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Delplanque M, Benech N, Rolhion N, Oeuvray C, Straube M, Galbert C, Brot L, Henry T, Jamilloux Y, Savey L, Grateau G, Sokol H, Georgin-Lavialle S. Gut microbiota alterations are associated with phenotype and genotype in familial Mediterranean fever. Rheumatology (Oxford) 2024; 63:1039-1048. [PMID: 37402619 DOI: 10.1093/rheumatology/kead322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 05/23/2023] [Accepted: 06/17/2023] [Indexed: 07/06/2023] Open
Abstract
OBJECTIVE FMF is the most common monogenic autoinflammatory disease associated with MEFV mutations. Disease phenotype and response to treatment vary from one patient to another, despite similar genotype, suggesting the role of environmental factors. The objective of this study was to analyse the gut microbiota of a large cohort of FMF patients in relation to disease characteristics. METHODS The gut microbiotas of 119 FMF patients and 61 healthy controls were analysed using 16 s rRNA gene sequencing. Associations between bacterial taxa, clinical characteristics, and genotypes were evaluated using multivariable association with linear models (MaAslin2), adjusting on age, sex, genotype, presence of AA amyloidosis (n = 17), hepatopathy (n = 5), colchicine intake, colchicine resistance (n = 27), use of biotherapy (n = 10), CRP levels, and number of daily faeces. Bacterial network structures were also analysed. RESULTS The gut microbiotas of FMF patients differ from those of controls in having increased pro-inflammatory bacteria, such as the Enterobacter, Klebsiella and Ruminococcus gnavus group. Disease characteristics and resistance to colchicine correlated with homozygous mutations and were associated with specific microbiota alteration. Colchicine treatment was associated with the expansion of anti-inflammatory taxa such as Faecalibacterium and Roseburia, while FMF severity was associated with expansion of the Ruminococcus gnavus group and Paracoccus. Colchicine-resistant patients exhibited an alteration of the bacterial network structure, with decreased intertaxa connectivity. CONCLUSION The gut microbiota of FMF patients correlates with disease characteristics and severity, with an increase in pro-inflammatory taxa in the most severe patients. This suggests a specific role for the gut microbiota in shaping FMF outcomes and response to treatment.
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Affiliation(s)
- Marion Delplanque
- Sorbonne Université, Service Médecine Interne, Centre de Référence des Maladies Autoinflammatoires et des Amyloses (CEREMAIA), APHP, Hôpital Tenon, Paris, France
- Gastroenterology Department, Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, French Group of Faecal Microbiota Transplantation (GFTF), Paris, France
- Paris Center for Microbiome Medicine, Fédération Hospitalo-Universitaire, Paris, France
| | - Nicolas Benech
- Gastroenterology Department, Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, French Group of Faecal Microbiota Transplantation (GFTF), Paris, France
- Paris Center for Microbiome Medicine, Fédération Hospitalo-Universitaire, Paris, France
| | - Nathalie Rolhion
- Gastroenterology Department, Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, French Group of Faecal Microbiota Transplantation (GFTF), Paris, France
- Paris Center for Microbiome Medicine, Fédération Hospitalo-Universitaire, Paris, France
| | - Cyriane Oeuvray
- Gastroenterology Department, Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, French Group of Faecal Microbiota Transplantation (GFTF), Paris, France
- Paris Center for Microbiome Medicine, Fédération Hospitalo-Universitaire, Paris, France
| | - Marjolène Straube
- Gastroenterology Department, Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, French Group of Faecal Microbiota Transplantation (GFTF), Paris, France
- Paris Center for Microbiome Medicine, Fédération Hospitalo-Universitaire, Paris, France
| | - Chloé Galbert
- Gastroenterology Department, Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, French Group of Faecal Microbiota Transplantation (GFTF), Paris, France
- Paris Center for Microbiome Medicine, Fédération Hospitalo-Universitaire, Paris, France
| | - Loic Brot
- Gastroenterology Department, Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, French Group of Faecal Microbiota Transplantation (GFTF), Paris, France
- Paris Center for Microbiome Medicine, Fédération Hospitalo-Universitaire, Paris, France
| | - Thomas Henry
- CIRI, Centre International de Recherche en Infectiologie, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, University Lyon, Lyon, Rhônes, France
| | - Yvan Jamilloux
- CIRI, Centre International de Recherche en Infectiologie, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, University Lyon, Lyon, Rhônes, France
| | - Léa Savey
- Sorbonne Université, Service Médecine Interne, Centre de Référence des Maladies Autoinflammatoires et des Amyloses (CEREMAIA), APHP, Hôpital Tenon, Paris, France
| | - Gilles Grateau
- Sorbonne Université, Service Médecine Interne, Centre de Référence des Maladies Autoinflammatoires et des Amyloses (CEREMAIA), APHP, Hôpital Tenon, Paris, France
