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Creus-Martí I, Moya A, Santonja FJ. Methodology for microbiome data analysis: An overview. Comput Biol Med 2025; 192:110157. [PMID: 40279974 DOI: 10.1016/j.compbiomed.2025.110157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Revised: 03/07/2025] [Accepted: 04/04/2025] [Indexed: 04/29/2025]
Abstract
It is known that microbiome and health are related, in addition, recent research has found that microbiome has potential clinical uses. These facts highlight the importance of the microbiome in actual science. However, microbiome data has some characteristics that makes its statistical study challenging. In recent years, longitudinal and non-longitudinal methods have been designed to analyze the microbiota and knowing more about the bacterial behavior. In this article in the form of a review we summarize the characteristics of microbiome data and the statistical methods most widespread to analyze it. We have taken into account if the strategies are longitudinal or not. We also classify the methods based on their specific analytical objectives and based on their mathematical characteristics. The methods are structured according to their biological goals and mathematical features, ensuring that the insights provided are both relevant and accessible to professionals in biology and statistics. We present this review as a reference for the most widely used methods in microbiome data analysis and as a foundation for identifying potential areas for future research. We want to point out that this review can be particularly useful to remark the importance of the methodology designed in order to study microbiome longitudinal datasets.
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Affiliation(s)
- Irene Creus-Martí
- Department of Applied Mathematics, Universitat Politècnica de València, Valencia, Spain.
| | - Andrés Moya
- Institute for Integrative Systems Biology (I2Sysbio), Universitat de València and CSIC, València, Spain; The Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO), Valencia, Spain; CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Francisco J Santonja
- Department of Statistics and Operation Research, Universitat de València, Valencia, Spain
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Duclot F, Wu L, Wilkinson CS, Kabbaj M, Knackstedt LA. Ceftriaxone alters the gut microbiome composition and reduces alcohol intake in male and female Sprague-Dawley rats. Alcohol 2024; 120:169-178. [PMID: 38290696 DOI: 10.1016/j.alcohol.2024.01.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 01/26/2024] [Accepted: 01/26/2024] [Indexed: 02/01/2024]
Abstract
Ceftriaxone is an antibiotic that increases central nervous system (CNS) protein expression of the glutamate transporters GLT-1 and xCT and ameliorates pathological behaviors in rodent models of neurological disease and substance use disorder. However, little ceftriaxone passes through the blood-brain barrier, the CNS binding partner of ceftriaxone is unknown, and ceftriaxone does not consistently upregulate GLT-1 and xCT in cell culture. Ceftriaxone alters the gut microbiome composition in rodents and humans, and the microbiome-gut-brain axis regulates drug-seeking. Thus, here we test the hypothesis that ceftriaxone reduces alcohol intake while ameliorating alcohol-induced disruption of the gut microbiome composition. Male and female Sprague-Dawley rats received intermittent access to alcohol (IAA) while controls received access to only water. Following 17 IAA sessions, ceftriaxone/vehicle treatment was given for 5 days. Analysis of the gut microbiome composition was assessed by 16S rRNA gene amplicon sequencing conducted on fecal pellets collected prior to and after alcohol consumption and following ceftriaxone treatment. Male rats displayed escalated alcohol intake and preference over the course of the 17 sessions; however, total alcohol intake did not differ between the sexes. Ceftriaxone reduced alcohol intake and preference in male and female rats. While alcohol affected a diverse set of amplicon sequencing variants (ASV), ceftriaxone markedly reduced the diversity of microbial communities reflected by a blooming of the Enterococcaceae family. The remaining effects of ceftriaxone, however, encompassed families both affected and unaffected by prior alcohol drinking and highlight the Ruminococcaceae and Muribaculaceae families as bidirectionally modulated by alcohol and ceftriaxone. Altogether, our study confirms that ceftriaxone reduces alcohol intake in rats and partially reverses alcohol-induced dysbiosis.
