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Seo KW, Do KH, Lee WK. Comparative Genetic Characterization of CTX-M-Producing Escherichia coli Isolated from Humans and Pigs with Diarrhea in Korea Using Next-Generation Sequencing. Microorganisms 2023; 11:1922. [PMID: 37630482 PMCID: PMC10458018 DOI: 10.3390/microorganisms11081922] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/19/2023] [Accepted: 07/21/2023] [Indexed: 08/27/2023] Open
Abstract
Pathogenic E. coli causes intra- and extraintestinal diseases in humans and pigs and third-generation cephalosporins are the primary option for the treatment of these diseases. The objective of this study was to investigate the characteristics and correlation between CTX-M-producing E. coli from humans and pigs regarding CTX-M-producing E. coli using next-generation sequencing and bioinformatic tools. Among the 24 CTX-M-producing E. coli, three types of CTX-M genes (CTX-M-12, CTX-M-14, and CTX-M-15) were detected in humans and four types of CTX-M genes (CTX-M-14, CTX-M-15, CTX-M-55, and CTX-M-101) were detected in pigs. A total of 24 CTX-M-producing E. coli isolates also showed the following antimicrobial resistance genes: other B-Lactam resistance gene (75.0%); aminoglycoside resistance genes (75.0%); phenicol resistance genes (70.8%); tetracycline resistance genes (70.8%); sulfonamide resistance genes (66.7%); quinolone resistance genes (62.5%); trimethoprim resistance genes (54.2%); and fosfomycin resistance genes (8.3%). FII (92.3%) and FIB (90.9%) were the most common plasmid replicon in humans and pigs, respectively. A total of thirty-eight different genes associated with virulence 24 CTX-M-producing E. coli and all isolates contained at least more than one virulence gene. A total of 24 CTX-M-producing E. coli isolates showed 15 diverse sequence types (STs): thirteen isolates from human belonged to 6 different STs, and 11 isolates from pig belonged to 9 different STs. The presence of virulence genes in E. coli together with antimicrobial resistance genes (including CTX-M genes) emphasizes the necessity of comprehensive surveillance and persistent monitoring of the food chain to avoid all types of bacterial contamination, regardless of human or pig origin.
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Affiliation(s)
- Kwang-Won Seo
- College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Republic of Korea; (K.-W.S.)
| | - Kyung-Hyo Do
- College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Republic of Korea; (K.-W.S.)
| | - Wan-Kyu Lee
- College of Veterinary Medicine, Chungbuk National University, Cheongju 28644, Republic of Korea; (K.-W.S.)
- GutBiomeTech, Cheongju 28644, Republic of Korea
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202
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Moon J, Lee AR, Kim H, Jhun J, Lee SY, Choi JW, Jeong Y, Park MS, Ji GE, Cho ML, Park SH. Faecalibacterium prausnitzii alleviates inflammatory arthritis and regulates IL-17 production, short chain fatty acids, and the intestinal microbial flora in experimental mouse model for rheumatoid arthritis. Arthritis Res Ther 2023; 25:130. [PMID: 37496081 PMCID: PMC10373287 DOI: 10.1186/s13075-023-03118-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 07/15/2023] [Indexed: 07/28/2023] Open
Abstract
BACKGROUND Rheumatoid arthritis (RA) is a systemic chronic inflammatory disease that leads to joint destruction and functional disability due to the targeting of self-antigens present in the synovium, cartilage, and bone. RA is caused by a number of complex factors, including genetics, environment, dietary habits, and altered intestinal microbial flora. Microorganisms in the gut bind to nod-like receptors and Toll-like receptors to regulate the immune system and produce various metabolites, such as short-chain fatty acids (SCFAs) that interact directly with the host. Faecalibacterium prausnitzii is a representative bacterium that produces butyrate, a well-known immunomodulatory agent in the body, and this microbe exerts anti-inflammatory effects in autoimmune diseases. METHODS In this study, F. prausnitzii was administered in a mouse model of RA, to investigate RA pathology and changes in the intestinal microbial flora. Using collagen-induced arthritic mice, which is a representative animal model of RA, we administered F. prausnitzii orally for 7 weeks. RESULTS The arthritis score and joint tissue damage were decreased in the mice administered F. prausnitzii compared with the vehicle-treated group. In addition, administration of F. prausnitzii reduced the abundance of systemic immune cells that secrete the pro-inflammatory cytokine IL-17 and induced changes in SCFA concentrations and the intestinal microbial flora composition. It also resulted in decreased lactate and acetate concentrations, an increased butyrate concentration, and altered compositions of bacteria known to exacerbate or improve RA. CONCLUSION These results suggest that F. prausnitzii exerts a therapeutic effect on RA by regulation of IL-17 producing cells. In addition, F. prausnitzii modify the microbial flora composition and short chain fatty acids in experimental RA mouse model.
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Affiliation(s)
- Jeonghyeon Moon
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - A Ram Lee
- Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
- Rheumatism Research Center, College of Medicine, Catholic Research Institute of Medical Science, The Catholic University of Korea, Seoul, 06591, Korea
- Lab of Translational ImmunoMedicine, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, 222, Banpo-Daero, Seocho-Gu, Seoul, 06591, Republic of Korea
| | - Heejung Kim
- Department of Food and Nutrition, Research Institute of Human Ecology, Seoul National University, Seoul, South Korea
| | - JooYeon Jhun
- Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
- Rheumatism Research Center, College of Medicine, Catholic Research Institute of Medical Science, The Catholic University of Korea, Seoul, 06591, Korea
- Lab of Translational ImmunoMedicine, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, 222, Banpo-Daero, Seocho-Gu, Seoul, 06591, Republic of Korea
| | - Seon-Yeong Lee
- Rheumatism Research Center, College of Medicine, Catholic Research Institute of Medical Science, The Catholic University of Korea, Seoul, 06591, Korea
- Lab of Translational ImmunoMedicine, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, 222, Banpo-Daero, Seocho-Gu, Seoul, 06591, Republic of Korea
| | - Jeong Won Choi
- Rheumatism Research Center, College of Medicine, Catholic Research Institute of Medical Science, The Catholic University of Korea, Seoul, 06591, Korea
- Lab of Translational ImmunoMedicine, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, 222, Banpo-Daero, Seocho-Gu, Seoul, 06591, Republic of Korea
| | - Yunju Jeong
- Harvard Medical School, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Geun Eog Ji
- Department of Food and Nutrition, Research Institute of Human Ecology, Seoul National University, Seoul, South Korea
- Research Center, BIFIDO Co., Ltd., Hongcheon, South Korea
| | - Mi-La Cho
- Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea.
- Rheumatism Research Center, College of Medicine, Catholic Research Institute of Medical Science, The Catholic University of Korea, Seoul, 06591, Korea.
- Lab of Translational ImmunoMedicine, Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, 222, Banpo-Daero, Seocho-Gu, Seoul, 06591, Republic of Korea.
- Department of Medical Life Sciences, College of Medicine, The Catholic University of Korea, 222, Banpo-Daero, Seocho-Gu, Seoul, 06591, Republic of Korea.
| | - Sung-Hwan Park
- Rheumatism Research Center, College of Medicine, Catholic Research Institute of Medical Science, The Catholic University of Korea, Seoul, 06591, Korea.
- Division of Rheumatology, Department of Internal Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Korea.
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Liu G, Li T, Zhu X, Zhang X, Wang J. An independent evaluation in a CRC patient cohort of microbiome 16S rRNA sequence analysis methods: OTU clustering, DADA2, and Deblur. Front Microbiol 2023; 14:1178744. [PMID: 37560524 PMCID: PMC10408458 DOI: 10.3389/fmicb.2023.1178744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 06/14/2023] [Indexed: 08/11/2023] Open
Abstract
16S rRNA is the universal gene of microbes, and it is often used as a target gene to obtain profiles of microbial communities via next-generation sequencing (NGS) technology. Traditionally, sequences are clustered into operational taxonomic units (OTUs) at a 97% threshold based on the taxonomic standard using 16S rRNA, and methods for the reduction of sequencing errors are bypassed, which may lead to false classification units. Several denoising algorithms have been published to solve this problem, such as DADA2 and Deblur, which can correct sequencing errors at single-nucleotide resolution by generating amplicon sequence variants (ASVs). As high-resolution ASVs are becoming more popular than OTUs and only one analysis method is usually selected in a particular study, there is a need for a thorough comparison of OTU clustering and denoising pipelines. In this study, three of the most widely used 16S rRNA methods (two denoising algorithms, DADA2 and Deblur, along with de novo OTU clustering) were thoroughly compared using 16S rRNA amplification sequencing data generated from 358 clinical stool samples from the Colorectal Cancer (CRC) Screening Cohort. Our findings indicated that all approaches led to similar taxonomic profiles (with P > 0.05 in PERMNAOVA and P <0.001 in the Mantel test), although the number of ASVs/OTUs and the alpha-diversity indices varied considerably. Despite considerable differences in disease-related markers identified, disease-related analysis showed that all methods could result in similar conclusions. Fusobacterium, Streptococcus, Peptostreptococcus, Parvimonas, Gemella, and Haemophilus were identified by all three methods as enriched in the CRC group, while Roseburia, Faecalibacterium, Butyricicoccus, and Blautia were identified by all three methods as enriched in the healthy group. In addition, disease-diagnostic models generated using machine learning algorithms based on the data from these different methods all achieved good diagnostic efficiency (AUC: 0.87-0.89), with the model based on DADA2 producing the highest AUC (0.8944 and 0.8907 in the training set and test set, respectively). However, there was no significant difference in performance between the models (P >0.05). In conclusion, this study demonstrates that DADA2, Deblur, and de novo OTU clustering display similar power levels in taxa assignment and can produce similar conclusions in the case of the CRC cohort.
