynaecology, The First Affiliated Hospital of Xi’an Jiaotong University, Maternal & Child Health Centre, Xi’an, Shaanxi People’s Republic of China
| | - Zhonghai Zhu
- grid.43169.390000 0001 0599 1243School of Public Health, Xi’an Jiaotong University Health Science Centre, Xi’an, Shaanxi People’s Republic of China
| | - Lingxia Zeng
- grid.43169.390000 0001 0599 1243School of Public Health, Xi’an Jiaotong University Health Science Centre, Xi’an, Shaanxi People’s Republic of China ,grid.43169.390000 0001 0599 1243Key Laboratory of Environment and Genes Related to Diseases (Xi’an Jiaotong University), Ministry of Education, Xi’an, Shaanxi People’s Republic of China
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Prado C, Abatti MR, Michels M, Córneo E, Cucker L, Borges H, Dias R, Rocha LB, Dal-Pizzol F, Ritter C. Comparative effects of fresh and sterile fecal microbiota transplantation in an experimental animal model of necrotizing enterocolitis. J Pediatr Surg 2022; 57:183-191. [PMID: 35058059 DOI: 10.1016/j.jpedsurg.2021.12.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 12/01/2021] [Accepted: 12/08/2021] [Indexed: 12/27/2022]
Abstract
INTRODUCTION Necrotizing Enterocolitis (NEC) is a serious intestinal disease that affects premature neonates, causing high mortality, despite the technological development in neonatal intensive care, with antibiotics, parenteral nutrition, surgery, and advanced life support. The correction of dysbiosis with fecal microbiome transplantation (FMT) has shown beneficial effects in experimental models of the disease. The different forms of administration and conservation of FMT and mixed results depending on several factors lead to questions about the mechanism of action of FMT. This study aimed to compare the effectiveness of fresh, sterile FMT and probiotic treatment under parameters of inflammation, oxidative stress, and tissue damage in a neonatal model of NEC. METHODS One-day-old Wistar rats were used to induce NEC model. Animals were divided in five groups: Control + saline; NEC + saline; NEC + fresh FMT; NEC + sterile FMT and NEC+ probiotics. Parameters of inflammatory response and oxidative damage were measured in the gut, brain, and serum. It was also determined gut histopathological alterations. RESULTS Proinflammatory cytokines were increased in the NEC group, and IL-10 levels decreased in the gut, brain, and serum. Fresh and sterile FMT decreased inflammation when compared to the use of probiotics. Oxidative and histological damage to the intestine was apparent in the NEC group, and both FMT treatments had a protective effect. CONCLUSION Fresh and sterile FMT effectively reduced the inflammatory response, oxidative damage, and histological alterations in the gut and brain compared to an experimental NEC model.
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Affiliation(s)
- Christian Prado
- Laboratory of Experimental Pathophysiology, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciúma, SC, 88806-000, Brazil
| | - Mariane Rocha Abatti
- Laboratory of Experimental Pathophysiology, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciúma, SC, 88806-000, Brazil
| | - Monique Michels
- Laboratory of Experimental Pathophysiology, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciúma, SC, 88806-000, Brazil
| | - Emily Córneo
- Laboratory of Experimental Pathophysiology, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciúma, SC, 88806-000, Brazil.
| | - Luana Cucker
- Laboratory of Experimental Pathophysiology, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciúma, SC, 88806-000, Brazil
| | - Heloisa Borges
- Laboratory of Experimental Pathophysiology, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciúma, SC, 88806-000, Brazil
| | - Rodrigo Dias
- Laboratory of Experimental Pathophysiology, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciúma, SC, 88806-000, Brazil
| | - Luana Bezerra Rocha
- Laboratory of Experimental Pathophysiology, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciúma, SC, 88806-000, Brazil
| | - Felipe Dal-Pizzol
- Laboratory of Experimental Pathophysiology, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciúma, SC, 88806-000, Brazil
| | - Cristiane Ritter
- Laboratory of Experimental Pathophysiology, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciúma, SC, 88806-000, Brazil
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Brunse A, Offersen SM, Mosegaard JJ, Deng L, Damborg P, Nielsen DS, Sangild PT, Thymann T, Nguyen DN. Enteral broad-spectrum antibiotics antagonize the effect of fecal microbiota transplantation in preterm pigs. Gut Microbes 2022; 13:1-16. [PMID: 33382952 PMCID: PMC7781584 DOI: 10.1080/19490976.2020.1849997] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Preterm infants are at risk of multiple morbidities including necrotizing enterocolitis (NEC). Suspected NEC patients receive intravenous antibiotics (AB) to prevent sepsis, although enteral AB is arguably more effective at reducing NEC but is rarely used due to the risk of AB resistance. Fecal microbiota transplantation (FMT) has shown protective effects against NEC in animal experiments, but the interaction between AB and FMT has not been investigated in neonates. We hypothesized that administration of enteral AB followed by rectal FMT would effectively prevent NEC with negligible changes in AB resistance and systemic immunity. Using preterm piglets, we examined host and gut microbiota responses to AB, FMT, or a sequential combination thereof, with emphasis on NEC development. In a saline-controlled experiment, preterm piglets (n = 67) received oro-gastric neomycin (50 mg/kg/d) and amoxicillin-clavulanate (50/12.5 mg/kg/d) (hereafter AB) for four days after cesarean delivery, and were subsequently given rectal FMT from healthy suckling piglet donors. Whereas AB protected the stomach and small intestine, and FMT primarily protected the colon, the sequential combination treatment surprisingly provided no NEC protection. Furthermore, minor changes in the gut microbiota composition were observed in response to either treatment, although AB treatment decreased species diversity and increased AB resistance among coliform bacteria and Enterococci, which were both partly reversed by FMT. Besides, enteral AB treatment suppressed cellular and functional systemic immune development, which was not prevented by subsequent FMT. We discovered an antagonistic relationship between enteral AB and FMT in terms of NEC development. The outcome may depend on choice of AB compounds, FMT composition, doses, treatment duration, and administration routes, but these results challenge the applicability of enteral AB and FMT in preterm infants.