| | - Harry Sokol
- Gastroenterology Department, Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, French Group of Faecal Microbiota Transplantation (GFTF), Paris, France
- Paris Center for Microbiome Medicine, Fédération Hospitalo-Universitaire, Paris, France
- INRAE, UMR1319 Micalis & AgroParisTech, Jouy en Josas, Yvelines, France
| | - Sophie Georgin-Lavialle
- Sorbonne Université, Service Médecine Interne, Centre de Référence des Maladies Autoinflammatoires et des Amyloses (CEREMAIA), APHP, Hôpital Tenon, Paris, France
- Gastroenterology Department, Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, French Group of Faecal Microbiota Transplantation (GFTF), Paris, France
- Paris Center for Microbiome Medicine, Fédération Hospitalo-Universitaire, Paris, France
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Bailey S, Fraser K. Advancing our understanding of the influence of drug induced changes in the gut microbiome on bone health. Front Endocrinol (Lausanne) 2023; 14:1229796. [PMID: 37867525 PMCID: PMC10588641 DOI: 10.3389/fendo.2023.1229796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 08/07/2023] [Indexed: 10/24/2023] Open
Abstract
The gut microbiome has been implicated in a multitude of human diseases, with emerging evidence linking its microbial diversity to osteoporosis. This review article will explore the molecular mechanisms underlying perturbations in the gut microbiome and their influence on osteoporosis incidence in individuals with chronic diseases. The relationship between gut microbiome diversity and bone density is primarily mediated by microbiome-derived metabolites and signaling molecules. Perturbations in the gut microbiome, induced by chronic diseases can alter bacterial diversity and metabolic profiles, leading to changes in gut permeability and systemic release of metabolites. This cascade of events impacts bone mineralization and consequently bone mineral density through immune cell activation. In addition, we will discuss how orally administered medications, including antimicrobial and non-antimicrobial drugs, can exacerbate or, in some cases, treat osteoporosis. Specifically, we will review the mechanisms by which non-antimicrobial drugs disrupt the gut microbiome's diversity, physiology, and signaling, and how these events influence bone density and osteoporosis incidence. This review aims to provide a comprehensive understanding of the complex interplay between orally administered drugs, the gut microbiome, and osteoporosis, offering new insights into potential therapeutic strategies for preserving bone health.
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Affiliation(s)
- Stacyann Bailey
- Department of Biomedical Engineering, University of Massachusetts Amherst, Amherst, MA, United States
- Institute for Applied Life Sciences, University of Massachusetts Amherst, Amherst, MA, United States
| | - Keith Fraser
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, United States
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
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Schneider-Crease IA, Feder JA, Baniel A, McCann C, Haile AA, Abebe B, Fitzgerald L, Gomery MA, Simberloff RA, Petrie ZL, Gabriel S, Dorny P, Fashing PJ, Nguyen N, Bergman TJ, Beehner JC, Snyder-Mackler N, Lu A. Urinary neopterin reflects immunological variation associated with age, helminth parasitism, and the microbiome in a wild primate. Sci Rep 2022; 12:21307. [PMID: 36494454 PMCID: PMC9734142 DOI: 10.1038/s41598-022-25298-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022] Open
Abstract
Neopterin, a product of activated white blood cells, is a marker of nonspecific inflammation that can capture variation in immune investment or disease-related immune activity and can be collected noninvasively in urine. Mounting studies in wildlife point to lifetime patterns in neopterin related to immune development, aging, and certain diseases, but rarely are studies able to assess whether neopterin can capture multiple concurrent dimensions of health and disease in a single system. We assessed the relationship between urinary neopterin stored on filter paper and multiple metrics of health and disease in wild geladas (Theropithecus gelada), primates endemic to the Ethiopian highlands. We tested whether neopterin captures age-related variation in inflammation arising from developing immunity in infancy and chronic inflammation in old age, inflammation related to intramuscular tapeworm infection, helminth-induced anti-inflammatory immunomodulation, and perturbations in the gastrointestinal microbiome. We found that neopterin had a U-shaped relationship with age, no association with larval tapeworm infection, a negative relationship with metrics related to gastrointestinal helminth infection, and a negative relationship with microbial diversity. Together with growing research on neopterin and specific diseases, our results demonstrate that urinary neopterin can be a powerful tool for assessing multiple dimensions of health and disease in wildlife.