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Affiliation(s)
- Guang Liu
- School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
- Guangdong Hongyuan Pukong Medical Technology Co., Ltd., Guangzhou, China
| | - Tong Li
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China
| | - Xiaoyan Zhu
- School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Xuanping Zhang
- School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Jiayin Wang
- School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
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Jan S, Fratzke AP, Felgner J, Hernandez-Davies JE, Liang L, Nakajima R, Jasinskas A, Supnet M, Jain A, Felgner PL, Davies DH, Gregory AE. Multivalent vaccines demonstrate immunogenicity and protect against Coxiella burnetii aerosol challenge. Front Immunol 2023; 14:1192821. [PMID: 37533862 PMCID: PMC10390735 DOI: 10.3389/fimmu.2023.1192821] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/16/2023] [Indexed: 08/04/2023] Open
Abstract
Vaccines are among the most cost-effective public health measures for controlling infectious diseases. Coxiella burnetii is the etiological agent of Q fever, a disease with a wide clinical spectrum that ranges from mild symptoms, such as fever and fatigue, to more severe disease, such as pneumonia and endocarditis. The formalin-inactivated whole-cell vaccine Q-VAX® contains hundreds of antigens and confers lifelong protection in humans, but prior sensitization from infection or vaccination can result in deleterious reactogenic responses to vaccination. Consequently, there is great interest in developing non-reactogenic alternatives based on adjuvanted recombinant proteins. In this study, we aimed to develop a multivalent vaccine that conferred protection with reduced reactogenicity. We hypothesized that a multivalent vaccine consisting of multiple antigens would be more immunogenic and protective than a monovalent vaccine owing to the large number of potential protective antigens in the C. burnetii proteome. To address this, we identified immunogenic T and B cell antigens, and selected proteins were purified to evaluate with a combination adjuvant (IVAX-1), with or without C. burnetii lipopolysaccharide (LPS) in immunogenicity studies in vivo in mice and in a Hartley guinea pig intratracheal aerosol challenge model using C. burnetii strain NMI RSA 493. The data showed that multivalent vaccines are more immunogenic than monovalent vaccines and more closely emulate the protection achieved by Q-VAX. Although six antigens were the most immunogenic, we also discovered that multiplexing beyond four antigens introduces detectable reactogenicity, indicating that there is an upper limit to the number of antigens that can be safely included in a multivalent Q-fever vaccine. C. burnetii LPS also demonstrates efficacy as a vaccine antigen in conferring protection in an otherwise monovalent vaccine formulation, suggesting that its addition in multivalent vaccines, as demonstrated by a quadrivalent formulation, would improve protective responses.
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Affiliation(s)
- Sharon Jan
- Vaccine Research & Development Center, Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, United States
| | - Alycia P. Fratzke
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX, United States
- Department of Pathology, Charles River Laboratories, Reno, NV, United States
| | - Jiin Felgner
- Vaccine Research & Development Center, Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, United States
| | - Jenny E. Hernandez-Davies
- Vaccine Research & Development Center, Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, United States
| | - Li Liang
- Vaccine Research & Development Center, Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, United States
| | - Rie Nakajima
- Vaccine Research & Development Center, Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, United States
| | - Algimantas Jasinskas
- Vaccine Research & Development Center, Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, United States
| | - Medalyn Supnet
- Vaccine Research & Development Center, Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, United States
| | - Aarti Jain
- Vaccine Research & Development Center, Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, United States
| | - Philip L. Felgner
- Vaccine Research & Development Center, Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, United States
| | - D. Huw Davies
- Vaccine Research & Development Center, Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, United States
| | - Anthony E. Gregory
- Vaccine Research & Development Center, Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, United States
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205
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Abbasi A, Bazzaz S, Da Cruz AG, Khorshidian N, Saadat YR, Sabahi S, Ozma MA, Lahouty M, Aslani R, Mortazavian AM. A Critical Review on Akkermansia muciniphila: Functional Mechanisms, Technological Challenges, and Safety Issues. Probiotics Antimicrob Proteins 2023:10.1007/s12602-023-10118-x. [PMID: 37432597 DOI: 10.1007/s12602-023-10118-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2023] [Indexed: 07/12/2023]
Abstract
Due to its physiological benefits from in vitro and in vivo points of view, Akkermansia muciniphila, a common colonizer in the human gut mucous layer, has consistently been identified as an option for the next-generation probiotic. A. muciniphila is a significant bacterium that promotes host physiology. However, it also has a great deal of potential to become a probiotic due to its physiological advantages in a variety of therapeutic circumstances. Therefore, it can be established that the abundance of A. muciniphila in the gut environment, which is controlled by many genetic and dietary variables, is related to the biological behaviors of the intestinal microbiota and gut dysbiosis/eubiosis circumstances. Before A. muciniphila is widely utilized as a next-generation probiotic, regulatory obstacles, the necessity for significant clinical trials, and the sustainability of manufacturing must be eliminated. In this review, the outcomes of recent experimental and clinical reports are comprehensively reviewed, and common colonization patterns, main factors involved in the colonization of A. muciniphila in the gut milieu, their functional mechanisms in establishing homeostasis in the metabolic and energy pathways, the promising delivery role of microencapsulation, potential genetic engineering strategies, and eventually safety issues of A. muciniphila have been discussed.
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Affiliation(s)
- Amin Abbasi
- Student Research Committee, Department of Food Science and Technology, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Science and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sara Bazzaz
- Department of Food Science and Technology, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Science and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Adriano G Da Cruz
- Department of Food Processing, Federal Institute of Science and Technology Education of Rio de Janeiro (IFRJ) - Campus Maracanã, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Nasim Khorshidian
- Department of Food Science and Technology, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Science and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Sahar Sabahi
- Department of Nutrition, School of Allied Medical Sciences, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mahdi Asghari Ozma
- Department of Medical Bacteriology and Virology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Masoud Lahouty
- Department of Microbiology, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Ramin Aslani
- Food Safety and Hygiene Division, Department of Environmental Health Engineering, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Amir M Mortazavian
- Department of Food Science and Technology, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Science and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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206
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Lyu X, Wang S, Zhong J, Cai L, Zheng Y, Zhou Y, Zhou Y, Chen Q, Li Q. Gut microbiome interacts with pregnancy hormone metabolites in gestational diabetes mellitus. Front Microbiol 2023; 14:1175065. [PMID: 37492251 PMCID: PMC10364628 DOI: 10.3389/fmicb.2023.1175065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 06/09/2023] [Indexed: 07/27/2023] Open
Abstract
Introduction Change in the composition of intestinal microbiota is associated with metabolic disorders such as gestational diabetes mellitus (GDM). Methods To understand how the microbiota impacts the development of gestational diabetes mellitus, we profiled the intestinal microbiome of 54 pregnant women, including 27 GDM subjects, by employing 16S rRNA gene sequencing. Additionally, we conducted targeted metabolomics assays to validate the identified pathways with overrepresented metabolites. Results We evaluated the patterns of changing abundances of operational taxonomic units (OTU) between GDM and the healthy counterparts over three timepoints. Based on the significant OTUs, we inferred 132 significantly altered metabolic pathways in GDM. And identified two overrepresented metabolites of pregnancy hormone, butyrate and mevalonate, as potential intermediary metabolites of intestinal microbiota in GDM. Finally, we validated the impacts of the intestinal microbiota on GDM by demonstrating consistent changes of the serum levels of progesterone, estradiol, butyrate, and mevalonate in an independent cohort. Discussion Our findings confirm that alterations in the microbiota play a role in the development of GDM by impacting the metabolism of pregnancy hormones. This provides a novel perspective on the pathogenesis of GDM and introduces potential biomarkers that can be used for early diagnosis and prevention of the disease.
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Affiliation(s)
- Xuejing Lyu
- Clinical Medical Research Center for Obstetrics and Gynecology Diseases of Fujian Province, Laboratory of Research and Diagnosis of Gynecological Diseases of Xiamen City, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- School of Medicine, National Institute of Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Shaona Wang
- The Third Clinical Medical College, Fujian Medical University, Fuzhou, China
- Department of Women’s Health, Xiamen Haicang District Maternity and Child Health Care Hospital, Xiamen, China
| | - Jiaxin Zhong
- School of Medicine, National Institute of Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Lingzhu Cai
- Clinical Medical Research Center for Obstetrics and Gynecology Diseases of Fujian Province, Laboratory of Research and Diagnosis of Gynecological Diseases of Xiamen City, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- The Third Clinical Medical College, Fujian Medical University, Fuzhou, China
| | - Yanhui Zheng
- Clinical Medical Research Center for Obstetrics and Gynecology Diseases of Fujian Province, Laboratory of Research and Diagnosis of Gynecological Diseases of Xiamen City, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- The Third Clinical Medical College, Fujian Medical University, Fuzhou, China
| | - Ying Zhou
- Clinical Medical Research Center for Obstetrics and Gynecology Diseases of Fujian Province, Laboratory of Research and Diagnosis of Gynecological Diseases of Xiamen City, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- The Third Clinical Medical College, Fujian Medical University, Fuzhou, China
| | - Ying Zhou
- School of Medicine, National Institute of Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Qionghua Chen
- Clinical Medical Research Center for Obstetrics and Gynecology Diseases of Fujian Province, Laboratory of Research and Diagnosis of Gynecological Diseases of Xiamen City, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- The Third Clinical Medical College, Fujian Medical University, Fuzhou, China
| | - Qiyuan Li
- School of Medicine, National Institute of Data Science in Health and Medicine, Xiamen University, Xiamen, China
- Department of Pediatrics, The First Affiliated Hospital of Xiamen University, Xiamen, China
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Martín R, Rios-Covian D, Huillet E, Auger S, Khazaal S, Bermúdez-Humarán LG, Sokol H, Chatel JM, Langella P. Faecalibacterium: a bacterial genus with promising human health applications. FEMS Microbiol Rev 2023; 47:fuad039. [PMID: 37451743 PMCID: PMC10410495 DOI: 10.1093/femsre/fuad039] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 06/08/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023] Open
Abstract
In humans, many diseases are associated with alterations in gut microbiota, namely increases or decreases in the abundance of specific bacterial groups. One example is the genus Faecalibacterium. Numerous studies have underscored that low levels of Faecalibacterium are correlated with inflammatory conditions, with inflammatory bowel disease (IBD) in the forefront. Its representation is also diminished in the case of several diseases, including colorectal cancer (CRC), dermatitis, and depression. Additionally, the relative presence of this genus is considered to reflect, at least in part, intestinal health status because Faecalibacterium is frequently present at reduced levels in individuals with gastrointestinal diseases or disorders. In this review, we first thoroughly describe updates to the taxonomy of Faecalibacterium, which has transformed a single-species taxon to a multispecies taxon over the last decade. We then explore the links discovered between Faecalibacterium abundance and various diseases since the first IBD-focused studies were published. Next, we examine current available strategies for modulating Faecalibacterium levels in the gut. Finally, we summarize the mechanisms underlying the beneficial effects that have been attributed to this genus. Together, epidemiological and experimental data strongly support the use of Faecalibacterium as a next-generation probiotic (NGP) or live biotherapeutic product (LBP).