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Affiliation(s)
- Florian Duclot
- Florida State University, Biomedical Sciences Department, Tallahassee, FL, United States.
| | - Lizhen Wu
- University of Florida, Psychology Department, Gainesville, FL, United States.
| | - Courtney S Wilkinson
- University of Florida, Psychology Department, Gainesville, FL, United States; Center for Addiction Research and Education, University of Florida, Gainesville, FL, United States.
| | - Mohamed Kabbaj
- Florida State University, Biomedical Sciences Department, Tallahassee, FL, United States.
| | - Lori A Knackstedt
- University of Florida, Psychology Department, Gainesville, FL, United States; Center for Addiction Research and Education, University of Florida, Gainesville, FL, United States.
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Hong Y, Li H, Chen L, Su H, Zhang B, Luo Y, Li C, Zhao Z, Shao Y, Guo L. Short-term exposure to antibiotics begets long-term disturbance in gut microbial metabolism and molecular ecological networks. MICROBIOME 2024; 12:80. [PMID: 38715137 PMCID: PMC11075301 DOI: 10.1186/s40168-024-01795-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 03/14/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND Antibiotic exposure can occur in medical settings and from environmental sources. Long-term effects of brief antibiotic exposure in early life are largely unknown. RESULTS Post a short-term treatment by ceftriaxone to C57BL/6 mice in early life, a 14-month observation was performed using 16S rRNA gene-sequencing technique, metabolomics analysis, and metagenomics analysis on the effects of ceftriaxone exposure. Firstly, the results showed that antibiotic pre-treatment significantly disturbed gut microbial α and β diversities (P < 0.05). Both Chao1 indices and Shannon indices manifested recovery trends over time, but they didn't entirely recover to the baseline of control throughout the experiment. Secondly, antibiotic pre-treatment reduced the complexity of gut molecular ecological networks (MENs). Various network parameters were affected and manifested recovery trends over time with different degrees, such as nodes (P < 0.001, R2 = 0.6563), links (P < 0.01, R2 = 0.4543), number of modules (P = 0.0672, R2 = 0.2523), relative modularity (P = 0.6714, R2 = 0.0155), number of keystones (P = 0.1003, R2 = 0.2090), robustness_random (P = 0.79, R2 = 0.0063), and vulnerability (P = 0.0528, R2 = 0.28). The network parameters didn't entirely recover. Antibiotic exposure obviously reduced the number of key species in gut MENs. Interestingly, new keystones appeared during the recovery process of network complexity. Changes in network stability might be caused by variations in network complexity, which supports the ecological theory that complexity begets stability. Besides, the metabolism profiles of the antibiotic group and control were significantly different. Correlation analysis showed that antibiotic-induced differences in gut microbial metabolism were related to MEN changes. Antibiotic exposure also caused long-term effects on gut microbial functional networks in mice. CONCLUSIONS These results suggest that short-term antibiotic exposure in early life will cause long-term negative impacts on gut microbial diversity, MENs, and microbial metabolism. Therefore, great concern should be raised about children's brief exposure to antibiotics if the results observed in mice are applicable to humans. Video Abstract.
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Affiliation(s)
- Yuehui Hong
- Dongguan Key Laboratory of Public Health Laboratory Science, The First Dongguan Affiliated Hospital, School of Public Health, Guangdong Medical University, Dongguan, 523808, China
- Jiangmen Key Laboratory of Traditional Chinese Medicine Ingredients and Their Mechanisms of Action, Guangdong Jiangmen Chinese Medicine College, Jiangmen, 529000, China
| | - Hao Li
- Dongguan Key Laboratory of Public Health Laboratory Science, The First Dongguan Affiliated Hospital, School of Public Health, Guangdong Medical University, Dongguan, 523808, China
| | - Linkang Chen
- Dongguan Key Laboratory of Public Health Laboratory Science, The First Dongguan Affiliated Hospital, School of Public Health, Guangdong Medical University, Dongguan, 523808, China
| | - Hongtian Su
- Dongguan Key Laboratory of Public Health Laboratory Science, The First Dongguan Affiliated Hospital, School of Public Health, Guangdong Medical University, Dongguan, 523808, China
| | - Bin Zhang
- Dongguan Key Laboratory of Public Health Laboratory Science, The First Dongguan Affiliated Hospital, School of Public Health, Guangdong Medical University, Dongguan, 523808, China
| | - Yu Luo
- Dongguan Key Laboratory of Public Health Laboratory Science, The First Dongguan Affiliated Hospital, School of Public Health, Guangdong Medical University, Dongguan, 523808, China
| | - Chengji Li
- Dongguan Key Laboratory of Public Health Laboratory Science, The First Dongguan Affiliated Hospital, School of Public Health, Guangdong Medical University, Dongguan, 523808, China
| | - Zuguo Zhao
- Dongguan Key Laboratory of Public Health Laboratory Science, The First Dongguan Affiliated Hospital, School of Public Health, Guangdong Medical University, Dongguan, 523808, China
| | - Yiming Shao
- Dongguan Key Laboratory of Sepsis Translational Medicine, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523808, China.
