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Panzer JJ, Maples C, Meyer MP, Tillotson G, Theis KR, Chopra T. Gut microbiome alpha diversity decreases in relation to body weight, antibiotic exposure, and infection with multidrug-resistant organisms. Am J Infect Control 2024; 52:707-711. [PMID: 38176539 DOI: 10.1016/j.ajic.2023.12.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/23/2023] [Accepted: 12/27/2023] [Indexed: 01/06/2024]
Abstract
BACKGROUND The human gastrointestinal tract is home to a dense and diverse microbiome, predominated by bacteria. Despite the conservation of critical functionality across most individuals, the composition of the gut microbiome is highly individualized, leading to differential responses to perturbations such as oral antibiotics or multidrug-resistant organism (MDRO) infection. Herein, subject responses to these perturbations based on their body weight were evaluated. METHODS Fecal samples were collected from 45 subjects at the Detroit Medical Center to evaluate the effects of perturbations on subjects' gut microbiome composition. Bacterial profiling was completed using 16S rRNA gene sequencing. RESULTS Subjects with multiple MDROs, subjects weighing greater than 80 kg infected with MDRO E coli, and subjects weighing less than 80 kg with exposure to vancomycin and carbapenem antibiotics during hospitalization had significantly decreased gut microbiome richness. CONCLUSIONS Both administration of oral antibiotics and MDRO infections decreased gut microbiome alpha diversity, but the magnitude of these gut microbiome perturbations was body weight dependent.
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Affiliation(s)
- Jonathan J Panzer
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI
| | - Catherine Maples
- Department of Infectious Diseases, Wayne State University, Detroit, MI
| | | | | | - Kevin R Theis
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI.
| | - Teena Chopra
- Department of Infectious Diseases, Wayne State University, Detroit, MI.
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2
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Brar NK, Dhariwal A, Åmdal HA, Junges R, Salvadori G, Baker JL, Edlund A, Petersen FC. Exploring ex vivo biofilm dynamics: consequences of low ampicillin concentrations on the human oral microbiome. NPJ Biofilms Microbiomes 2024; 10:37. [PMID: 38565843 PMCID: PMC10987642 DOI: 10.1038/s41522-024-00507-7] [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: 08/28/2023] [Accepted: 03/20/2024] [Indexed: 04/04/2024] Open
Abstract
Prolonged exposure to antibiotics at low concentration can promote processes associated with bacterial biofilm formation, virulence and antibiotic resistance. This can be of high relevance in microbial communities like the oral microbiome, where commensals and pathogens share a common habitat and where the total abundance of antibiotic resistance genes surpasses the abundance in the gut. Here, we used an ex vivo model of human oral biofilms to investigate the impact of ampicillin on biofilm viability. The ecological impact on the microbiome and resistome was investigated using shotgun metagenomics. The results showed that low concentrations promoted significant shifts in microbial taxonomic profile and could enhance biofilm viability by up to 1 to 2-log. For the resistome, low concentrations had no significant impact on antibiotic resistance gene (ARG) diversity, while ARG abundance decreased by up to 84%. A positive correlation was observed between reduced microbial diversity and reduced ARG abundance. The WHO priority pathogens Streptococcus pneumoniae and Staphylococcus aureus were identified in some of the samples, but their abundance was not significantly altered by ampicillin. Most of the antibiotic resistance genes that increased in abundance in the ampicillin group were associated with streptococci, including Streptococcus mitis, a well-known potential donor of ARGs to S. pneumoniae. Overall, the results highlight the potential of using the model to further our understanding of ecological and evolutionary forces driving antimicrobial resistance in oral microbiomes.
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Affiliation(s)
- N K Brar
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - A Dhariwal
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - H A Åmdal
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - R Junges
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - G Salvadori
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - J L Baker
- Department of Oral Rehabilitation & Biosciences, Oregon Health & Science University, Portland, OR, USA
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, USA
- Department of Pediatrics, UC San Diego School of Medicine, La Jolla, CA, USA
| | - A Edlund
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, USA
- Department of Pediatrics, UC San Diego School of Medicine, La Jolla, CA, USA
| | - F C Petersen
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway.
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Wang D, Zeng J, Wujin C, Ullah Q, Su Z. Lactobacillus reuteri derived from horse alleviates Escherichia coli-induced diarrhea by modulating gut microbiota. Microb Pathog 2024; 188:106541. [PMID: 38224920 DOI: 10.1016/j.micpath.2024.106541] [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: 11/10/2023] [Revised: 12/31/2023] [Accepted: 01/08/2024] [Indexed: 01/17/2024]
Abstract
Diarrhea is a prevalent health issue in farm animals and poses a significant challenge to the progress of animal husbandry. Recent evidence suggested that probiotics can alleviate diarrhea by maintaining gut microbial balance and enhancing the integrity of the intestinal barrier. However, there is a scarcity of studies investigating the efficacy of equine Lactobacillus reuteri in relieving E. coli-induced diarrhea. Hence, this study aimed to examine the potential of equine-derived Lactobacillus reuteri in alleviating E. coli diarrhea from the perspective of gut microbiota. Results demonstrated that supplementation of Lactobacillus reuteri had the potential to alleviate diarrhea induced by E. coli infection and restore the decline of tight junction genes, such as Claudin-1 and ZO-1. Additionally, Lactobacillus reuteri supplementation can restore the expression of inflammatory factors (IL-6, IL-10, TNF-α, and IFN-γ) and reduce colon inflammatory damage. Diversity analysis, based on amplicon sequencing, revealed a significant reduction in the diversity of gut microbiota during E. coli-induced diarrhea. Moreover, there were notable statistical differences in the composition and structure of gut microbiota among the different treatment groups. E. coli could induce gut microbial dysbiosis by decreasing the abundance of beneficial bacteria, including Lactobacillus, Bifidobacterium, Ligilactobacillus, Enterorhabdus, and Lachnospiraceae_UCG_001, in comparison to the control group. Conversely, supplementation with Lactobacillus reuteri could restore the abundance of beneficial bacteria and increase the diversity of the gut microbiota, thereby reshaping gut microbiota. Additionally, we also observed that supplementation with Lactobacillus reuteri alone improved the gut microbial composition and structure. In summary, the findings suggest that Lactobacillus reuteri can alleviate E. coli-induced diarrhea by preserving the integrity of the intestinal barrier and modulating the composition of the gut microbiota. These results not only contribute to understanding of the mechanism underlying the beneficial effects of Lactobacillus reuteri in relieving diarrhea, but also provide valuable insights for the development of probiotic products aimed at alleviating diarrheal diseases.