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Affiliation(s)
- Rebeca Martín
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - David Rios-Covian
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Eugénie Huillet
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Sandrine Auger
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Sarah Khazaal
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Luis G Bermúdez-Humarán
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Harry Sokol
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Gastroenterology Department, F-75012 Paris, France
- Paris Centre for Microbiome Medicine (PaCeMM) FHU, F-75012, Paris, France
| | - Jean-Marc Chatel
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Philippe Langella
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
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208
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Gu F, Larsen N, Pascale N, Petersen SA, Khakimov B, Respondek F, Jespersen L. Age-related effects on the modulation of gut microbiota by pectins and their derivatives: an in vitro study. Front Microbiol 2023; 14:1207837. [PMID: 37476669 PMCID: PMC10354267 DOI: 10.3389/fmicb.2023.1207837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 06/13/2023] [Indexed: 07/22/2023] Open
Abstract
Introduction The present study investigates whether supplementation with pectin-type polysaccharides has potential to improve aging-associated dysbiosis of the gut microbiota. The influence of different types of pectins on the gut microbiota composition and short-chain fatty acids (SCFAs) profiles of elderly was compared to younger adults. Methods Pectins studied included a pectin polysaccharide (PEC), a partially hydrolyzed pectin (PPH), and a pectin oligosaccharide (POS). Additionally, inulin was used as a reference prebiotic substrate. Individual fecal samples were collected from healthy elderly volunteers (70-75 years) and younger adults (30-35 years). In vitro fermentations were performed using the CoMiniGut model with controlled temperature and pH. Samples were withdrawn at baseline and after 24 h fermentation for measurement of SCFAs production and microbiota composition by 16S rRNA gene sequencing. Results and Discussion The results showed that fermentations with PEC and PPH resulted in a specific stimulation of Faecalibacterium prausnitzii regardless of the age groups. Collinsella aerofaciens became a dominating species in the young adult group with fermentations of all three pectins, which was not observed in the elderly group. No significant differences in SCFAs production were found among the pectins, indicating a high level of functional redundancy. Pectins boosted various bacterial groups differently from the reference prebiotic substrate (inulin). We also found inulin had reduced butyrogenic and bifidogenic effects in the elderly group compared to the younger adult group. In conclusion, the in vitro modulating effects of pectins on elderly gut microbiota showed potential of using pectins to improve age-related dysbiosis.
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Affiliation(s)
- Fangjie Gu
- Department of Food Science, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
- CP Kelco ApS, Lille Skensved, Denmark
| | - Nadja Larsen
- Department of Food Science, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | | | | | - Bekzod Khakimov
- Department of Food Science, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | | | - Lene Jespersen
- Department of Food Science, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
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209
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Ahmed EA, Ahmed SM, Zakaria NH, Baddour NM, Header DA. Study of the gut microbiome in Egyptian patients with active ulcerative colitis. REVISTA DE GASTROENTEROLOGIA DE MEXICO (ENGLISH) 2023; 88:246-255. [PMID: 35906158 DOI: 10.1016/j.rgmxen.2022.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 10/13/2021] [Indexed: 11/24/2022]
Abstract
INTRODUCTION AND AIM Ulcerative colitis (UC) is characterized by chronic, uncontrolled inflammation of the intestinal mucosa. Gut microbiota dysbiosis was reported to be a factor in intestinal inflammation. The aim of the present study was to study changes in the gut microbiome in Egyptian patients with active UC. MATERIALS AND METHODS In this cross-sectional study, the gut bacterial microbiome of 21 UC patients and 20 control subjects was analyzed using the quantitative SYBR Green real-time PCR technique, targeting the 16S rRNA gene of selected bacterial phyla/genera and/or species. RESULTS UC patients showed marked dysbiosis evidenced by a significant decrease in the Firmicutes and F. prausnitzii anti-inflammatory bacteria. The Firmicutes/Bacteroidetes ratio was also lower in the UC cases (1.65), compared with the healthy controls (2.93). In addition, the UC cases showed a statistically significant decrease in Ruminococcus, compared with the control group. However, there were no statistically significant differences between UC patients and the controls, regarding A. muciniphila, Bifidobacterium, Lactobacillus, Bacteroides, and Prevotella. One UC case was positive for the pathogenic bacterium, Clostridioides difficile, with low relative abundance. CONCLUSION The current study showed differences in the gut microbiome of UC patients, compared with healthy controls. This may help in identifying the gut microbiome and specific bacterial changes that can be targeted for treatment of UC.
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Affiliation(s)
- E A Ahmed
- Departamento de Medicina Interna, Unidad de Gastroenterología, Facultad de Medicina, Universidad de Alejandría, Alejandría, Egypt
| | - S M Ahmed
- Departamento de Microbiología e Inmunología Médica, Facultad de Medicina, Universidad de Alejandría, Alejandría, Egypt
| | - N H Zakaria
- Departamento de Patología Clínica, Facultad de Medicina, Universidad de Alejandría, Alejandría, Egypt
| | - N M Baddour
- Departamento de Patología, Facultad de Medicina, Universidad de Alejandría, Alejandría, Egypt
| | - D A Header
- Departamento de Medicina Interna, Unidad de Gastroenterología, Facultad de Medicina, Universidad de Alejandría, Alejandría, Egypt.
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210
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Fatani AMN, Suh JH, Auger J, Alabasi KM, Wang Y, Segal MS, Dahl WJ. Pea hull fiber supplementation does not modulate uremic metabolites in adults receiving hemodialysis: a randomized, double-blind, controlled trial. Front Nutr 2023; 10:1179295. [PMID: 37457968 PMCID: PMC10349378 DOI: 10.3389/fnut.2023.1179295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 06/08/2023] [Indexed: 07/18/2023] Open
Abstract
Background Fiber is a potential therapeutic to suppress microbiota-generated uremic molecules. This study aimed to determine if fiber supplementation decreased serum levels of uremic molecules through the modulation of gut microbiota in adults undergoing hemodialysis. Methods A randomized, double-blinded, controlled crossover study was conducted. Following a 1-week baseline, participants consumed muffins with added pea hull fiber (PHF) (15 g/d) and control muffins daily, each for 4 weeks, separated by a 4-week washout. Blood and stool samples were collected per period. Serum p-cresyl sulfate (PCS), indoxyl sulfate (IS), phenylacetylglutamine (PAG), and trimethylamine N-oxide (TMAO) were quantified by LC-MS/MS, and fecal microbiota profiled by 16S rRNA gene amplicon sequencing and specific taxa of interest by qPCR. QIIME 2 sample-classifier was used to discover unique microbiota profiles due to the consumption of PHF. Results Intake of PHF contributed an additional 9 g/d of dietary fiber to the subjects' diet due to compliance. No significant changes from baseline were observed in serum PCS, IS, PAG, or TMAO, or for the relative quantification of Akkermansia muciniphila, Faecalibacterium prausnitzii, Bifidobacterium, or Roseburia, taxa considered health-enhancing. Dietary protein intake and IS (r = -0.5, p = 0.05) and slow transit stool form and PCS (r = 0.7, p < 0.01) were significantly correlated at baseline. PHF and control periods were not differentiated; however, using machine learning, taxa most distinguishing the microbiota composition during the PHF periods compared to usual diet alone were enriched Gemmiger, Collinsella, and depleted Lactobacillus, Ruminococcus, Coprococcus, and Mogibacteriaceae. Conclusion PHF supplementation did not mitigate serum levels of targeted microbial-generated uremic molecules. Given the high cellulose content, which may be resistant to fermentation, PHF may not exert sufficient effects on microbiota composition to modulate its activity at the dose consumed.
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Affiliation(s)
- Asmaa M. N. Fatani
- Department of Food Science and Human Nutrition, University of Florida, Gainesville, FL, United States
- Food and Nutrition Department, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Joon Hyuk Suh
- Department of Food Science and Human Nutrition, University of Florida, Gainesville, FL, United States
| | - Jérémie Auger
- Rosell Institute for Microbiome and Probiotics, Lallemand Health Solutions, Montréal, QC, Canada
| | - Karima M. Alabasi
- Department of Food Science and Human Nutrition, University of Florida, Gainesville, FL, United States
- Foods and Nutrition Department, School of Health Science and Wellness, Northwest Missouri State University, Maryville, MO, United States
| | - Yu Wang
- Department of Food Science and Human Nutrition, University of Florida, Gainesville, FL, United States
| | - Mark S. Segal
- Department of Nephrology, Hypertension and Renal Transplantation, College of Medicine, University of Florida, Gainesville, FL, United States
- North Florida South Georgia VHS, Gainesville, FL, United States
| | - Wendy J. Dahl
- Department of Food Science and Human Nutrition, University of Florida, Gainesville, FL, United States
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211
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Cozzi G, Scagnellato L, Lorenzin M, Savarino E, Zingone F, Ometto F, Favero M, Doria A, Vavricka SR, Ramonda R. Spondyloarthritis with inflammatory bowel disease: the latest on biologic and targeted therapies. Nat Rev Rheumatol 2023:10.1038/s41584-023-00984-8. [PMID: 37386288 DOI: 10.1038/s41584-023-00984-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2023] [Indexed: 07/01/2023]
Abstract
Spondyloarthritis (SpA) encompasses a heterogeneous group of chronic inflammatory diseases that can affect both axial and peripheral joints, tendons and entheses. Among the extra-articular manifestations, inflammatory bowel disease (IBD) is associated with considerable morbidity and effects on quality of life. In everyday clinical practice, treatment of these conditions requires a close collaboration between gastroenterologists and rheumatologists to enable early detection of joint and intestinal manifestations during follow-up and to choose the most effective therapeutic regimen, implementing precision medicine for each patient's subtype of SpA and IBD. The biggest issue in this field is the dearth of drugs that are approved for both diseases, as only TNF inhibitors are currently approved for the treatment of full-spectrum SpA-IBD. Janus tyrosine kinase inhibitors are among the most promising drugs for the treatment of peripheral and axial SpA, as well as for intestinal manifestations. Other therapies such as inhibitors of IL-23 and IL-17, phosphodiesterase 4 inhibitor, α4β7 integrin blockers and faecal microbiota transplantation seem to only be able to control some disease domains, or require further studies. Given the growing interest in the development of novel drugs to treat both conditions, it is important to understand the current state of the art and the unmet needs in the management of SpA-IBD.