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Affiliation(s)
- India A Schneider-Crease
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.
| | - Jacob A Feder
- Interdepartmental Doctoral Program in Anthropological Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Alice Baniel
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Colleen McCann
- Department of Mammals, Bronx Zoo, Wildlife Conservation Society, New York, NY, USA
- New York Consortium in Evolutionary Primatology, New York, NY, USA
| | | | - Belayneh Abebe
- African Wildlife Foundation, Simien Mountains Landscape Conservation and Management Project, Debark, Ethiopia
| | | | - Megan A Gomery
- Simien Mountains Gelada Research Project, Debark, Ethiopia
| | - Ruth A Simberloff
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, USA
| | | | - Sarah Gabriel
- Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
| | - Pierre Dorny
- Department of Biomedical Sciences, Institute for Tropical Medicine, Antwerp, Belgium
| | - Peter J Fashing
- Department of Anthropology, California State University Fullerton, Fullerton, CA, USA
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Nga Nguyen
- Department of Anthropology, California State University Fullerton, Fullerton, CA, USA
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Thore J Bergman
- Department of Ecology and Evolution, University of Michigan, Ann Arbor, MI, USA
- Department of Psychology, University of Michigan, Ann Arbor, MI, USA
| | - Jacinta C Beehner
- Department of Psychology, University of Michigan, Ann Arbor, MI, USA
- Department of Anthropology, University of Michigan, Ann Arbor, MI, USA
| | - Noah Snyder-Mackler
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Amy Lu
- Department of Anthropology, Stony Brook University, Stony Brook, NY, USA
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Bohard L, Patry I, Sergent P, Leclerc G, Leroy J, Chirouze C, Bouiller K. Factors associated with late microbiological documentation of prosthetic joint infection. Future Microbiol 2022; 17:1115-1124. [PMID: 35860979 DOI: 10.2217/fmb-2021-0310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Purpose: To describe the number of prosthetic joint infections (PJIs) with late documentation and to identify associated factors. Methods: Bacterial PJIs with surgical management between November 2015 and November 2019 in a French center were analyzed. Results of short (72 h) and late culture (at 14 days) were analyzed. Results: A total of 160 PJIs were reported with 215 bacteria. Twenty-nine patients had late documentation (18.1%). The bacteria most involved were coagulase-negative staphylococci and Cutibacterium spp. (60%). In multivariate analysis, late chronic PJI (odds ratio = 2.47) and antibiotic therapy before surgery (odds ratio = 3.13) were associated with late-documented infection. Conclusion: A better knowledge of the factors associated with late-documented infections is essential in order to simplify antibiotic treatment at the appropriate time.