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Affiliation(s)
- Dongjing Wang
- Institute of Animal Husbandry and Veterinary, Tibet Autonomous Region Academy of Agricultural Sciences, Lhasa, Tibet, 850009, China
| | - Jiangyong Zeng
- Institute of Animal Husbandry and Veterinary, Tibet Autonomous Region Academy of Agricultural Sciences, Lhasa, Tibet, 850009, China
| | - Cuomu Wujin
- Institute of Animal Husbandry and Veterinary, Tibet Autonomous Region Academy of Agricultural Sciences, Lhasa, Tibet, 850009, China
| | - Qudrat Ullah
- Department of Theriogenology, Faculty of Veterinary and Animal Sciences, The University of Agriculture, Dera Ismail Khan, 29111, Pakistan
| | - Zhonghua Su
- Tibet Autonomous Region Animal Disease Prevention and Control Center, Lhasa, Tibet, 850009, China.
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4
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Alvarez-Zapata M, Franco-Vega A, Rondero AG, Guerra RS, Flores BIJ, Comas-García M, Ovalle CO, Schneider B, Ratering S, Schnell S, Martinez-Gutierrez F. Modulation of the Altered Intestinal Microbiota by Use of Antibiotics with a Novel Synbiotic on Wistar Rats. Probiotics Antimicrob Proteins 2023:10.1007/s12602-023-10204-0. [PMID: 38127241 DOI: 10.1007/s12602-023-10204-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2023] [Indexed: 12/23/2023]
Abstract
The use of antibiotics unbalances the intestinal microbiota. Probiotics, prebiotics, and synbiotics are alternatives for these unbalances. The effects of a new synbiotic composed of probiotic Saccharomyces boulardii CNCM I-745 and fructans from Agave salmiana (fAs) as prebiotics were assessed to modulate the intestinal microbiota. Two probiotic presentations, the commercial probiotic (CP) and the microencapsulated probiotic (MP) to improve those effects, were used to prepare the synbiotics and feed Wistar rats subjected to antibiotics (AB). Eight groups were studied, including five controls and three groups to modulate the microbiota after the use of antibiotics: G5: AB + MP-synbiotic, G6: AB + CP-synbiotic, and G8: AB + fAs. All treatments were administered daily for 7 days. On days 7 and 21, euthanasia was performed, cecum tissue was recovered and used to evaluate histological analysis and to study microphotograph by TEM, and finally, bacterial DNA was extracted and 16S rRNA gene metabarcode sequencing was performed. Histological analysis showed less epithelial damage and more abundance of the intestinal microbiota in the groups G5, G6, and G8 in comparison with the AB control group after 7 days. Microphotograph of the cecum at 2 weeks post treatment showed that G5 and G6 presented beneficial effects in epithelial reconstruction. Interestingly, in the groups that used the synbiotic without AB (G3 and G4) in addition to contributing to the recovery of the autochthonous microbiota, it promotes the development of beneficial microorganisms; those results were also achieved in the groups that used the synbiotic with AB enhancing the bacterial diversity and regulating the impact of AB.
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Affiliation(s)
- Miguel Alvarez-Zapata
- Laboratorio de Antimicrobianos, Biopelículas y Microbiota, Facultad de Ciencias Químicas, U.A.S.L.P., Av. Dr. Manuel Nava No. 6 Zona Universitaria, CP 78210, San Luis Potosí, S.L.P., México
| | - Avelina Franco-Vega
- Laboratorio de Tecnologías Emergentes, Facultad de Ciencias Químicas, U.A.S.L.P., San Luis Potosí, México
| | - Adriana Ganem Rondero
- Laboratorio de Investigación y Posgrado en Tecnología Farmacéutica (L-322), Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Mexico City, Estado de México, México
| | - Ruth Soria Guerra
- Laboratorio de Biotecnología de plantas, Facultad de Ciencias Químicas, U.A.S.L.P., San Luis Potosí, México
| | | | - Mauricio Comas-García
- Sección de Genómica Médica, Centro de Investigación en Biomedicina y Salud, U.A.S.L.P., San Luis Potosí, México
- Sección de Microscopía de Alta Resolución, Centro de Investigación en Biomedicina y Salud, U.A.S.L.P., San Luis Potosí, Mexico
- Facultad de Ciencias, U.A.S.L.P., San Luis Potosi, Mexico
| | | | - Belinda Schneider
- Institute of Applied Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Stefan Ratering
- Institute of Applied Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Fidel Martinez-Gutierrez
- Laboratorio de Antimicrobianos, Biopelículas y Microbiota, Facultad de Ciencias Químicas, U.A.S.L.P., Av. Dr. Manuel Nava No. 6 Zona Universitaria, CP 78210, San Luis Potosí, S.L.P., México.
- Sección de Genómica Médica, Centro de Investigación en Biomedicina y Salud, U.A.S.L.P., San Luis Potosí, México.