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Affiliation(s)
- Giacomo Cozzi
- Rheumatology Unit, Department of Medicine-DIMED, Padova University Hospital, Padova, Italy
| | - Laura Scagnellato
- Rheumatology Unit, Department of Medicine-DIMED, Padova University Hospital, Padova, Italy
| | - Mariagrazia Lorenzin
- Rheumatology Unit, Department of Medicine-DIMED, Padova University Hospital, Padova, Italy
| | - Edoardo Savarino
- Gastroenterology Unit, Department of Surgery, Oncology and Gastroenterology, University Hospital of Padova, Padova, Italy
| | - Fabiana Zingone
- Gastroenterology Unit, Department of Surgery, Oncology and Gastroenterology, University Hospital of Padova, Padova, Italy
| | - Francesca Ometto
- Rheumatology Unit, Department of Medicine-DIMED, Padova University Hospital, Padova, Italy
| | - Marta Favero
- Rheumatology Unit, Department of Medicine-DIMED, Padova University Hospital, Padova, Italy
| | - Andrea Doria
- Rheumatology Unit, Department of Medicine-DIMED, Padova University Hospital, Padova, Italy
| | - Stephan R Vavricka
- Department of Gastroenterology and Hepatology, University Hospital Zürich and Center for Gastroenterology and Hepatology, Zürich, Switzerland
| | - Roberta Ramonda
- Rheumatology Unit, Department of Medicine-DIMED, Padova University Hospital, Padova, Italy.
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212
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Liu F, Li R, Zhong Y, Liu X, Deng W, Huang X, Price M, Li J. Age-related alterations in metabolome and microbiome provide insights in dietary transition in giant pandas. mSystems 2023; 8:e0025223. [PMID: 37273228 PMCID: PMC10308887 DOI: 10.1128/msystems.00252-23] [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: 03/24/2023] [Accepted: 04/04/2023] [Indexed: 06/06/2023] Open
Abstract
We conducted UPLC-MS-based metabolomics, 16S rRNA, and metagenome sequencing on the fecal samples of 44 captive giant pandas (Ailuropoda melanoleuca) from four age groups (i.e., Cub, Young, Adult, and Old) to comprehensively understand age-related changes in the metabolism and gut microbiota of giant pandas. We characterized the metabolite profiles of giant pandas based on 1,376 identified metabolites, with 152 significantly differential metabolites (SDMs) found across the age groups. We found that the metabolites and the composition/function of the gut microbiota changed in response to the transition from a milk-dominant diet in panda cubs to a bamboo-specific diet in young and adult pandas. Lipid metabolites such as choline and hippuric acid were enriched in the Cub group, and many plant secondary metabolites were significantly higher in the Young and Adult groups, while oxidative stress and inflammatory related metabolites were only found in the Old group. However, there was a decrease in the α-diversity of gut microbiota in adult and old pandas, who exclusively consume bamboo. The abundance of bacteria related to the digestion of cellulose-rich food, such as Firmicutes, Streptococcus, and Clostridium, significantly increased from the Cub to the Adult group, while the abundance of beneficial bacteria such as Faecalibacterium, Sarcina, and Blautia significantly decreased. Notably, several potential pathogenic bacteria had relatively high abundances, especially in the Young group. Metagenomic analysis identified 277 CAZyme genes including cellulose degrading genes, and seven of the CAZymes had abundances that significantly differed between age groups. We also identified 237 antibiotic resistance genes (ARGs) whose number and diversity increased with age. We also found a significant positive correlation between the abundance of bile acids and gut bacteria, especially Lactobacillus and Bifidobacterium. Our results from metabolome, 16S rRNA, and metagenome data highlight the important role of the gut microbiota-bile acid axis in the regulation of age-related metabolism and provide new insights into the lipid metabolism of giant pandas. IMPORTANCE The giant panda is a member of the order Carnivora but is entirely herbivorous. The giant panda's specialized diet and related metabolic mechanisms have not been fully understood. It is therefore crucial to investigate the dynamic changes in metabolites as giant pandas grow and physiologically adapt to their herbivorous diet. This study conducted UPLC-MS-based metabolomics 16S rRNA, and metagenome sequencing on the fecal samples of captive giant pandas from four age groups. We found that metabolites and the composition/function of gut microbiota changed in response to the transition from a milk-dominant diet in cubs to a bamboo-specific diet in young and adult pandas. The metabolome, 16S rRNA, and metagenome results highlight that the gut microbiota-bile acid axis has an important role in the regulation of age-related metabolism, and our study provides new insights into the lipid metabolism of giant pandas.
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Affiliation(s)
- Fangyuan Liu
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Rengui Li
- China Conservation and Research Center for the Giant Panda, Dujiangyan, Sichuan, China
- Key Laboratory of State Forestry and Grassland Administration on Conservation Biology for Rare Animals of the Giant Panda State Park, Dujiangyan, Sichuan, China
| | - Yi Zhong
- China Wildlife Conservation Association, Beijing, China
| | - Xu Liu
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Wenwen Deng
- China Conservation and Research Center for the Giant Panda, Dujiangyan, Sichuan, China
- Key Laboratory of State Forestry and Grassland Administration on Conservation Biology for Rare Animals of the Giant Panda State Park, Dujiangyan, Sichuan, China
| | - Xiaoyu Huang
- China Conservation and Research Center for the Giant Panda, Dujiangyan, Sichuan, China
- Key Laboratory of State Forestry and Grassland Administration on Conservation Biology for Rare Animals of the Giant Panda State Park, Dujiangyan, Sichuan, China
| | - Megan Price
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Jing Li
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
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Fan Q, Du E, Chen F, Tao W, Zhao N, Huang S, Guo W, Huang J, Wei J. Maternal Magnolol Supplementation during Pregnancy and Lactation Promotes Antioxidant Capacity, Improves Gut Health, and Alters Gut Microbiota and Metabolites of Weanling Piglets. Metabolites 2023; 13:797. [PMID: 37512505 PMCID: PMC10383630 DOI: 10.3390/metabo13070797] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/14/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
Maternal nutrition exerts a profound effect on the postnatal performance of offspring, especially during the weaning period. The multifunctional bioactive component magnolol (MAG) has shown promise as a dietary supplement. This study aimed to explore the effects of maternal MAG supplementation on the antioxidant capacity, gut health, gut microbiome, and metabolome composition of weanling piglets. Fifty pregnant sows were randomly divided into two equally sized groups, the control group and the group supplemented with 100 g/t MAG during the gestation and lactation periods, and 7 days postweaning, the pups were euthanized. The microbiome and metabolome features of weanling piglet colons were compared. Our results revealed that maternal MAG supplementation modified the serum redox status of weanling piglets by decreasing malondialdehyde concentration and increasing superoxide dismutase activity and total antioxidant capacity. Moreover, the decreased indicators of diarrhea were accompanied by improved gut barrier function, in which serum diamine oxidase concentration was decreased, and expressions of zona occludens-1, claudin-1, and intestinal alkaline phosphatase were increased in the colon of weanling piglets from sows supplemented with MAG. Further analysis of the gut microbiota indicated that maternal MAG supplementation significantly increased the relative abundance of beneficial bacteria in the colon of weanling piglets, including Faecalibacterium prausnitzii and Oscillospira. Metabolome analysis identified 540 differential metabolites in the colon of piglets from MAG-fed dams, of which glycerophospholipid classes were highly correlated with progeny gut health and key beneficial bacteria. Our findings indicated that maternal MAG supplementation can improve the oxidative status and gut health of weanling piglets, possibly due to alterations in the gut microbiota and metabolites.