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Affiliation(s)
- Anders Brunse
- Section for Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Simone Margaard Offersen
- Section for Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Josefine Juliane Mosegaard
- Section for Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ling Deng
- Section of Food Microbiology and Fermentation, Department of Food Science, Faculty of Science, Copenhagen University, Copenhagen, Denmark
| | - Peter Damborg
- Section for Veterinary Clinical Microbiology, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Dennis Sandris Nielsen
- Section of Food Microbiology and Fermentation, Department of Food Science, Faculty of Science, Copenhagen University, Copenhagen, Denmark
| | - Per Torp Sangild
- Section for Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Thymann
- Section for Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Duc Ninh Nguyen
- Section for Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark,CONTACT Duc Ninh Nguyen Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Burkholderiaceae and Multidrug Resistance Genes Are Key Players in Resistome Development in a Germfree Soil Model. mSystems 2021; 6:e0098821. [PMID: 34726494 PMCID: PMC8562478 DOI: 10.1128/msystems.00988-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Assembly of a resistome in parallel with the establishment of a microbial community is not well understood. Germfree models can reveal microbiota interactions and shed light on bacterial colonization and resistance development under antibiotic pressure. In this study, we exposed germfree soil (GS), GS with diluted nontreated soil (DS), and nontreated soil (NS) to various concentrations of tetracycline (TET) in a nongermfree environment for 10 weeks, followed by 2 weeks of exposure to water. High-throughput sequencing was used to profile bacterial communities and antibiotic resistance genes (ARGs) in the soils. The initial bacterial loads were found to shape the profiles of bacterial communities and the resistomes. GS and DS treated with TET and the same soils left untreated had similar profiles, whereas NS showed different profiles. Soils with the same initial bacterial loads had their profiles shifted by TET treatment. Multidrug resistance (MDR) genes were the most abundant ARG types in all soils, with multidrug efflux pump genes being the discriminatory ARGs in GS regardless of different TET treatments and in GS, DS, and NS after TET. Furthermore, MDR genes were significantly enriched by TET treatment. In contrast, tetracycline resistance genes were either absent or low in relative abundance. The family Burkholderiaceae was predominant in all soils (except in NS treated with water) and was positively selected for by TET treatment. Most importantly, Burkholderiaceae were the primary carrier of ARGs, including MDR genes. IMPORTANCE This is the first study to examine how resistomes develop and evolve using GS. GS can be used to study the colonization and establishment of bacterial communities under antibiotic selection. Surprisingly, MDR genes were the main ARGs detected in GS, and TET treatments did not positively select for specific tetracycline resistance genes. Additionally, Burkholderiaceae were the key bacterial hosts for MDR genes in the current GS model under the conditions investigated. These results show that the family Burkholderiaceae underpins the development of resistome and serves as a source of ARGs. The ease of establishment of Burkholderiaceae and MDR genes in soils has serious implications for human health, since these bacteria are versatile and ubiquitous in the environment.