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Affiliation(s)
- Louis Bohard
- Department of Infectious Diseases, CHU Besancon, Besancon, 25000, France
| | - Isabelle Patry
- Department of Bacteriology, CHU Besancon, Besancon, 25000, France
| | - Pauline Sergent
- Department of Orthopedic, Trauma, Plastic & Reconstructive Surgery & Hand Clinic, CHU Besancon, Besancon, 25000, France
| | - Grégoire Leclerc
- Department of Orthopedic, Trauma, Plastic & Reconstructive Surgery & Hand Clinic, CHU Besancon, Besancon, 25000, France
| | - Joël Leroy
- Department of Infectious Diseases, CHU Besancon, Besancon, 25000, France
| | - Catherine Chirouze
- Department of Infectious Diseases, CHU Besancon, Besancon, 25000, France.,UMR-CNRS 6249 Chrono-Environnement, Université Bourgogne Franche-Comté, Besancon, Besancon, 25000, France
| | - Kevin Bouiller
- Department of Infectious Diseases, CHU Besancon, Besancon, 25000, France.,UMR-CNRS 6249 Chrono-Environnement, Université Bourgogne Franche-Comté, Besancon, Besancon, 25000, France
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Zhao X, Tang W, Wan H, Lan Z, Qin H, Lin Q, Hu Y, Yu G, Jiang N, Yu B. Altered Gut Microbiota as an Auxiliary Diagnostic Indicator for Patients With Fracture-Related Infection. Front Microbiol 2022; 13:723791. [PMID: 35495685 PMCID: PMC9048737 DOI: 10.3389/fmicb.2022.723791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 02/16/2022] [Indexed: 12/02/2022] Open
Abstract
Preoperative diagnosis of fracture-related infection (FRI) is difficult for patients without obvious signs of infection. However, specific profiles of gut microbiota may be used as a potential diagnostic tool for FRI as suggested by a previous study. The fecal microbiome was compared between 20 FRI patients (FRI group), 18 fracture healed patients (FH group), and 12 healthy controls (HC group) included after collection of fecal samples and evaluation. The α and β diversity indices were used to characterize the fecal microbiome. Dysbiosis indexes were constructed based on the characteristic high-dimensional biomarkers identified in the fecal microbiota from the three groups by linear discriminant analysis and generalized linear model analysis to quantify the dysbiosis of fecal microbiota. The effectiveness of α and β diversity indices and dysbiosis indexes was assessed in distinguishing the fecal microbiome among the three groups. The influences of serum inflammatory factors on gut microbiota were also addressed. The α diversity indices were significantly different between the three groups, the highest in HC group and the lowest in FRI group (P < 0.05). The β diversity indices showed significant phylogenetic dissimilarity of gut microbiome composition among the three groups (P < 0.001). The dysbiosis indexes were significantly higher in FRI group than in FH and HC groups (P < 0.001). The area under Receiver operating characteristic curve showed the characteristics of gut microbiota and the gut microbiota was found as effective in distinguishing the three groups. The dysbiosis in the FRI patients was associated with systemic inflammatory factors. In addition, significant differences in the gut microbiota were not observed between the FRI patients versus without sinus tract or pus before operation. Since FRI patients, with or without sinus tract or pus, have a characteristic profile of gut microbiota, their gut microbiota may be used as an auxiliary diagnostic tool for suspected FRI.
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Affiliation(s)
- Xingqi Zhao
- Division of Orthopaedics and Traumatology, Department of Orthopaedics, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Bone and Cartilage Regenerative Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Wenli Tang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Haoyang Wan
- Division of Orthopaedics and Traumatology, Department of Orthopaedics, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Bone and Cartilage Regenerative Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zixin Lan
- The Second Clinical Medical College, Southern Medical University, Guangzhou, China
| | - Hanjun Qin
- Division of Orthopaedics and Traumatology, Department of Orthopaedics, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Bone and Cartilage Regenerative Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Qingrong Lin
- Division of Orthopaedics and Traumatology, Department of Orthopaedics, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Bone and Cartilage Regenerative Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yanjun Hu
- Division of Orthopaedics and Traumatology, Department of Orthopaedics, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Bone and Cartilage Regenerative Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Guangchuang Yu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- *Correspondence: Guangchuang Yu,
| | - Nan Jiang
- Division of Orthopaedics and Traumatology, Department of Orthopaedics, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Bone and Cartilage Regenerative Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Nan Jiang,
| | - Bin Yu
- Division of Orthopaedics and Traumatology, Department of Orthopaedics, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Bone and Cartilage Regenerative Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Bin Yu,
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McPherson EJ, Dipane MV, Chowdhry M, Wassef AJ. Fabrication of antibiotic-loaded dissolvable calcium sulfate beads: an in vitro mixing lab utilizing various antibiotic mixing formulas. J Bone Jt Infect 2021; 6:405-412. [PMID: 34804775 PMCID: PMC8600463 DOI: 10.5194/jbji-6-405-2021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 10/25/2021] [Indexed: 11/11/2022] Open
Abstract
Chronic periprosthetic joint infection (PJI) is a devastating
complication that requires an aggressive eradication protocol. Local
antimicrobial delivery via dissolvable calcium sulfate (CaSO4) using
small-sized beads (3–8 mm) has been utilized as an adjunctive treatment
combined with implant exchange, radical debridement, and antimicrobial
loaded acrylic spacers. The non-exothermic setting of CaSO4 theoretically allows for any antimicrobial agent to be used, so long as
mixing methods provide a consistent fabrication within a reasonable set
time. This study performed the first in vitro mixing study, in which various
antimicrobial agents, used singularly and in combination, were mixed with a
synthetic CaSO4 product to observe and document their interactions. The
study was performed in a simulated operating room environment. We report a
standard mix formula with set times, testing 22 different antimicrobial
agents, combinations, and doses. For some antimicrobials and combinations,
set times using the standard formula were either too fast or exceedingly
slow. For these 14 antimicrobial agents and combinations, we were able to
arrive at individualized mixing methods. We present all mixing formulas and
set times. In all, we were able to establish mixing methods that incorporate
all antimicrobial agents and combinations that we have seen utilized via
surgeon-directed use.