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Affiliation(s)
- Qiwen Fan
- Key Laboratory of Animal Embryo Engineering and Molecular Breeding of Hubei Province, Wuhan 430064, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Wuhan 430064, China
| | - Encun Du
- Key Laboratory of Animal Embryo Engineering and Molecular Breeding of Hubei Province, Wuhan 430064, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Wuhan 430064, China
| | - Fang Chen
- Key Laboratory of Animal Embryo Engineering and Molecular Breeding of Hubei Province, Wuhan 430064, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Wuhan 430064, China
| | - Wenjing Tao
- Key Laboratory of Animal Embryo Engineering and Molecular Breeding of Hubei Province, Wuhan 430064, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Wuhan 430064, China
| | - Na Zhao
- Key Laboratory of Animal Embryo Engineering and Molecular Breeding of Hubei Province, Wuhan 430064, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Wuhan 430064, China
| | - Shaowen Huang
- Key Laboratory of Animal Embryo Engineering and Molecular Breeding of Hubei Province, Wuhan 430064, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Wuhan 430064, China
| | - Wanzheng Guo
- Key Laboratory of Animal Embryo Engineering and Molecular Breeding of Hubei Province, Wuhan 430064, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Wuhan 430064, China
| | - Jing Huang
- Key Laboratory of Animal Embryo Engineering and Molecular Breeding of Hubei Province, Wuhan 430064, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Wuhan 430064, China
| | - Jintao Wei
- Key Laboratory of Animal Embryo Engineering and Molecular Breeding of Hubei Province, Wuhan 430064, China
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis (Ministry of Agriculture), Wuhan 430064, China
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214
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Roshini J, Patro LPP, Sundaresan S, Rathinavelan T. Structural diversity among Acinetobacter baumannii K-antigens and its implication in the in silico serotyping. Front Microbiol 2023; 14:1191542. [PMID: 37415807 PMCID: PMC10320297 DOI: 10.3389/fmicb.2023.1191542] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 05/30/2023] [Indexed: 07/08/2023] Open
Abstract
Acinetobacter baumannii is an emerging opportunistic pathogen. It exhibits multi-, extreme-, and pan-drug resistance against several classes of antibiotics. Capsular polysaccharide (CPS or K-antigen) is one of the major virulence factors which aids A. baumannii in evading the host immune system. K-antigens of A. baumannii exploit the Wzx/Wzy-dependent pathway that involves 13 different proteins for its assembly and transport onto the outer membrane. A total of 64 (out of 237 K-locus(KL) types) known K-antigen sugar repeating structures are discussed here and are classified into seven groups based on their initial sugars, QuiNAc4NAc, GalNAc, GlcNAc, Gal, QuiNAc/FucNAc, FucNAc, and GlcNAc along with Leg5Ac7Ac/Leg5Ac7R. Thus, the corresponding seven initializing glycosyltransferases (ItrA1, ItrA2, ItrA3, ItrA4, ItrB1, ItrB3, and ItrA3 along with ItrB2) exhibit serotype specificity. The modeled 3D-structural repository of the 64 K-antigens can be accessed at https://project.iith.ac.in/ABSD/k_antigen.html. The topology of K-antigens further reveals the presence of 2-6 and 0-4 sugar monomers in the main and side chains, respectively. The presence of negatively (predominant) or neutrally charged K-antigens is observed in A. baumannii. Such diversity in the K-antigen sugar composition provides the K-typing specificity (viz., 18-69% in terms of reliability) for Wza, Wzb, Wzc, Wzx, and Wzy proteins involved in the Wzx/Wzy-dependent pathway. Interestingly, the degree of uniqueness of these proteins among different K-types is estimated to be 76.79%, considering the 237 reference sequences. This article summarizes the A. baumannii K-antigen structural diversity and creation of a K-antigen digital repository and provides a systematic analysis of the K-antigen assembly and transportation marker proteins.
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215
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Robinson I, Hochmair MJ, Schmidinger M, Absenger G, Pichler M, Nguyen VA, Richtig E, Rainer BM, Ay L, Jansen C, Pacífico C, Knabl A, Sladek B, Gasche N, Valipour A. Assessing the Performance of a Novel Stool-Based Microbiome Test That Predicts Response to First Line Immune Checkpoint Inhibitors in Multiple Cancer Types. Cancers (Basel) 2023; 15:3268. [PMID: 37444378 DOI: 10.3390/cancers15133268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 07/15/2023] Open
Abstract
The intestinal microbiome is by now an undebatable key player in the clinical outcome of ICI therapies. However, no microbiome profiling method to aid therapy decision is yet validated. We conducted a multi-centric study in patients with stage III/IV melanoma, NSCLC, or RCC receiving ICI treatment. The stool microbiome profile of 63 patients was analyzed with BiomeOne®, a microbiome-based algorithm that anticipates whether a patient will achieve clinical benefit with ICIs prior to therapy initiation. Classification of patient samples as Rs and NRs was achieved with a sensitivity of 81% and a specificity of 50% in this validation cohort. An ICI-favorable response was characterized by an intestinal microbiome rich in bacteria such as Oscillospira sp., Clostridia UCG-014, Lachnospiraceae UCG-010 sp., Prevotella copri, and a decrease in Sutterella sp., Lactobacillales, and Streptococcus sp. Patients who developed immune-related adverse events (irAEs) had an overall increased microbial diversity and richness, and a stool microbiome depleted in Agathobacter. When compared with the programmed death-ligand 1 (PD-L1) expression test in the subcohort of NSCLC patients (n = 38), BiomeOne® exhibited a numerically higher sensitivity (78.6%) in identifying responders when compared with the PD-L1 test (67.9%). This study provides an evaluation of BiomeOne®, the first microbiome-based test for prediction of ICI response, to achieve market authorization. Validation with further indications and expansion to other microbiome-based interventions will be essential to bring microbiome-based diagnostics into standard clinical practice.
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Affiliation(s)
- Irina Robinson
- Department of Respiratory and Critical Care Medicine, Karl Landsteiner Institute for Lung Research and Pulmonary Oncology, Klinik Floridsdorf, Vienna Healthcare Group, 1210 Vienna, Austria
| | - Maximilian Johannes Hochmair
- Department of Respiratory and Critical Care Medicine, Karl Landsteiner Institute for Lung Research and Pulmonary Oncology, Klinik Floridsdorf, Vienna Healthcare Group, 1210 Vienna, Austria
| | - Manuela Schmidinger
- Department of Urology, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Gudrun Absenger
- Department of Internal Medicine, Division of Oncology, Medical University of Graz, 8036 Graz, Austria
| | - Martin Pichler
- Department of Internal Medicine, Division of Oncology, Medical University of Graz, 8036 Graz, Austria
| | - Van Anh Nguyen
- Department of Dermatology, Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Erika Richtig
- Department of Dermatology, Medical University of Graz, 8036 Graz, Austria
| | | | - Leyla Ay
- Department of Respiratory and Critical Care Medicine, Karl Landsteiner Institute for Lung Research and Pulmonary Oncology, Klinik Floridsdorf, Vienna Healthcare Group, 1210 Vienna, Austria
| | | | | | | | | | | | - Arschang Valipour
- Department of Respiratory and Critical Care Medicine, Karl Landsteiner Institute for Lung Research and Pulmonary Oncology, Klinik Floridsdorf, Vienna Healthcare Group, 1210 Vienna, Austria
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216
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Ferreiro AL, Choi J, Ryou J, Newcomer EP, Thompson R, Bollinger RM, Hall-Moore C, Ndao IM, Sax L, Benzinger TLS, Stark SL, Holtzman DM, Fagan AM, Schindler SE, Cruchaga C, Butt OH, Morris JC, Tarr PI, Ances BM, Dantas G. Gut microbiome composition may be an indicator of preclinical Alzheimer's disease. Sci Transl Med 2023; 15:eabo2984. [PMID: 37315112 PMCID: PMC10680783 DOI: 10.1126/scitranslmed.abo2984] [Citation(s) in RCA: 51] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/26/2023] [Indexed: 06/16/2023]
Abstract
Alzheimer's disease (AD) pathology is thought to progress from normal cognition through preclinical disease and ultimately to symptomatic AD with cognitive impairment. Recent work suggests that the gut microbiome of symptomatic patients with AD has an altered taxonomic composition compared with that of healthy, cognitively normal control individuals. However, knowledge about changes in the gut microbiome before the onset of symptomatic AD is limited. In this cross-sectional study that accounted for clinical covariates and dietary intake, we compared the taxonomic composition and gut microbial function in a cohort of 164 cognitively normal individuals, 49 of whom showed biomarker evidence of early preclinical AD. Gut microbial taxonomic profiles of individuals with preclinical AD were distinct from those of individuals without evidence of preclinical AD. The change in gut microbiome composition correlated with β-amyloid (Aβ) and tau pathological biomarkers but not with biomarkers of neurodegeneration, suggesting that the gut microbiome may change early in the disease process. We identified specific gut bacterial taxa associated with preclinical AD. Inclusion of these microbiome features improved the accuracy, sensitivity, and specificity of machine learning classifiers for predicting preclinical AD status when tested on a subset of the cohort (65 of the 164 participants). Gut microbiome correlates of preclinical AD neuropathology may improve our understanding of AD etiology and may help to identify gut-derived markers of AD risk.
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Affiliation(s)
- Aura L. Ferreiro
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - JooHee Choi
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jian Ryou
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Erin P. Newcomer
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Regina Thompson
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Rebecca M. Bollinger
- Program in Occupational Therapy, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Carla Hall-Moore
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - I. Malick Ndao
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Laurie Sax
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Tammie L. S. Benzinger
- Department of Radiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Charles F. and Joanne Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Susan L. Stark
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Program in Occupational Therapy, Washington University School of Medicine, St. Louis, MO 63110, USA
- Charles F. and Joanne Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - David M. Holtzman
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Charles F. and Joanne Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Anne M. Fagan
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Charles F. and Joanne Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Suzanne E. Schindler
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Charles F. and Joanne Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Carlos Cruchaga
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Omar H. Butt
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - John C. Morris
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Charles F. and Joanne Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Phillip I. Tarr
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Beau M. Ances
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Radiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Charles F. and Joanne Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Gautam Dantas
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
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Garofalo C, Cristiani CM, Ilari S, Passacatini LC, Malafoglia V, Viglietto G, Maiuolo J, Oppedisano F, Palma E, Tomino C, Raffaeli W, Mollace V, Muscoli C. Fibromyalgia and Irritable Bowel Syndrome Interaction: A Possible Role for Gut Microbiota and Gut-Brain Axis. Biomedicines 2023; 11:1701. [PMID: 37371796 DOI: 10.3390/biomedicines11061701] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/06/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Fibromyalgia (FM) is a serious chronic pain syndrome, characterised by muscle and joint stiffness, insomnia, fatigue, mood disorders, cognitive dysfunction, anxiety, depression and intestinal irritability. Irritable Bowel Syndrome (IBS) shares many of these symptoms, and FM and IBS frequently co-exist, which suggests a common aetiology for the two diseases. The exact physiopathological mechanisms underlying both FM and IBS onset are unknown. Researchers have investigated many possible causes, including alterations in gut microbiota, which contain billions of microorganisms in the human digestive tract. The gut-brain axis has been proven to be the link between the gut microbiota and the central nervous system, which can then control the gut microbiota composition. In this review, we will discuss the similarities between FM and IBS. Particularly, we will focus our attention on symptomatology overlap between FM and IBS as well as the similarities in microbiota composition between FM and IBS patients. We will also briefly discuss the potential therapeutic approaches based on microbiota manipulations that are successfully used in IBS and could be employed also in FM patients to relieve pain, ameliorate the rehabilitation outcome, psychological distress and intestinal symptoms.