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Shahin M, Ji B, Dixit PD. EMBED: Essential MicroBiomE Dynamics, a dimensionality reduction approach for longitudinal microbiome studies. NPJ Syst Biol Appl 2023; 9:26. [PMID: 37339950 PMCID: PMC10282069 DOI: 10.1038/s41540-023-00285-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 05/23/2023] [Indexed: 06/22/2023] Open
Abstract
Dimensionality reduction offers unique insights into high-dimensional microbiome dynamics by leveraging collective abundance fluctuations of multiple bacteria driven by similar ecological perturbations. However, methods providing lower-dimensional representations of microbiome dynamics both at the community and individual taxa levels are not currently available. To that end, we present EMBED: Essential MicroBiomE Dynamics, a probabilistic nonlinear tensor factorization approach. Like normal mode analysis in structural biophysics, EMBED infers ecological normal modes (ECNs), which represent the unique orthogonal modes capturing the collective behavior of microbial communities. Using multiple real and synthetic datasets, we show that a very small number of ECNs can accurately approximate microbiome dynamics. Inferred ECNs reflect specific ecological behaviors, providing natural templates along which the dynamics of individual bacteria may be partitioned. Moreover, the multi-subject treatment in EMBED systematically identifies subject-specific and universal abundance dynamics that are not detected by traditional approaches. Collectively, these results highlight the utility of EMBED as a versatile dimensionality reduction tool for studies of microbiome dynamics.
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Affiliation(s)
- Mayar Shahin
- Department of Physics, University of Florida, Gainesville, FL, 32611, USA.
| | - Brian Ji
- Physician-Scientist Training Pathway, Department of Medicine, UCSD, San Diego, CA, 92103, USA
| | - Purushottam D Dixit
- Department of Physics, University of Florida, Gainesville, FL, 32611, USA.
- Genetics Institute, University of Florida, Gainesville, FL, 32611, USA.
- Department of Chemical Engineering, University of Florida, Gainesville, FL, 32611, USA.
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06511, USA.
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6
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Yu J, Guo Z, Yan J, Bu C, Peng C, Li C, Mao R, Zhang J, Wang Z, Chen S, Yao M, Xie Z, Yang C, Yang YY, Yuan P, Ding X. Gastric Acid-Responsive ROS Nanogenerators for Effective Treatment of Helicobacter pylori Infection without Disrupting Homeostasis of Intestinal Flora. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023:e2206957. [PMID: 37127895 PMCID: PMC10369278 DOI: 10.1002/advs.202206957] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 04/15/2023] [Indexed: 05/03/2023]
Abstract
Helicobacter pylori (H. pylori) has infected more than half of the world's population, and is the major cause of gastric cancer. The efficacy of standard antibiotic-based triple therapy is declining due to drug resistance development. Herein, a pH-responsive reactive oxygen species (ROS) nanogenerator (Fe-HMME@DHA@MPN) composed of acid-responsive metal polyphenol network (MPN) shell and mesoporous metal-organic nanostructure core [Fe-HMME (hematoporphyrin monomethyl ether, sonosensitizer)] loaded with dihydroartemisinin (DHA) is reported. These nanoparticles generate more ROS singlet oxygen than sonosensitizer HMME under ultrasonication, and this sonodynamic process is fueled by oxygen generated through Fenton/Fenton-like reactions of the degraded product in gastric acid Fe (II) and hydrogen peroxide (H2 O2 ) in the infection microenvironment. The encapsulated DHA, as a hydroperoxide source, is found to enhance the peroxidase-like activity of the Fe-HMME@DHA@MPN to generate ROS hydroxyl radical, beneficial for the microenvironment without sufficient H2 O2 . In vitro experiments demonstrate that the ROS nanogenerators are capable of killing multidrug-resistant H. pylori and removing biofilm, and ROS nanogenerators show high therapeutic efficacy in a H. pylori infection mouse model. Unlike the triple therapy, the nanogenerators display negligible side effects toward the normal gut microbiota. Taken together, these self-enhanced ROS nanogenerators have a great potential for treatment of H. pylori infection.
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Affiliation(s)
- Jiayin Yu
- School of Pharmaceutical Science (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, P. R. China
| | - Zhihao Guo
- School of Pharmaceutical Science (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, P. R. China
| | - Jiachang Yan
- School of Pharmaceutical Science (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, P. R. China
| | - Changxin Bu
- School of Pharmaceutical Science (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, P. R. China
| | - Chang Peng
- School of Pharmaceutical Science (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, P. R. China
| | - Cuie Li
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Science, 190 Kaiyuan Avenue, Guangzhou Science Park, Luogang District, Guangzhou, 510080, P. R. China
| | - Rui Mao
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Science, 190 Kaiyuan Avenue, Guangzhou Science Park, Luogang District, Guangzhou, 510080, P. R. China
| | - Jian Zhang
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Science, 190 Kaiyuan Avenue, Guangzhou Science Park, Luogang District, Guangzhou, 510080, P. R. China
| | - Zhi Wang
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Science, 190 Kaiyuan Avenue, Guangzhou Science Park, Luogang District, Guangzhou, 510080, P. R. China
| | - Shi Chen
- The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510655, P. R. China
| | - Meicun Yao
- School of Pharmaceutical Science (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, P. R. China
| | - Zhiyong Xie
- School of Pharmaceutical Science (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, P. R. China
| | - Chuan Yang
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, Centros #06-01, Singapore, 138668, Singapore
| | - Yi Yan Yang
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, Centros #06-01, Singapore, 138668, Singapore
- Department of Orthopaedic Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119288, Singapore
| | - Peiyan Yuan
- School of Pharmaceutical Science (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, P. R. China
| | - Xin Ding
- School of Pharmaceutical Science (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, P. R. China
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D'Achille G, Morroni G. Side effects of antibiotics and perturbations of mitochondria functions. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2023; 377:121-139. [PMID: 37268348 DOI: 10.1016/bs.ircmb.2023.03.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Antibiotics are one of the greatest discoveries of medicine of the past century. Despite their invaluable contribution to infectious disease, their administration could lead to side effects that in some cases are serious. The toxicity of some antibiotics is in part due to their interaction with mitochondria: these organelles derive from a bacterial ancestor and possess specific translation machinery that shares similarities with the bacterial counterpart. In other cases, the antibiotics could interfere with mitochondrial functions even if their main bacterial targets are not shared with the eukaryotic cells. The purpose of this review is to summarize the effects of antibiotics administration on mitochondrial homeostasis and the opportunity that some of these molecules could represent in cancer treatment. The importance of antimicrobial therapy is unquestionable, but the identification of interaction with eukaryotic cells and in particular with mitochondria is crucial to reduce the toxicity of these drugs and to explore other useful medical applications.