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Yuan X, Chang C, Chen X, Li K. Emerging trends and focus of human gastrointestinal microbiome research from 2010-2021: a visualized study. J Transl Med 2021; 19:327. [PMID: 34332587 PMCID: PMC8325541 DOI: 10.1186/s12967-021-03009-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 07/23/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The gastrointestinal microbiome is an important component of the human body and is closely related to human health and disease. This study describes the hotspots of the human gastrointestinal microbiome research and its evolution in the past decade, evaluates the scientific cooperation network, and finally predicts the field's future development trend using bibliometric analysis and a visualized study. METHODS We searched the original articles from January 2010 to February 2021 in the Scopus database using the term "gastrointestinal microbiome" and its synonyms. CiteSpace was used to construct country and author co-occurrence map; conduct journal, citation cocitation analysis, and reference co-citation knowledge map; and form a keywords co-occurrence map, a clustering knowledge map, timeline view of keywords, and burst term map. RESULT A total of 4444 documents published from January 2010 to February 2021 were analysed. In approximately the past decade, the number of articles on the human gastrointestinal microbiome has increased rapidly, and the research topics focus on different populations, research methods, and detection methods. All countries and regions in the world, led by the US, are studying the human gastrointestinal microbiome, and many research teams with close cooperation have been formed. The research has been published extensively in microbiology journals and clinical medicine journals, and the highly cited articles mainly describe the relationship between gastrointestinal microorganisms and human health and disease. Regarding the research emphasis, researchers' exploration of the human gastrointestinal microbiome (2011-2013) was at a relatively macro and superficial stage and sought to determine how the gastrointestinal microbiome relates to humans. From 2014 to 2017, increasingly more studies were conducted to determine the interaction between human gastrointestinal flora and various organs and systems. In addition, researchers (2018-2021) focused on the gastrointestinal microbial community and the diversity of certain types of microbes. CONCLUSION Over time, the scope of the research on the clinical uses of the gastrointestinal microbiome gradually increased, and the contents were gradually deepened and developed towards a more precise level. The study of the human gastrointestinal microbiome is an ongoing research hotspot and contributes to human health.
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Affiliation(s)
- Xingzhu Yuan
- West China School of Nursing/ West China Hospital, Sichuan University, No.8 Teaching Building, Chengdu City, 610041, Sichuan province, China
| | - Chengting Chang
- West China School of Nursing/ West China Hospital, Sichuan University, No.8 Teaching Building, Chengdu City, 610041, Sichuan province, China
| | - Xinrong Chen
- West China School of Nursing/ West China Hospital, Sichuan University, No.8 Teaching Building, Chengdu City, 610041, Sichuan province, China
| | - Ka Li
- West China School of Nursing/ West China Hospital, Sichuan University, No.8 Teaching Building, Chengdu City, 610041, Sichuan province, China.
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Major histocompatibility complex class II genetic diversity and the genetic influence on gut microbiota in Guizhou minipigs. Folia Microbiol (Praha) 2021; 66:997-1008. [PMID: 34309822 DOI: 10.1007/s12223-021-00903-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 07/20/2021] [Indexed: 10/20/2022]
Abstract
Major histocompatibility complex (MHC) is an important complex that presents antigen to T cells. The second exon of swine MHC (SLA) class II genes has antigen binding sites that bind with extracellular antigen. Populations with high MHC gene diversity result in low gut microbiota, and individuals with MHC gene heterozygote have lower gut microbiota diversity than that of homozygote. The pig is an animal with organs physiologically and anatomically similar to humans than any other mammal, and the pig is also suitably developed as a laboratory animal to establish the animal models of human disease. However, the relationship between SLA genetic diversity and the gut microbes of the pig is ambiguous. We studied the characterization of SLA class II genes and calculated the genetic diversity, and then we selected experimental animal groups divided by different SLA genotypes to investigate the gut microbiota composition by sequencing V3 to V4 hypervariable regions of bacterial 16 s rRNA from fecal samples. Our results showed that Guizhou minipigs had a low SLA genetic diversity, which may be due to the small founder population. The Guizhou minipig population deviated from neutral selection and balancing selection, which shows that Guizhou minipigs experience a strong artificial selection in recent years. We observed that the sex differences influenced gut microbiota much more deeply than that of genetics. Our results also showed that the individual with heterozygote of genes at the SLA class II region had much higher abundant gut microbiota than that of the homozygote.