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Affiliation(s)
- Edward J McPherson
- Department of Orthopaedic Surgery, David Geffen School of Medicine at UCLA, Santa Monica, 90404, USA
| | - Matthew V Dipane
- Department of Orthopaedic Surgery, David Geffen School of Medicine at UCLA, Santa Monica, 90404, USA
| | | | - Andrew J Wassef
- Long Beach Lakewood Orthopedic Institute, Long Beach, 90808, USA
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Impact of Antibiotic Therapies on Resistance Genes Dynamic and Composition of the Animal Gut Microbiota. Animals (Basel) 2021; 11:ani11113280. [PMID: 34828011 PMCID: PMC8614244 DOI: 10.3390/ani11113280] [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: 10/10/2021] [Revised: 11/03/2021] [Accepted: 11/11/2021] [Indexed: 11/16/2022] Open
Abstract
Antibiotics are major disruptors of the gastrointestinal microbiota, depleting bacterial species beneficial for the host health and favoring the emergence of potential pathogens. Furthermore, the intestine is a reactor of antibiotic resistance emergence, and the presence of antibiotics exacerbates the selection of resistant bacteria that can disseminate in the environment and propagate to further hosts. We reviewed studies analyzing the effect of antibiotics on the intestinal microbiota and antibiotic resistance conducted on animals, focusing on the main food-producing and companion animals. Irrespective of antibiotic classes and animal hosts, therapeutic dosage decreased species diversity and richness favoring the bloom of potential enteropathogens and the selection of antibiotic resistance. These negative effects of antibiotic therapies seem ineluctable but often were mitigated when an antibiotic was administered by parenteral route. Sub-therapeutic dosages caused the augmentation of taxa involved in sugar metabolism, suggesting a link with weight gain. This result should not be interpreted positively, considering that parallel information on antibiotic resistance selection was rarely reported and selection of antibiotic resistance is known to occur also at low antibiotic concentration. However, studies on the effect of antibiotics as growth promoters put the basis for understanding the gut microbiota composition and function in this situation. This knowledge could inspire alternative strategies to antibiotics, such as probiotics, for improving animal performance. This review encompasses the analysis of the main animal hosts and all antibiotic classes, and highlights the future challenges and gaps of knowledge that should be filled. Further studies are necessary for elucidating pharmacodynamics in animals in order to improve therapy duration, antibiotic dosages, and administration routes for mitigating negative effects of antibiotic therapies. Furthermore, this review highlights that studies on aminoglycosides are almost inexistent, and they should be increased, considering that aminoglycosides are the first most commonly used antibiotic family in companion animals. Harmonization of experimental procedures is necessary in this research field. In fact, current studies are based on different experimental set-up varying for antibiotic dosage, regimen, administration, and downstream microbiota analysis. In the future, shotgun metagenomics coupled with long-reads sequencing should become a standard experimental approach enabling to gather comprehensive knowledge on GIM in terms of composition and taxonomic functions, and of ARGs. Decorticating GIM in animals will unveil revolutionary strategies for medication and improvement of animals' health status, with positive consequences on global health.
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