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Affiliation(s)
- Gloria D'Achille
- Microbiology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy
| | - Gianluca Morroni
- Microbiology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy.
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Xu Z, Wu X, Zhang J, Cheng P, Xu Z, Sun W, Zhong Y, Wang Y, Yu G, Liu H. Microplastics existence intensified bloom of antibiotic resistance in livestock feces transformed by black soldier fly. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 317:120845. [PMID: 36496063 DOI: 10.1016/j.envpol.2022.120845] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/27/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
Efficient degradation of residual antibiotics in livestock and poultry feces by black soldier flies (BSFs) has been widely reported. Nevertheless, the effects of widely detected microplastics in feces on the dynamic reduction of antibiotics and the transfer of gut bacterial resistome remain unclear. In this study, red fluorescence-labeled microplastics are observed to be abundantly distributed in BSFs gut, which caused epithelial cell damage along with gut peristalsis and friction, thereby releasing reactive oxygen species and activating the antioxidant enzyme system. In addition, they result in not only in inflammatory cytokine release to induce gut inflammation, but fecal hardening because of mucus released from the BSFs, thereby hindering organic mineralization and antibiotic degradation. Besides, the gut pathogenic bacteria easily obtain growth energy and crowded out ecological niches by reducing nitrate produced by inflammatory host cells to nitrite with nitrate reductase. Consequently, linear discriminant analysis effect size and detrended correspondence analysis found that microplastic intake significantly reshape the microbial community structure and cause the significant reduction of several important organic-decomposing bacteria and probiotics (e.g., Pseudomonadales, Coriobacteriales, Lachnospirales, and Ruminococcaceae). In addition, a large number of pathogenic bacteria (e.g., Enterococcaceae, Hungateiclostridiaceae, and Clostridia) are enriched in feces and BSFs gut. Weighted correlation network analysis and bubble diagram analysis indicate that microplastic intake intensified gut colonization of pathogenic bacteria carrying antibiotic-resistant genes/mobile genetic elements, driving the bloom of antibiotic resistance in transformed fecal piles. Therefore, microplastics in feces should be isolated as much as possible before insect transformation.
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Affiliation(s)
- Zhimin Xu
- College of Resources and Environment, Innovative Institute of Animal Healthy Breeding, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China; Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Xinyue Wu
- College of Resources and Environment, Innovative Institute of Animal Healthy Breeding, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Jiexiang Zhang
- Guangzhou Radio & TV Measurement & Testing Co., Ltd., Guangzhou, 510656, China
| | - Ping Cheng
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Zhihao Xu
- Department of Public Health and Preventive Medicine, School of Medicine, Jinggangshan University, Jian, 343009, China
| | - Weimin Sun
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management Institute of Environmental and Soil Sciences, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Yuming Zhong
- College of Resources and Environment, Innovative Institute of Animal Healthy Breeding, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Yifan Wang
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Guohui Yu
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China.
| | - Hui Liu
- College of Resources and Environment, Innovative Institute of Animal Healthy Breeding, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
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9
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Advances in Lactobacillus Restoration for β-Lactam Antibiotic-Induced Dysbiosis: A System Review in Intestinal Microbiota and Immune Homeostasis. Microorganisms 2023; 11:microorganisms11010179. [PMID: 36677471 PMCID: PMC9861108 DOI: 10.3390/microorganisms11010179] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/13/2023] Open
Abstract
A balanced gut microbiota and their metabolites are necessary for the maintenance of the host's health. The antibiotic-induced dysbiosis can cause the disturbance of the microbial community, influence the immune homeostasis and induce susceptibility to metabolic- or immune-mediated disorders and diseases. The Lactobacillus and their metabolites or components affect the function of the host's immune system and result in microbiota-mediated restoration. Recent data have indicated that, by altering the composition and functions of gut microbiota, antibiotic exposure can also lead to a number of specific pathologies, hence, understanding the potential mechanisms of the interactions between gut microbiota dysbiosis and immunological homeostasis is very important. The Lactobacillus strategies for detecting the associations between the restoration of the relatively imbalanced microbiome and gut diseases are provided in this discussion. In this review, we discuss the recently discovered connections between microbial communities and metabolites in the Lactobacillus treatment of β-lactam antibiotic-induced dysbiosis, and establish the relationship between commensal bacteria and host immunity under this imbalanced homeostasis of the gut microbiota.