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Affiliation(s)
- Cinzia Garofalo
- Department of Experimental and Clinical Medicine, "Magna Græcia" University of Catanzaro, 88100 Catanzaro, Italy
| | - Costanza Maria Cristiani
- Department of Medical and Surgical Sciences, Neuroscience Research Center, "Magna Græcia" University of Catanzaro, 88100 Catanzaro, Italy
| | - Sara Ilari
- Physiology and Pharmacology of Pain, IRCCS San Raffaele Roma, 00166 Rome, Italy
| | - Lucia Carmela Passacatini
- Department of Health Science, Institute of Research for Food Safety & Health (IRC-FSH), "Magna Græcia" University of Catanzaro, 88100 Catanzaro, Italy
| | | | - Giuseppe Viglietto
- Department of Experimental and Clinical Medicine, "Magna Græcia" University of Catanzaro, 88100 Catanzaro, Italy
| | - Jessica Maiuolo
- Department of Health Science, Institute of Research for Food Safety & Health (IRC-FSH), "Magna Græcia" University of Catanzaro, 88100 Catanzaro, Italy
| | - Francesca Oppedisano
- Department of Health Science, Institute of Research for Food Safety & Health (IRC-FSH), "Magna Græcia" University of Catanzaro, 88100 Catanzaro, Italy
| | - Ernesto Palma
- Department of Health Science, Institute of Research for Food Safety & Health (IRC-FSH), "Magna Græcia" University of Catanzaro, 88100 Catanzaro, Italy
| | - Carlo Tomino
- Scientific Direction, IRCCS San Raffaele Roma, 00166 Rome, Italy
| | - William Raffaeli
- Institute for Research on Pain, ISAL Foundation, Torre Pedrera, 47922 Rimini, Italy
| | - Vincenzo Mollace
- Department of Health Science, Institute of Research for Food Safety & Health (IRC-FSH), "Magna Græcia" University of Catanzaro, 88100 Catanzaro, Italy
| | - Carolina Muscoli
- Department of Health Science, Institute of Research for Food Safety & Health (IRC-FSH), "Magna Græcia" University of Catanzaro, 88100 Catanzaro, Italy
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López-Siles M, Moure Z, Muadica AS, Sánchez S, Cruces R, Ávila A, Lara N, Köster PC, Dashti A, Oteo-Iglesias J, Carmena D, McConnell MJ. Fecal carriage of extended-spectrum beta-lactamase-producing Enterobacterales in healthy Spanish schoolchildren. Front Microbiol 2023; 14:1035291. [PMID: 37362938 PMCID: PMC10288999 DOI: 10.3389/fmicb.2023.1035291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 05/16/2023] [Indexed: 06/28/2023] Open
Abstract
Background Extended-spectrum ß-lactamase-producing Enterobacterales (ESBL-E) are a serious threat among emerging antibiotic resistant bacteria. Particularly, the number of cases of ESBL-E infections reported in children has been increasing in recent years, and approved antibiotic treatments for this age group are limited. However, information regarding the prevalence of colonization in European children, risk factors associated with colonization, and the characteristics of the colonizing strains is scarce. The aims of this study were to determine the prevalence of ESBL-E colonization in fecal samples of apparently healthy schoolchildren, to identify lifestyle routines associated with colonization, and to characterize clonal relationships and mechanisms of resistance in ESBL-E isolates. Methods A cohort of 887 healthy children (3-13 years old) from seven primary and secondary schools in the Madrid metropolitan area was recruited between April-June 2018, and sociodemographic information and daily habits were collected. Fecal samples were screened for ESBL-E carriage in selective medium. ESBL-E isolates were further characterized by assessing molecular epidemiology (PFGE and MLST), ESBL gene carriage, and antibiotic resistance profile. This information was analyzed in conjunction with the metadata of the participants in order to identify external factors associated with ESBL-E carriage. Results Twenty four ESBL-E, all but one Escherichia coli, were detected in 23 children (prevalence: 2.6%; 95% CI: 1.6-3.6%). Of these, seven contained the blaCTX-M-14 allele, five the blaCTX-M-15, five the blaSHV-12, three the blaCTX-M-27, three the blaCTX-M-32, and one the blaCTX-M-9. Significant clonal diversity was observed among the isolates that grouped into 22 distinct clusters (at <85% similarity of PFGE profile). ESBL-producing E. coli isolates belonged to 12 different STs, with ST10 (25%) and ST131 (17%) being the most frequent. Apart from ß-lactams, resistance to trimethoprim/sulfamethoxazole (46%), ciprofloxacin (33%), levofloxacin (33%), tobramycin (21%), and gentamicin (8%) were the most frequently detected. Conclusion The prevalence of ESBL-E in the studied cohort of children was lower than the average colonization rate previously detected in Europe for both children and adults. E. coli was the main ESBL-producing species detected and CTX-M were the most frequently identified ESBLs. High ST diversity suggests polyclonal dissemination. Compared to other STs, ST131 isolates were associated with resistance to various antimicrobials.
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Affiliation(s)
- Mireia López-Siles
- Intrahospital Infections Unit, Reference and Research Laboratory in Resistance to Antibiotics and Infections Related to Healthcare, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Serra Húnter Fellow, Microbiology of Intestinal Diseases, Biology Department, Universitat de Girona, Girona, Spain
| | - Zaira Moure
- Reference and Research Laboratory in Resistance to Antibiotics and Infections Related to Healthcare, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla, Instituto de Investigación Sanitaria, (IDIVAL), Santander, Spain
| | - Aly Salimo Muadica
- Parasitology Reference and Research Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- Departamento de Ciências e Tecnologia, Universidade Licungo, Quelimane, Mozambique
| | - Sergio Sánchez
- Reference and Research Laboratory of Food and Waterborne Bacterial Infections, National Center for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Raquel Cruces
- Intrahospital Infections Unit, Reference and Research Laboratory in Resistance to Antibiotics and Infections Related to Healthcare, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Alicia Ávila
- Reference and Research Laboratory in Resistance to Antibiotics and Infections Related to Healthcare, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Noelia Lara
- Reference and Research Laboratory in Resistance to Antibiotics and Infections Related to Healthcare, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Pamela Carolina Köster
- Parasitology Reference and Research Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Alejandro Dashti
- Parasitology Reference and Research Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Jesús Oteo-Iglesias
- Reference and Research Laboratory in Resistance to Antibiotics and Infections Related to Healthcare, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- Spanish Network for Research in Infectious Diseases (REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - David Carmena
- Parasitology Reference and Research Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Michael J. McConnell
- Intrahospital Infections Unit, Reference and Research Laboratory in Resistance to Antibiotics and Infections Related to Healthcare, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
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Fernandes A, Oliveira A, Carvalho AL, Soares R, Barata P. Faecalibacterium prausnitzii in Differentiated Thyroid Cancer Patients Treated with Radioiodine. Nutrients 2023; 15:2680. [PMID: 37375584 DOI: 10.3390/nu15122680] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Faecalibacterium prausnitzii, one of the most important bacteria of the human gut microbiota, produces butyrate (a short-chain fatty acid). Short-chain fatty acids are known to influence thyroid physiology and thyroid cancer's response to treatment. We aimed to analyze the relative abundance of Faecalibacterium prausnitzii on the gut microbiota of differentiated thyroid cancer patients compared to controls and its variation after radioiodine therapy (RAIT). METHODS Fecal samples were collected from 37 patients diagnosed with differentiated thyroid cancer before and after radioiodine therapy and from 10 volunteers. The abundance of F. prausnitzii was determined using shotgun metagenomics. RESULTS Our study found that the relative abundance of F. prausnitzii is significantly reduced in thyroid cancer patients compared to volunteers. We also found that there was a mixed response to RAIT, with an increase in the relative and absolute abundances of this bacterium in most patients. CONCLUSIONS Our study confirms that thyroid cancer patients present a dysbiotic gut microbiota, with a reduction in F. prausnitzii's relative abundance. In our study, radioiodine did not negatively affect F. prausnitzii, quite the opposite, suggesting that this bacterium might play a role in resolving radiation aggression issues.
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Affiliation(s)
- Ana Fernandes
- Department of Nuclear Medicine, Centro Hospitalar Universitário de São João, E.P.E., 4200-319 Porto, Portugal
| | - Ana Oliveira
- Department of Nuclear Medicine, Centro Hospitalar Universitário de São João, E.P.E., 4200-319 Porto, Portugal
| | - Ana Luísa Carvalho
- Department of Nuclear Medicine, Centro Hospitalar Universitário de São João, E.P.E., 4200-319 Porto, Portugal
| | - Raquel Soares
- Department of Biomedicine, Faculdade de Medicina da Universidade do Porto, 4200-319 Porto, Portugal
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Pedro Barata
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- Department of Pharmaceutical Science, Faculdade de Ciências da Saúde da Universidade Fernando Pessoa, 4249-004 Porto, Portugal
- Department of Pathology, Centro Hospitalar Universitário do Porto, 4099-001 Porto, Portugal
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Estevinho MM, Cabeda J, Santiago M, Machado E, Silva R, Duro M, Pita I, Morais R, Macedo G, Bull TJ, Magro F, Sarmento A. Viable Mycobacterium avium subsp. paratuberculosis Colonizes Peripheral Blood of Inflammatory Bowel Disease Patients. Microorganisms 2023; 11:1520. [PMID: 37375022 DOI: 10.3390/microorganisms11061520] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/31/2023] [Accepted: 06/04/2023] [Indexed: 06/29/2023] Open
Abstract
Pathobionts, particularly Mycobacterium avium subsp. paratuberculosis (MAP) and Escherichia coli isolates with adherence/invasive ability (AIEC) have been associated with inflammatory bowel disease (IBD), particularly Crohn's disease (CD). This study aimed to evaluate the frequency of viable MAP and AIEC in a cohort of IBD patients. As such, MAP and E. coli cultures were established from faecal and blood samples (with a total n = 62 for each) of patients with CD (n = 18), ulcerative colitis (UC, n = 15), or liver cirrhosis (n = 7), as well as from healthy controls (HC, n = 22). Presumptive positive cultures were tested by polymerase chain reaction (PCR), for a positive confirmation of MAP or E. coli identity. E. coli-confirmed isolates were then tested for AIEC identity using adherence and invasion assays in the epithelial cell line of Caco-2 and survival and replication assays in the macrophage cell line of J774. MAP sub-culture and genome sequencing were also performed. MAP was more frequently cultured from the blood and faecal samples of patients with CD and cirrhosis. E. coli presumptive colonies were isolated from the faecal samples of most individuals, in contrast to what was registered for the blood samples. Additionally, from the confirmed E. coli isolates, only three had an AIEC-like phenotype (i.e., one CD patient and two UC patients). This study confirmed the association between MAP and CD; however, it did not find a strong association between the presence of AIEC and CD. It may be hypothesized that the presence of viable MAP in the bloodstream of CD patients contributes to disease reactivation.