| | - Lianxian Guo
- Dongguan Key Laboratory of Public Health Laboratory Science, The First Dongguan Affiliated Hospital, School of Public Health, Guangdong Medical University, Dongguan, 523808, China.
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Bouiller K, Gbaguidi-Haore H, Hocquet D, Crépin T, Wendling D, Borot S, Chirouze C, Bertrand X. The effects of switching from ceftriaxone to cefotaxime on the occurrence of third-generation cephalosporin-resistant Enterobacterales: A stepped-wedge cluster randomized trial. Infect Dis Now 2024; 54:104806. [PMID: 37838305 DOI: 10.1016/j.idnow.2023.104806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 10/03/2023] [Accepted: 10/07/2023] [Indexed: 10/16/2023]
Abstract
OBJECTIVES To evaluate the effects of the replacement of ceftriaxone by cefotaxime on the incidence of third-generation cephalosporin-resistant Enterobacterales (3GC-RE). PATIENTS AND METHODS We conducted a 24-month monocentric prospective, stepped-wedge cluster randomized controlled trial. During the control phase of the study, clinicians prescribed either ceftriaxone or cefotaxime. During the intervention phase, they systematically prescribed cefotaxime. RESULTS The cefotaxime/ceftriaxone ratio was inversely correlated with the incidence of 3GC-RE. All in all, 3GC-RE incidence was 1.05 (27/25,692) acquired cases/1000 hospitalization days during the control phase and 0.54 (11/20,419) acquired cases/1000 hospitalization days during the intervention phase (incidence rate ratio [IRR] = 0.51 [0.22-1.07], p = 0.06). In multivariable analysis, intervention phase (versus control phase) (p = 0.007), cefotaxime/ceftriaxone ratio (p = 0.003) and imported 3GC-RE (p = 0.005) were associated with the incidence of acquired cases of 3GC-RE. CONCLUSIONS We found that replacing ceftriaxone with cefotaxime reduced the occurrence of 3GC-RE isolates. More studies are needed to confirm these results.
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Affiliation(s)
- Kevin Bouiller
- Service de Maladies Infectieuses et Tropicales - CHU, Besancon, France; UMR-CNRS 6249 Chrono-environnement, Université de Franche-Comté, 25000, Besançon, France.