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10
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Zhang YW, Cao MM, Li YJ, Zhang RL, Wu MT, Yu Q, Rui YF. Fecal microbiota transplantation as a promising treatment option for osteoporosis. J Bone Miner Metab 2022; 40:874-889. [PMID: 36357745 PMCID: PMC9649400 DOI: 10.1007/s00774-022-01375-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 10/04/2022] [Indexed: 11/12/2022]
Abstract
Osteoporosis is a systemic metabolic bone disease characterized by the descending bone mass and destruction of bone microstructure, which tends to result in the increased bone fragility and associated fractures, as well as high disability rate and mortality. The relation between gut microbiota and bone metabolism has gradually become a research hotspot, and it has been verified that gut microbiota is closely associated with reduction of bone mass and incidence of osteoporosis recently. As a novel "organ transplantation" technique, fecal microbiota transplantation (FMT) mainly refers to the transplantation of gut microbiota from healthy donors to recipients with gut microbiota imbalance, so that the gut microbiota in recipients can be reshaped and play a normal function, and further prevent or treat the diseases related to gut microbiota disorder. Herein, based on the gut-bone axis and proven regulatory effects of gut microbiota on osteoporosis, this review expounds relevant basic researches and clinical practice of FMT on osteoporosis, thus demonstrating the potentials of FMT as a therapeutic option for osteoporosis and further providing certain reference for the future researches.
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Affiliation(s)
- Yuan-Wei Zhang
- Department of Orthopaedics, Zhongda Hospital, School of Medicine, Southeast University, No. 87 Ding Jia Qiao, Nanjing, 210009, Jiangsu, People's Republic of China
- Multidisciplinary Team (MDT) for Geriatric Hip Fracture Management, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu, People's Republic of China
- School of Medicine, Southeast University, Nanjing, Jiangsu, People's Republic of China
- Orthopaedic Trauma Institute (OTI), Southeast University, Nanjing, Jiangsu, People's Republic of China
| | - Mu-Min Cao
- Department of Orthopaedics, Zhongda Hospital, School of Medicine, Southeast University, No. 87 Ding Jia Qiao, Nanjing, 210009, Jiangsu, People's Republic of China
- Multidisciplinary Team (MDT) for Geriatric Hip Fracture Management, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu, People's Republic of China
- School of Medicine, Southeast University, Nanjing, Jiangsu, People's Republic of China
- Orthopaedic Trauma Institute (OTI), Southeast University, Nanjing, Jiangsu, People's Republic of China
| | - Ying-Juan Li
- Multidisciplinary Team (MDT) for Geriatric Hip Fracture Management, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu, People's Republic of China
- Department of Geriatrics, School of Medicine, Zhongda Hospital, Southeast University, Nanjing, Jiangsu, People's Republic of China
| | - Ruo-Lan Zhang
- School of Medicine, Southeast University, Nanjing, Jiangsu, People's Republic of China
| | - Meng-Ting Wu
- School of Medicine, Southeast University, Nanjing, Jiangsu, People's Republic of China
| | - Qian Yu
- Multidisciplinary Team (MDT) for Geriatric Hip Fracture Management, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu, People's Republic of China
- Department of Gastroenterology, School of Medicine, Zhongda Hospital, Southeast University, Nanjing, Jiangsu, People's Republic of China
| | - Yun-Feng Rui
- Department of Orthopaedics, Zhongda Hospital, School of Medicine, Southeast University, No. 87 Ding Jia Qiao, Nanjing, 210009, Jiangsu, People's Republic of China.
- Multidisciplinary Team (MDT) for Geriatric Hip Fracture Management, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu, People's Republic of China.
- School of Medicine, Southeast University, Nanjing, Jiangsu, People's Republic of China.
- Orthopaedic Trauma Institute (OTI), Southeast University, Nanjing, Jiangsu, People's Republic of China.
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11
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Exposure to Veterinary Antibiotics via Food Chain Disrupts Gut Microbiota and Drives Increased Escherichia coli Virulence and Drug Resistance in Young Adults. Pathogens 2022; 11:pathogens11091062. [PMID: 36145494 PMCID: PMC9500718 DOI: 10.3390/pathogens11091062] [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: 07/01/2022] [Revised: 08/15/2022] [Accepted: 09/14/2022] [Indexed: 11/17/2022] Open
Abstract
Exposure to veterinary antibiotics (VAs) and preferred as veterinary antibiotics (PVAs) via the food chain is unavoidable for their extensive use not only for treating bacterial infections, but also for use as growth promoters in livestock and aquaculture. One of the consequences is the disturbance of gut microbiota. However, its impact on the virulence and drug resistance of opportunistic pathogens is still unclear. In this study, a total of 26 antibiotics were detected in the urine of 300 young undergraduates in Anhui Province. We found that excessive intake of milk was positively correlated to high levels of VAs and PVAs. It led to the dysbiosis of gut microbiota characterized by high abundance of Bacteroidetes and Proteobacteria. The increase in Proteobacteria was mainly due to a single operational taxonomic unit (OTU) of Escherichia coli (E. coli). We isolated several E. coli strains from participants and compared their drug resistance and virulence using PCR assay and virulence-related assays. We observed that exposure to high levels of VAs and PVAs induced more resistant genes and drove E. coli strain to become more virulent. At last, we conducted transcriptome analysis to investigate the molecular mechanism of virulent and drug-resistant regulators in the highly virulent E. coli strain. We noted that there were multiple pathways involved in the drug resistance and virulence of the highly virulent strain. Our results demonstrated that participants with high-level VAs and PVAs exposure have a disrupted gut microbiota following the appearance of highly drug-resistant and virulent E. coli and, therefore may be at elevated risk for long-term health complications.