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Affiliation(s)
- Maria Manuela Estevinho
- Department of Gastroenterology, Vila Nova de Gaia/Espinho Hospital Center, 4434-502 Vila Nova de Gaia, Portugal
- Department of Biomedicine, Unit of Pharmacology and Therapeutics, Faculty of Medicine, University of Porto, 4050-313 Porto, Portugal
| | - José Cabeda
- FP-I3ID, Universidade Fernando Pessoa, 4200-150 Porto, Portugal
- Escola Superior de Saúde Fernando Pessoa, 4200-253 Porto, Portugal
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR, CIMAR), 4450-208 Matosinhos, Portugal
| | - Mafalda Santiago
- Department of Biomedicine, Unit of Pharmacology and Therapeutics, Faculty of Medicine, University of Porto, 4050-313 Porto, Portugal
| | - Elisabete Machado
- FP-I3ID, Universidade Fernando Pessoa, 4200-150 Porto, Portugal
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Faculdade de Ciências da Saúde, Universidade Fernando Pessoa, 4200-150 Porto, Portugal
| | - Ricardo Silva
- FP-I3ID, Universidade Fernando Pessoa, 4200-150 Porto, Portugal
- Escola Superior de Saúde Fernando Pessoa, 4200-253 Porto, Portugal
| | - Mary Duro
- FP-I3ID, Universidade Fernando Pessoa, 4200-150 Porto, Portugal
- Escola Superior de Saúde Fernando Pessoa, 4200-253 Porto, Portugal
- LAQV@REQUIMTE, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Inês Pita
- Department of Gastroenterology, Entre Douro e Vouga Hospital Center, 4520-211 Santa Maria da Feira, Portugal
| | - Rui Morais
- Department of Gastroenterology, São João University Hospital Center, 4200-319 Porto, Portugal
| | - Guilherme Macedo
- Department of Gastroenterology, São João University Hospital Center, 4200-319 Porto, Portugal
| | - Tim J Bull
- Institute of Infection and Immunity, St George's University of London, London SW17 ORE, UK
| | - Fernando Magro
- Department of Biomedicine, Unit of Pharmacology and Therapeutics, Faculty of Medicine, University of Porto, 4050-313 Porto, Portugal
- Department of Gastroenterology, São João University Hospital Center, 4200-319 Porto, Portugal
| | - Amélia Sarmento
- FP-I3ID, Universidade Fernando Pessoa, 4200-150 Porto, Portugal
- Faculdade de Ciências da Saúde, Universidade Fernando Pessoa, 4200-150 Porto, Portugal
- I3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-150 Porto, Portugal
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Wade H, Pan K, Duan Q, Kaluzny S, Pandey E, Fatumoju L, Saraswathi V, Wu R, Harris EN, Su Q. Akkermansia muciniphila and its membrane protein ameliorates intestinal inflammatory stress and promotes epithelial wound healing via CREBH and miR-143/145. J Biomed Sci 2023; 30:38. [PMID: 37287024 DOI: 10.1186/s12929-023-00935-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 05/30/2023] [Indexed: 06/09/2023] Open
Abstract
BACKGROUND The intestinal epithelial barrier is the interface for interaction between gut microbiota and host metabolic systems. Akkermansia muciniphila (A. muciniphila) is a key player in the colonic microbiota that resides in the mucus layer, whose abundance is selectively decreased in the faecal microbiota of inflammatory bowel disease (IBD) patients. This study aims to investigate the regulatory mechanism among A. muciniphila, a transcription factor cAMP-responsive element-binding protein H (CREBH), and microRNA-143/145 (miR-143/145) in intestinal inflammatory stress, gut barrier integrity and epithelial regeneration. METHODS A novel mouse model with increased colonization of A muciniphila in the intestine of CREBH knockout mice, an epithelial wound healing assay and several molecular biological techniques were applied in this study. Results were analysed using a homoscedastic 2-tailed t-test. RESULTS Increased colonization of A. muciniphila in mouse gut enhanced expression of intestinal CREBH, which was associated with the mitigation of intestinal endoplasmic reticulum (ER) stress, gut barrier leakage and blood endotoxemia induced by dextran sulfate sodium (DSS). Genetic depletion of CREBH (CREBH-KO) significantly inhibited the expression of tight junction proteins that are associated with gut barrier integrity, including Claudin5 and Claudin8, but upregulated Claudin2, a tight junction protein that enhances gut permeability, resulting in intestinal hyperpermeability and inflammation. Upregulation of CREBH by A. muciniphila further coupled with miR-143/145 promoted intestinal epithelial cell (IEC) regeneration and wound repair via insulin-like growth factor (IGF) and IGFBP5 signalling. Moreover, the gene expressing an outer membrane protein of A. muciniphila, Amuc_1100, was cloned into a mammalian cell-expression vector and successfully expressed in porcine and human IECs. Expression of Amuc_1100 in IECs could recapitulate the health beneficial effect of A. muciniphila on the gut by activating CREBH, inhibiting ER stress and enhancing the expression of genes involved in gut barrier integrity and IEC's regeneration. CONCLUSIONS This study uncovers a novel mechanism that links A. muciniphila and its membrane protein with host CREBH, IGF signalling and miRNAs in mitigating intestinal inflammatory stress-gut barrier permeability and promoting intestinal wound healing. This novel finding may lend support to the development of therapeutic approaches for IBD by manipulating the interaction between host genes, gut bacteria and its bioactive components.
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Affiliation(s)
- Henry Wade
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, BT9 5DL, UK
| | - Kaichao Pan
- Department of Medicine, Section of Cardiology, University of Chicago, Chicago, USA
| | - Qihua Duan
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, BT9 5DL, UK
| | - Szczepan Kaluzny
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, BT9 5DL, UK
| | - Ekta Pandey
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Linda Fatumoju
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | | | - Rongxue Wu
- Department of Medicine, Section of Cardiology, University of Chicago, Chicago, USA
| | - Edward N Harris
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Qiaozhu Su
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, BT9 5DL, UK.
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Gong Y, Chen A, Zhang G, Shen Q, Zou L, Li J, Miao YB, Liu W. Cracking Brain Diseases from Gut Microbes-Mediated Metabolites for Precise Treatment. Int J Biol Sci 2023; 19:2974-2998. [PMID: 37416776 PMCID: PMC10321288 DOI: 10.7150/ijbs.85259] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 05/24/2023] [Indexed: 07/08/2023] Open
Abstract
The gut-brain axis has been a subject of significant interest in recent years. Understanding the link between the gut and brain axis is crucial for the treatment of disorders. Here, the intricate components and unique relationship between gut microbiota-derived metabolites and the brain are explained in detail. Additionally, the association between gut microbiota-derived metabolites and the integrity of the blood-brain barrier and brain health is emphasized. Meanwhile, gut microbiota-derived metabolites with their recent applications, challenges and opportunities their pathways on different disease treatment are focus discussed. The prospective strategy of gut microbiota-derived metabolites potential applies to the brain disease treatments, such as Parkinson's disease and Alzheimer's disease, is proposed. This review provides a broad perspective on gut microbiota-derived metabolites characteristics facilitate understand the connection between gut and brain and pave the way for the development of a new medication delivery system for gut microbiota-derived metabolites.
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Affiliation(s)
- Ying Gong
- Department of Haematology, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine of University of Electronic Science and Technology of China, No. 32, West Section 2, First Ring Road, Qingyang District, Chengdu 610000, China
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610041, China
| | - Anmei Chen
- Department of Haematology, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine of University of Electronic Science and Technology of China, No. 32, West Section 2, First Ring Road, Qingyang District, Chengdu 610000, China
| | - Guohui Zhang
- Key Laboratory of reproductive medicine, Sichuan Provincial maternity and Child Health Care Hospital, Chengdu 610000, China
| | - Qing Shen
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610041, China
| | - Liang Zou
- School of Food and Biological Engineering, Chengdu University, Chengdu 610106, Sichuan, China
| | - Jiahong Li
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610041, China
| | - Yang-Bao Miao
- Department of Haematology, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine of University of Electronic Science and Technology of China, No. 32, West Section 2, First Ring Road, Qingyang District, Chengdu 610000, China
| | - Weixin Liu
- Key Laboratory of reproductive medicine, Sichuan Provincial maternity and Child Health Care Hospital, Chengdu 610000, China
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Bouferraa Y, Fares C, Bou Zerdan M, Boyce Kennedy L. Microbial Influences on Immune Checkpoint Inhibitor Response in Melanoma: The Interplay between Skin and Gut Microbiota. Int J Mol Sci 2023; 24:ijms24119702. [PMID: 37298653 DOI: 10.3390/ijms24119702] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/29/2023] [Accepted: 05/31/2023] [Indexed: 06/12/2023] Open
Abstract
Immunotherapy has revolutionized the treatment of melanoma, but its limitations due to resistance and variable patient responses have become apparent. The microbiota, which refers to the complex ecosystem of microorganisms that inhabit the human body, has emerged as a promising area of research for its potential role in melanoma development and treatment response. Recent studies have highlighted the role of microbiota in influencing the immune system and its response to melanoma, as well as its influence on the development of immune-related adverse events associated with immunotherapy. In this article, we discuss the complex multifactorial mechanisms through which skin and gut microbiota can affect the development of melanoma including microbial metabolites, intra-tumor microbes, UV light, and the immune system. In addition, we will discuss the pre-clinical and clinical studies that have demonstrated the influence of different microbial profiles on response to immunotherapy. Additionally, we will explore the role of microbiota in the development of immune-mediated adverse events.