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Li L, Wang Q, Gao Y, Liu L, Duan Y, Mao D, Luo Y. Colistin and amoxicillin combinatorial exposure alters the human intestinal microbiota and antibiotic resistome in the simulated human intestinal microbiota. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 750:141415. [PMID: 32846251 DOI: 10.1016/j.scitotenv.2020.141415] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 05/26/2023]
Abstract
Antibiotics treatment could cause the dysbiosis of human intestinal microbiota and antibiotic resistome. Fecal microbiota transplantation (FMT) has been an efficacious treatment to restore the dysbiosis of intestinal microbiota in a variety of intestinal diseases. However, to data, the effect of the combinatorial antibiotic treatment on microbiota, antibiotic resistome and the FMT for restoration affected by combinatorial antibiotic exposure in the human intestinal microbiota remain unclear. In this study, we systematically investigated the effect of the colistin and amoxicillin combinatorial exposure in the simulator of the human intestinal microbial ecosystem (SHIME) and found that this combinatorial exposure significantly altered (p < 0.05) the human intestinal microbiota and antibiotic resistome. The shift of bacterial community and antibiotic resistome could incompletely recovery to baseline by FMT treatment after combinatorial antibiotic exposure. Additionally, the variance of antibiotic resistome was dominantly driven by the bacterial community (41.18%-68.03%) after the combinatorial antibiotic exposure. Overall, this study first to investigate the influence of the colistin and amoxicillin combinatorial exposure on the intestinal microbiota and antibiotic resistome, and assess the FMT recovery in the simulated human intestinal microbiota, which may potentially provide a correct administration of antibiotics and application of FMT in the clinic.
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Affiliation(s)
- Linyun Li
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Qing Wang
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China; College of Energy and Environmental Engineering, Hebei University of Engineering, Hebei Key Laboratory of Air Pollution Cause and Impact (preparatory), Handan 056038, China
| | - Yanyu Gao
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Lei Liu
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Yujing Duan
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Daqing Mao
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Yi Luo
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China.
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Zhou Y, Li Y, Zhang L, Wu Z, Huang Y, Yan H, Zhong J, Wang LJ, Abdullah HM, Wang HH. Antibiotic Administration Routes and Oral Exposure to Antibiotic Resistant Bacteria as Key Drivers for Gut Microbiota Disruption and Resistome in Poultry. Front Microbiol 2020; 11:1319. [PMID: 32733394 PMCID: PMC7358366 DOI: 10.3389/fmicb.2020.01319] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 05/25/2020] [Indexed: 01/05/2023] Open
Abstract
Previous studies have identified oral administration of antibiotics and gut-impacting drugs as critical drivers for fecal antibiotic resistance (AR) and microbiome disruption in lab mice, but the practical implications of these findings have yet to be validated in hosts nurtured in conventional environment. Using ampicillin (Amp) as a way to extrapolate the general effect of antibiotics, this project examined the impact of drug administration routes on fecal microbiota and resistome using poultry raised in a teaching farm. AR genes were found to be abundant in the feces of young Leghorn chicks without previous antibiotic treatment. In chickens seeded with bla CMY-2 + Escherichia coli, 300 mg/kg body weight of Amp was orally administered for 5 days. This led to the fecal microbiota switching from Firmicutes occupied (95.60 ± 2.62%) and Lactobacillus rich, to being dominated by Proteobacteria (70.91 ± 28.93%), especially Escherichia/Shigella. However, when Amp was given via muscle injection, Firmicutes was mostly retained (i.e., from 83.6 ± 24.4% pre- to 90.4 ± 15.2% post-treatment). In control chickens without seeding with bla CMY-2 + E. coli, oral Amp also led to the increase of Proteobacteria, dominated by Klebsiella and Escherichia/Shigella, and a reduction of Firmicutes. Specifically within Firmicutes, Enterococcus, Clostridium, etc. were enriched but Lactobacillus was diminished. The fecal resistome including Ampr genes was more abundant in chickens receiving oral Amp than those treated with muscle injection, but the difference was primarily within 1 log. The data illustrated that both drug administration routes and pre-existing gut microbiota have profound impacts on gut microbiome disruption when antibiotic treatment is given. In hosts nurtured in a conventional environment, drug administration route has the most evident impact on gut microbiota rather than the size of the targeted bla CMY-2 + gene pool, likely due to the pre-existing bacteria that are (i) less susceptible to Amp, and/or (ii) with Ampr- or multidrug resistance-encoding genes other than bla CMY-2 +. These results demonstrated the critical interplay among drug administration routes, microbiota seeded through the gastrointestinal tract, AR, gut microbiota disruption, and the rise of common opportunistic pathogens in hosts. The potential implications in human and animal health are discussed.
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Affiliation(s)
- Yang Zhou
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, United States.,Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yu Li
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, United States
| | - Lu Zhang
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, United States.,College of Food Science and Engineering of Technology, Guangzhou, China
| | - Zuowei Wu
- College of Veterinary Preventive Medicine, Iowa State University, Ames, IA, United States
| | - Ying Huang
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, United States.,College of Food Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - He Yan
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, United States.,College of Food Science and Engineering of Technology, Guangzhou, China
| | - Jiang Zhong
- Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Li-Ju Wang
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, United States
| | - Hafiz M Abdullah
- Department of Animal Science Poultry Facility, OARDC, Wooster, OH, United States
| | - Hua H Wang
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, United States.,Department of Microbiology, The Ohio State University, Columbus, OH, United States
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