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12
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Sumithra TG, Sharma KSR, Gangadharan S, Suresh G, Prasad V, Amala PV, Sayooj P, Gop AP, Anil MK, Patil PK, Achamveetil G. Dysbiosis and Restoration Dynamics of the Gut Microbiome Following Therapeutic Exposure to Florfenicol in Snubnose Pompano (Trachinotus blochii) to Aid in Sustainable Aquaculture Production Strategies. Front Microbiol 2022; 13:881275. [PMID: 35707172 PMCID: PMC9189426 DOI: 10.3389/fmicb.2022.881275] [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: 02/22/2022] [Accepted: 03/30/2022] [Indexed: 11/13/2022] Open
Abstract
Information on unintended effects of therapeutic exposure of antibiotics on the fish gut microbiome is a vital prerequisite for ensuring fish and environmental health during sustainable aquaculture production strategies. The present study forms the first report on the impact of florfenicol (FFC), a recommended antibiotic for aquaculture, on the gut microbiome of snubnose pompano (Trachinotus blochii), a high-value marine aquaculture candidate. Both culture-dependent and independent techniques were applied to identify the possible dysbiosis and restoration dynamics, pointing out the probable risks to the host and environment health. The results revealed the critical transient dysbiotic events in the taxonomic and functional metagenomic profiles and significant reductions in the bacterial load and diversity measures. More importantly, there was a complete restoration of gut microbiome density, diversity, functional metagenomic profiles, and taxonomic composition (up to class level) within 10–15 days of antibiotic withdrawal, establishing the required period for applying proper management measures to ensure animal and environment health, following FFC treatment. The observed transient increase in the relative abundance of opportunistic pathogens suggested the need to apply proper stress management measures and probiotics during the period. Simultaneously, the results demonstrated the inhibitory potential of FFC against marine pathogens (vibrios) and ampicillin-resistant microbes. The study pointed out the possible microbial signatures of stress in fish and possible probiotic microbes (Serratia sp., Methanobrevibacter sp., Acinetobacter sp., and Bacillus sp.) that can be explored to design fish health improvisation strategies. Strikingly, the therapeutic exposure of FFC neither caused any irreversible increase in antibiotic resistance nor promoted the FFC resistant microbes in the gut. The significant transient increase in the numbers of kanamycin-resistant bacteria and abundance of two multidrug resistance encoding genes (K03327 and K03585) in the treated fish gut during the initial 10 days post-withdrawal suggested the need for implementing proper aquaculture effluent processing measures during the period, thus, helps to reduce the spillover of antibiotic-resistant microbes from the gut of the treated fish to the environment. In brief, the paper generates interesting and first-hand insights on the implications of FFC treatment in the gut microbiome of a marine aquaculture candidate targeting its safe and efficient application in unavoidable circumstances. Implementation of mitigation strategies against the identified risks during the initial 15 days of withdrawal period is warranted to ensure cleaner and sustainable aquaculture production from aquatic animal and ecosystem health perspectives.
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Affiliation(s)
- T. G. Sumithra
- Marine Biotechnology Division, Indian Council of Agricultural Research (ICAR)-Central Marine Fisheries Research Institute, Kochi, India
| | - Krupesha S. R. Sharma
- Marine Biotechnology Division, Indian Council of Agricultural Research (ICAR)-Central Marine Fisheries Research Institute, Kochi, India
- *Correspondence: Krupesha S. R. Sharma,
| | - Suja Gangadharan
- Marine Biotechnology Division, Indian Council of Agricultural Research (ICAR)-Central Marine Fisheries Research Institute, Kochi, India
| | - Gayathri Suresh
- Marine Biotechnology Division, Indian Council of Agricultural Research (ICAR)-Central Marine Fisheries Research Institute, Kochi, India
| | - Vishnu Prasad
- Marine Biotechnology Division, Indian Council of Agricultural Research (ICAR)-Central Marine Fisheries Research Institute, Kochi, India
| | - P. V. Amala
- Marine Biotechnology Division, Indian Council of Agricultural Research (ICAR)-Central Marine Fisheries Research Institute, Kochi, India
| | - P. Sayooj
- Marine Biotechnology Division, Indian Council of Agricultural Research (ICAR)-Central Marine Fisheries Research Institute, Kochi, India
| | - Ambarish P. Gop
- Vizhinjam Regional Centre of ICAR-Central Marine Fisheries Research Institute, Thiruvananthapuram, India
| | - M. K. Anil
- Vizhinjam Regional Centre of ICAR-Central Marine Fisheries Research Institute, Thiruvananthapuram, India
| | - Prasanna Kumar Patil
- Aquatic Animal Health and Environment Division, ICAR-Central Institute of Brackishwater Aquaculture, Chennai, India
| | - Gopalakrishnan Achamveetil
- Marine Biotechnology Division, Indian Council of Agricultural Research (ICAR)-Central Marine Fisheries Research Institute, Kochi, India
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13
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Jeffery IB, Cotter PD, Scanlan PD. Collateral Damage in the Human Gut Microbiome - Blastocystis Is Significantly Less Prevalent in an Antibiotic-Treated Adult Population Compared to Non-Antibiotic Treated Controls. Front Cell Infect Microbiol 2022; 12:822475. [PMID: 35281435 PMCID: PMC8913940 DOI: 10.3389/fcimb.2022.822475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/04/2022] [Indexed: 12/14/2022] Open
Abstract
Antibiotics can drive the rapid loss of non-target, phylogenetically diverse microorganisms that inhabit the human gut. This so-called “collateral damage” has myriad consequences for host health and antibiotic mediated changes to the gut microbiota have been implicated in the aetiology of many chronic diseases. To date, studies have largely focused on how antibiotics affect the bacterial fraction of the gut microbiome and their impact on non-bacterial members, including prevalent eukaryal species, such as Blastocystis, remains largely unknown. Here we assessed the prevalence and diversity of Blastocystis in an elderly adult group that were in receipt of antibiotics (n = 86) and an equivalent non-antibiotic treated group (n = 88) using a PCR-based approach. This analysis revealed that although similar subtypes were present in both groups, Blastocystis was significantly less prevalent in the antibiotic-treated group (16%) compared to non-antibiotic treated controls (55%); Fisher’s Exact test, p < 0.0001). Given that antibiotics target structures and molecules of prokaryotic cells to kill or inhibit bacterial populations, the most likely explanation for differences in prevalence between both groups is due to secondary extinctions owing to the potential dependence of Blastocystis on bacteria present in the gut microbiome that were negatively affected by antibiotic treatment. Although further work is required to explore this hypothesis in greater detail, these data clearly show that Blastocystis prevalence in human populations is negatively associated with antibiotic treatment. This finding may be relevant to explaining patterns of variation for this microorganism in different human populations and cohorts of interest.