| | - Houssein Gbaguidi-Haore
- Service d'Hygiène Hospitalière - CHU, Besancon, France; UMR-CNRS 6249 Chrono-environnement, Université de Franche-Comté, 25000, Besançon, France
| | - Didier Hocquet
- Service d'Hygiène Hospitalière - CHU, Besancon, France; UMR-CNRS 6249 Chrono-environnement, Université de Franche-Comté, 25000, Besançon, France
| | | | | | - Sophie Borot
- Service d'Endocrinologie - CHU, Besancon, France
| | - Catherine Chirouze
- Service de Maladies Infectieuses et Tropicales - CHU, Besancon, France; UMR-CNRS 6249 Chrono-environnement, Université de Franche-Comté, 25000, Besançon, France
| | - Xavier Bertrand
- Service d'Hygiène Hospitalière - CHU, Besancon, France; UMR-CNRS 6249 Chrono-environnement, Université de Franche-Comté, 25000, Besançon, France
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Ishnaiwer M, Le Bastard Q, Naour M, Zeman M, Dailly E, Montassier E, Batard E, Dion M. Efficacy of an inulin-based treatment on intestinal colonization by multidrug-resistant E. coli: insight into the mechanism of action. Gut Microbes 2024; 16:2347021. [PMID: 38685762 PMCID: PMC11062366 DOI: 10.1080/19490976.2024.2347021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 04/19/2024] [Indexed: 05/02/2024] Open
Abstract
Inulin, an increasingly studied dietary fiber, alters intestinal microbiota. The aim of this study was to assess whether inulin decreases intestinal colonization by multidrug resistant E. coli and to investigate its potential mechanisms of action. Mice with amoxicillin-induced intestinal dysbiosis mice were inoculated with extended spectrum beta-lactamase producing E. coli (ESBL-E. coli). The combination of inulin and pantoprazole (IP) significantly reduced ESBL-E. coli fecal titers, whereas pantoprazole alone did not and inulin had a delayed and limited effect. Fecal microbiome was assessed using shotgun metagenomic sequencing and qPCR. The efficacy of IP was predicted by increased abundance of 74 taxa, including two species of Adlercreutzia. Preventive treatments with A. caecimuris or A. muris also reduced ESBL-E. coli fecal titers. Fecal microbiota of mice effectively treated by IP was enriched in genes involved in inulin catabolism, production of propionate and expression of beta-lactamases. They also had increased beta-lactamase activity and decreased amoxicillin concentration. These results suggest that IP act through production of propionate and degradation of amoxicillin by the microbiota. The combination of pantoprazole and inulin is a potential treatment of intestinal colonization by multidrug-resistant E. coli. The ability of prebiotics to promote propionate and/or beta-lactamase producing bacteria may be used as a screening tool to identify potential treatments of intestinal colonization by multidrug resistant Enterobacterales.
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Affiliation(s)
- Murad Ishnaiwer
- Nantes Université, CHU Nantes, Cibles et médicaments des infections et du cancer, IICiMed, Nantes, France
- College of Applied Sciences, Palestine Polytechnic University, Hebron, Palestine
| | - Quentin Le Bastard
- Nantes Université, CHU Nantes, Cibles et médicaments des infections et du cancer, IICiMed, Nantes, France
- Emergency Department, CHU Nantes, Nantes, France
| | | | - Michal Zeman
- Veterinary Research Institute, Brno, Czech Republic
| | - Eric Dailly
- Nantes Université, CHU Nantes, Cibles et médicaments des infections et du cancer, IICiMed, Nantes, France
- CHU Nantes, Clinical Pharmacology Department, Nantes, France
| | - Emmanuel Montassier
- Nantes Université, CHU Nantes, Cibles et médicaments des infections et du cancer, IICiMed, Nantes, France
- Emergency Department, CHU Nantes, Nantes, France
- Center for Research in Transplantation and Translational Immunology, Nantes Université, Inserm, CHU Nantes, Nantes, France
| | - Eric Batard
- Nantes Université, CHU Nantes, Cibles et médicaments des infections et du cancer, IICiMed, Nantes, France
- Emergency Department, CHU Nantes, Nantes, France
| | - Michel Dion
- Nantes Université, CHU Nantes, Cibles et médicaments des infections et du cancer, IICiMed, Nantes, France
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Wang F, Xiao Y, Lu Y, Deng ZY, Deng XY, Lin LB. Bacteriophage Lytic Enzyme P9ly as an Alternative Antibacterial Agent Against Antibiotic-Resistant Shigella dysenteriae and Staphylococcus aureus. Front Microbiol 2022; 13:821989. [PMID: 35237249 PMCID: PMC8882861 DOI: 10.3389/fmicb.2022.821989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/19/2022] [Indexed: 11/24/2022] Open
Abstract
Developing new strategies to replace or supplement antibiotics to combat bacterial infection is a pressing task in the field of microbiological research. In this study, we report a lytic enzyme named P9ly deriving from the bacteriophage PSD9 that could infect multidrug-resistant Shigella. This enzyme was identified through whole-genome sequencing of PSD9. The results show that P9ly contains a conserved T4-like_lys domain and belongs to the phage lysozyme family. Recombinant P9ly obtained from protein purification presented biological activity and could digest bacterial cell walls (CW), resulting in the destruction of cell structure and leakage of intracellular components. Furthermore, P9ly exhibited bacteriolytic and bactericidal activity on different strains, especially multidrug-resistant Gram-negative Shigella dysenteriae and Gram-positive Staphylococcus aureus. Additionally, combined use of P9ly with ceftriaxone sodium (CRO) could decrease necessary dose of the antibiotic used and improve the antibacterial effect. In summary, under the current backdrop of extensive antibiotic usage and the continuous emergence of bacterial resistance, this study provides an insight into developing bacteriophage-based antibacterial agents against both Gram-negative and Gram-positive pathogens.