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Affiliation(s)
- Ian B. Jeffery
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Paul D. Cotter
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
| | - Pauline D. Scanlan
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- *Correspondence: Pauline D. Scanlan,
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14
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Akbar S, Gu L, Sun Y, Zhang L, Lyu K, Huang Y, Yang Z. Understanding host-microbiome-environment interactions: Insights from Daphnia as a model organism. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 808:152093. [PMID: 34863741 DOI: 10.1016/j.scitotenv.2021.152093] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/21/2021] [Accepted: 11/27/2021] [Indexed: 06/13/2023]
Abstract
Microbes perform a variety of vital functions that are essential for healthy ecosystems, ranging from nutrient recycling, antibiotic production and waste decomposition. In many animals, microbes become an integral part by establishing diverse communities collectively termed as "microbiome/s". Microbiomes defend their hosts against pathogens and provide essential nutrients necessary for their growth and reproduction. The microbiome is a polygenic trait that is dependent on host genotype and environmental variables. However, the alteration of microbiomes by stressful condition and their recovery is still poorly understood. Despite rapid growth in host-associated microbiome studies, very little is known about how they can shape ecological processes. Here, we review current knowledge on the microbiome of Daphnia, its role in fitness, alteration by different stressors, and the ecological and evolutionary aspects of host microbiome interactions. We further discuss how variation in Daphnia physiology, life history traits, and microbiome interactive responses to biotic and abiotic factors could impact patterns of microbial diversity in the total environment, which drives ecosystem function in many freshwater environments. Our literature review provides evidence that microbiome is essential for Daphnia growth, reproduction and tolerance against stressors. Though the core and flexible microbiome of Daphnia is still debatable, it is clear that the Daphnia microbiome is highly dependent on interactions among host genotype, diet and the environment. Different environmental factors alter the microbiome composition and diversity of Daphnia and reduce their fitness. These interactions could have important implications in shaping microbial patterns and their recycling as Daphnia are keystone species in freshwater ecosystem. This review provides a framework for studying these complex relationships to gain a better understanding of the ecological and evolutionary roles of the microbiome.
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Affiliation(s)
- Siddiq Akbar
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Lei Gu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Yunfei Sun
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Lu Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Kai Lyu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Yuan Huang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China
| | - Zhou Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Biological Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210023, China.
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15
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Cabré S, Ratsika A, Rea K, Stanton C, Cryan JF. Animal Models for Assessing Impact of C-Section Delivery on Biological Systems. Neurosci Biobehav Rev 2022; 135:104555. [PMID: 35122781 DOI: 10.1016/j.neubiorev.2022.104555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 01/28/2022] [Accepted: 01/30/2022] [Indexed: 12/02/2022]
Abstract
There has been a significant increase in Caesarean section (C-section) births worldwide over the past two decades and although it is can be a life-saving procedure, the enduring effects on host physiology are now undergoing further scrutiny. Indeed, epidemiological data have linked C-section birth with multiple immune, metabolic and neuropsychiatric diseases. Birth by C-section is known to alter the colonisation of the neonatal gut microbiota (with C-section delivered infants lacking vaginal microbiota associated with passing along the birth canal), which in turn can impact the development and maintenance of many important biological systems. Appropriate animal models are key to disentangling the role of missing microbes in brain health and disease in C-section births. In this review of preclinical studies, we interrogate the effects of C-section birth on the development (and maintenance) of several biological systems and we discuss the involvement of the gut microbiome on C-section-related alterations.
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Affiliation(s)
- Sílvia Cabré
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Cork T12 YT20, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork T12 YT20, Ireland
| | - Anna Ratsika
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Cork T12 YT20, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork T12 YT20, Ireland
| | - Kieran Rea
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Cork T12 YT20, Ireland
| | - Catherine Stanton
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Cork T12 YT20, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork T12 YT20, Ireland; Teagasc Food Research Centre, Moorepark, Fermoy P61 C996, Ireland
| | - John F Cryan
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Cork T12 YT20, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork T12 YT20, Ireland.
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16
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Dynamic of the human gut microbiome under infectious diarrhea. Curr Opin Microbiol 2022; 66:79-85. [PMID: 35121284 DOI: 10.1016/j.mib.2022.01.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/06/2022] [Accepted: 01/11/2022] [Indexed: 11/20/2022]
Abstract
Despite the widespread implementation of sanitation, immunization and appropriate treatment, infectious diarrheal diseases still inflict a great health burden to children living in low resource settings. Conventional microbiology research in diarrhea have focused on the pathogen's biology and pathogenesis, but initial enteric infections could trigger subsequent perturbations in the gut microbiome, leading to short-term or long-term health effects. Conversely, such pre-existing perturbations could render children more vulnerable to enteropathogen colonization and diarrhea. Recent advances in DNA sequencing and bioinformatic analyses have been integrated in well-designed clinical and epidemiological studies, which allow us to track how the gut microbiome changes from disease onset to recovery. Here, we aim to summarize the current understanding on the diarrheal gut microbiome, stratified into different disease stages. Furthermore, we discuss how such perturbations could have impacts beyond an acute diarrhea episode, specifically on the child's nutritional status and the facilitation of antimicrobial resistance.
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17
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Isles NS, Mu A, Kwong JC, Howden BP, Stinear TP. Gut microbiome signatures and host colonization with multidrug-resistant bacteria. Trends Microbiol 2022; 30:853-865. [DOI: 10.1016/j.tim.2022.01.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 12/17/2022]
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18
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Evolution in a Community Context: towards Understanding the Causes and Consequences of Adaptive Evolution in the Human Gut Microbiota over Short Time Scales. mSystems 2021; 6:e0083221. [PMID: 34427532 PMCID: PMC8407120 DOI: 10.1128/msystems.00832-21] [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: 11/20/2022] Open
Abstract
How important is adaptive evolution to the unique diversity that we can observe for each individual human gut microbiome? How do gut microbes evolve in response to changes in their environment, and how does evolution in real time impact microbial functionality in the context of host health? My interdisciplinary research uses in vitro microcosm models to test how different abiotic and biotic factors impact microbial evolution in a community context. We complement this approach by tracking focal species as they evolve in real time and in their natural environment of the human gut. Our aim is to provide a better understanding of how the dynamics and outcomes of microbial evolution differ between individual gut environments, and in response to different selection pressures, so that we can move closer to rational gut microbiome treatments that promote host health and prevent and treat human disease.
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19
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Merenstein D, Fraser CM, Roberts RF, Liu T, Grant-Beurmann S, Tan TP, Smith KH, Cronin T, Martin OA, Sanders ME, Lucan SC, Kane MA. Bifidobacterium animalis subsp. lactis BB-12 Protects against Antibiotic-Induced Functional and Compositional Changes in Human Fecal Microbiome. Nutrients 2021; 13:nu13082814. [PMID: 34444974 PMCID: PMC8398419 DOI: 10.3390/nu13082814] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 08/11/2021] [Indexed: 01/04/2023] Open
Abstract
The administration of broad-spectrum antibiotics is often associated with antibiotic-associated diarrhea (AAD), and impacts gastrointestinal tract homeostasis, as evidenced by the following: (a) an overall reduction in both the numbers and diversity of the gut microbiota, and (b) decreased short-chain fatty acid (SCFA) production. Evidence in humans that probiotics may enhance the recovery of microbiota populations after antibiotic treatment is equivocal, and few studies have addressed if probiotics improve the recovery of microbial metabolic function. Our aim was to determine if Bifidobacterium animalis subsp. lactis BB-12 (BB-12)-containing yogurt could protect against antibiotic-induced fecal SCFA and microbiota composition disruptions. We conducted a randomized, allocation-concealed, controlled trial of amoxicillin/clavulanate administration (days 1-7), in conjunction with either BB-12-containing or control yogurt (days 1-14). We measured the fecal levels of SCFAs and bacterial composition at baseline and days 7, 14, 21, and 30. Forty-two participants were randomly assigned to the BB-12 group, and 20 participants to the control group. Antibiotic treatment suppressed the fecal acetate levels in both the control and probiotic groups. Following the cessation of antibiotics, the fecal acetate levels in the probiotic group increased over the remainder of the study and returned to the baseline levels on day 30 (-1.6% baseline), whereas, in the control group, the acetate levels remained suppressed. Further, antibiotic treatment reduced the Shannon diversity of the gut microbiota, for all the study participants at day 7. The magnitude of this change was larger and more sustained in the control group compared to the probiotic group, which is consistent with the hypothesis that BB-12 enhanced microbiota recovery. There were no significant baseline clinical differences between the two groups. Concurrent administration of amoxicillin/clavulanate and BB-12 yogurt, to healthy subjects, was associated with a significantly smaller decrease in the fecal SCFA levels and a more stable taxonomic profile of the microbiota over time than the control group.
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Affiliation(s)
- Daniel Merenstein
- Department of Family Medicine, Georgetown University Medical Center, Washington, DC 20057, USA; (T.P.T.); (K.H.S.); (T.C.)
- Department of Human Science, School of Nursing and Health Studies, Georgetown University Medical Center, Washington, DC 20057, USA
- Correspondence: (D.M.); (C.M.F.); (M.A.K.); Tel.: +1-202-687-2745 (D.M.); +1-410-706-3879 (C.M.F.); +1-410-706-5097 (M.A.K.)
| | - Claire M. Fraser
- Institute for Genomic Sciences, Departments of Medicine and Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; (S.G.-B.); (O.A.M.)
- Correspondence: (D.M.); (C.M.F.); (M.A.K.); Tel.: +1-202-687-2745 (D.M.); +1-410-706-3879 (C.M.F.); +1-410-706-5097 (M.A.K.)
| | - Robert F. Roberts
- Department of Food Science, The Pennsylvania State University, University Park, PA 16802, USA;
| | - Tian Liu
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA;
| | - Silvia Grant-Beurmann
- Institute for Genomic Sciences, Departments of Medicine and Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; (S.G.-B.); (O.A.M.)
| | - Tina P. Tan
- Department of Family Medicine, Georgetown University Medical Center, Washington, DC 20057, USA; (T.P.T.); (K.H.S.); (T.C.)
| | - Keisha Herbin Smith
- Department of Family Medicine, Georgetown University Medical Center, Washington, DC 20057, USA; (T.P.T.); (K.H.S.); (T.C.)
| | - Tom Cronin
- Department of Family Medicine, Georgetown University Medical Center, Washington, DC 20057, USA; (T.P.T.); (K.H.S.); (T.C.)
| | - Olivia A. Martin
- Institute for Genomic Sciences, Departments of Medicine and Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; (S.G.-B.); (O.A.M.)
- Department of Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | | | - Sean C. Lucan
- Department of Family and Social Medicine, Albert Einstein College of Medicine, Montefiore Health System, Bronx, NY 10461, USA;
| | - Maureen A. Kane
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA;
- Correspondence: (D.M.); (C.M.F.); (M.A.K.); Tel.: +1-202-687-2745 (D.M.); +1-410-706-3879 (C.M.F.); +1-410-706-5097 (M.A.K.)
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