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Affiliation(s)
- Feng Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yao Xiao
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Yao Lu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Zheng-Yu Deng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Xian-Yu Deng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Lian-Bing Lin
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
- Engineering Research Center for Replacement Technology of Feed Antibiotics of Yunnan College, Kunming, China
- *Correspondence: Lian-Bing Lin,
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Schönherr SG, Ranft D, Lippmann N, Lübbert C. Changes in antibiotic consumption, AMR and Clostridioides difficile infections in a large tertiary-care center following the implementation of institution-specific guidelines for antimicrobial therapy: A nine-year interrupted time series study. PLoS One 2021; 16:e0258690. [PMID: 34648594 PMCID: PMC8516227 DOI: 10.1371/journal.pone.0258690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 10/01/2021] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Institution-specific guidelines (ISGs) within the framework of antimicrobial stewardship programs offer locally tailored decision support taking into account local pathogen and resistance epidemiology as well as national and international guidelines. OBJECTIVES To assess the impact of ISGs for antimicrobial therapy on antibiotic consumption and subsequent changes in resistance rates and Clostridioides difficile infections (CDIs). METHODS The study was conducted at the Leipzig University Hospital, a 1,451-bed tertiary-care medical center, and covered the years 2012 to 2020. Since 2014, ISGs were provided to optimize empirical therapies, appropriate diagnostics, and antimicrobial prophylaxis. We used interrupted time series analysis (ITSA) and simple linear regression to analyze changes in antimicrobial consumption, resistance and CDIs. RESULTS Over the study period, 1,672,200 defined daily doses (DDD) of antibiotics were dispensed, and 85,645 bacterial isolates as well as 2,576 positive C. difficile cultures were collected. Total antimicrobial consumption decreased by 14% from 2012 to 2020, without clear impact of the deployment of ISGs. However, implementation of ISGs was associated with significant decreases in the use of substances that were rarely recommended (e.g., fluoroquinolones). Over the whole study period, we observed declining resistance rates to most antibiotic classes of up to 25% in Enterobacterales, staphylococci, and Pseudomonas aeruginosa. Switching from ceftriaxone to cefotaxime was associated with reduced resistance to third-generation cephalosporins. The number of CDI cases fell by 65%, from 501 in 2012 to 174 in 2020. CONCLUSIONS Well-implemented ISGs can have a significant, immediate, and lasting impact on the prescription behavior. ISGs might thereby contribute to reduce resistance rates and CDI incidences in the hospital setting.
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Affiliation(s)
- Sebastian G. Schönherr
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine II, Leipzig University Hospital, Leipzig, Germany
| | - Donald Ranft
- Hospital Pharmacy, Leipzig University Hospital, Leipzig, Germany
| | - Norman Lippmann
- Institute for Medical Microbiology and Virology, Leipzig University Hospital, Leipzig, Germany
- Interdisciplinary Center for Infectious Diseases (ZINF), Leipzig University Hospital, Leipzig, Germany
| | - Christoph Lübbert
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine II, Leipzig University Hospital, Leipzig, Germany
- Interdisciplinary Center for Infectious Diseases (ZINF), Leipzig University Hospital, Leipzig, Germany
- Department of Infectious Diseases/Tropical Medicine, Nephrology and Rheumatology, Hospital St. Georg, Leipzig, Germany
- * E-mail:
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