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Affiliation(s)
- Youssef Bouferraa
- Department of Internal Medicine, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
| | - Callie Fares
- Faculty of Medicine, American University of Beirut, Beirut 2020, Lebanon
| | - Maroun Bou Zerdan
- Department of Internal Medicine, SUNY Upstate Medical University, New York, NY 13205, USA
| | - Lucy Boyce Kennedy
- Department of Hematology and Medical Oncology, Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
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Nowicki C, Ray L, Engen P, Madrigrano A, Witt T, Lad T, Cobleigh M, Mutlu EA. Comparison of gut microbiome composition in colonic biopsies, endoscopically-collected and at-home-collected stool samples. Front Microbiol 2023; 14:1148097. [PMID: 37323911 PMCID: PMC10264612 DOI: 10.3389/fmicb.2023.1148097] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 05/09/2023] [Indexed: 06/17/2023] Open
Abstract
Aim The goal of this study is to compare microbiome composition in three different sample types in women, namely stool brought from home vs. solid stool samples obtained at the time of an unprepped sigmoidoscopy vs. biopsies of the colonic mucosa at the time of an unprepped sigmoidoscopy, using alpha- and beta-diversity metrics following bacterial 16S rRNA sequencing. The findings may have relevance to health and disease states in which bacterial metabolism has a significant impact on molecules/metabolites that are recirculated between the gut lumen and mucosa and systemic circulation, such as estrogens (as in breast cancer) or bile acids. Methods Concomitant at-home-collected stool, endoscopically-collected stool, and colonic biopsy samples were collected from 48 subjects (24 breast cancer, 24 control.) After 16S rRNA sequencing, an amplicon sequence variant (ASV) based approach was used to analyze the data. Alpha diversity metrics (Chao1, Pielou's Evenness, Faith PD, Shannon, and Simpson) and beta diversity metrics (Bray-Curtis, Weighted and Unweighted Unifrac) were calculated. LEfSe was used to analyze differences in the abundance of various taxa between sample types. Results Alpha and beta diversity metrics were significantly different between the three sample types. Biopsy samples were different than stool samples in all metrics. The highest variation in microbiome diversity was noted in the colonic biopsy samples. At-home and endoscopically-collected stool showed more similarities in count-based and weighted beta diversity metrics. There were significant differences in rare taxa and phylogenetically-diverse taxa between the two types of stool samples. Generally, there were higher levels of Proteobacteria in biopsy samples, with significantly more Actinobacteria and Firmicutes in stool (all p < 0.001, q-value < 0.05). Overall, there was a significantly higher relative abundance of Lachnospiraceae and Ruminococcaceae in stool samples (at-home collected and endoscopically-collected) and higher abundances of Tisserellaceae in biopsy samples (all p < 0.001, q-value < 0.05). Conclusion Our data shows that different sampling methods can impact results when looking at the composition of the gut microbiome using ASV-based approaches.
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Affiliation(s)
- Christina Nowicki
- Department of Internal Medicine, Division of Digestive Diseases and Nutrition, Rush University Medical Center, Chicago, IL, United States
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Illinois at Chicago, Chicago, IL, United States
| | - Lucille Ray
- Department of Internal Medicine, Division of Digestive Diseases and Nutrition, Rush University Medical Center, Chicago, IL, United States
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Illinois at Chicago, Chicago, IL, United States
| | - Philip Engen
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, United States
| | - Andrea Madrigrano
- Department of Surgery, Rush Medical College, Rush University Medical Center, Chicago, IL, United States
| | - Thomas Witt
- Department of Surgery, Rush Medical College, Rush University Medical Center, Chicago, IL, United States
| | - Thomas Lad
- Department of Oncology, Cook County Health and Hospital Systems, Chicago, IL, United States
| | - Melody Cobleigh
- Department of Internal Medicine, Division of Hematology, Oncology, and Cell Therapy, Rush University Medical Center, Chicago, IL, United States
| | - Ece A. Mutlu
- Department of Internal Medicine, Division of Digestive Diseases and Nutrition, Rush University Medical Center, Chicago, IL, United States
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Illinois at Chicago, Chicago, IL, United States
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225
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Boyanova L, Markovska R, Yordanov D, Gergova R, Hadzhiyski P. Anaerobes in specific infectious and noninfectious diseases: new developments. Anaerobe 2023; 81:102714. [PMID: 37349047 DOI: 10.1016/j.anaerobe.2023.102714] [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: 11/19/2022] [Revised: 01/21/2023] [Accepted: 02/03/2023] [Indexed: 06/24/2023]
Abstract
With the buildup of new research data, newer associations between anaerobic bacteria and diseases/conditions were evaluated. The aim of the mini-review was to draw attention and to encourage further multidisciplinary studies of the associations. We considered microbiome-disease correlations such as a decrease of fecal Faecalibacterium prausnitzii abundance in inflammatory bowel disease (IBD) and IBD recurrence, suggesting that F. prausnitzii could be a good biomarker for IBD. A link of subgingival Porphyromonas gingivalis with cardiovascular diseases was reported. Decreased Roseburia abundance was observed in the gut of Alzheimer's and Parkinson's disease patients. Akkermansia muciniphila was found to improve adipose/glucose metabolism, however, its intestinal abundance was observed in neurodegenerative diseases as well. Severe Clostridioides difficile infections have been reported in neonates and young children. Carcinogenic potential of anaerobes has been suggested. Fusobacterium nucleatum was implicated in the development of oral and colorectal cancer, Porphyromonas gingivalis and Tannerella forsythia were linked to esophageal cancer and Cutibacterium acnes subsp. defendens was associated with prostate cancer. However, there are some controversies about the results. In a Swedish longitudinal study, neither P. gingivalis nor T. forsythia exhibited oncogenic potential. The present data can enrich knowledge of anaerobic bacteria and their multifaceted significance for health and disease and can draw future research directions. However, more studies on large numbers of patients over prolonged periods are needed, taking into account the possible changes in the microbiota over time.
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Affiliation(s)
- Lyudmila Boyanova
- Department of Medical Microbiology, Medical University of Sofia, 2 Zdrave Str., 1431, Sofia, Bulgaria.
| | - Rumyana Markovska
- Department of Medical Microbiology, Medical University of Sofia, 2 Zdrave Str., 1431, Sofia, Bulgaria
| | - Daniel Yordanov
- Department of Medical Microbiology, Medical University of Sofia, 2 Zdrave Str., 1431, Sofia, Bulgaria
| | - Raina Gergova
- Department of Medical Microbiology, Medical University of Sofia, 2 Zdrave Str., 1431, Sofia, Bulgaria
| | - Petyo Hadzhiyski
- Specialized Hospital for Active Pediatric Treatment, Medical University of Sofia, "Acad. Ivan Evstatiev Geshov" Blvd, 1606, Sofia, Bulgaria
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226
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Kallassy J, Gagnon E, Rosenberg D, Silbart LK, McManus SA. Strains of Faecalibacterium prausnitzii and its extracts reduce blood glucose levels, percent HbA1c, and improve glucose tolerance without causing hypoglycemic side effects in diabetic and prediabetic mice. BMJ Open Diabetes Res Care 2023; 11:11/3/e003101. [PMID: 37277225 DOI: 10.1136/bmjdrc-2022-003101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 05/20/2023] [Indexed: 06/07/2023] Open
Abstract
INTRODUCTION The commensal bacterium Faecalibacterium prausnitzii is a prominent member of the microbiome of animals and humans, and it plays an important role in several physiological processes. Numerous studies have correlated the reduction of F. prausnitzii abundance with many disease states, including irritable bowel syndrome, Crohn's disease, obesity, asthma, major depressive disorder, and metabolic diseases in humans. Studies have also correlated F. prausnitzii with diseases in humans involved in altered glucose metabolism, including diabetes. RESEARCH DESIGN AND METHODS The aim of this study was to investigate the effects of compositions derived from three strains of F. prausnitzii (coined FPZ) on glucose metabolism in diet-induced obese male C57BL/6J prediabetic and type 2 diabetic mice. The primary endpoints of these studies were measuring changes in fasting blood glucose, glucose tolerance (as measured by a glucose tolerance test), and percent hemoglobin A1c (HbA1c) with longer term treatment. Two placebo-controlled trials were carried out using both live cell FPZ and killed cell FPZ and extracts. Two additional placebo-controlled trials were carried out in non-diabetic mice and mice that previously had type 2 diabetes (T2D). RESULTS Both trials in prediabetic and diabetic mice revealed that peroral administration of live FPZ or extracts from FPZ lowered fasting blood glucose levels and improved glucose tolerance compared with control mice. A trial administering longer FPZ treatment also resulted in lowered percent HbA1c compared with control mice. Additionally, trials in non-diabetic mice treated with FPZ demonstrated that FPZ treatment does not lead to hypoglycemia. CONCLUSIONS The trial results have shown that treatment with different formulations of FPZ result in lower blood glucose levels, lower percent HbA1c, and improved glucose response in mice compared with control prediabetic/diabetic mice. FPZ is a promising candidate as an orally administered probiotic or postbiotic to manage and improve pre-diabetes and T2D.
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Affiliation(s)
| | | | | | - Lawrence K Silbart
- Department of Allied Health Sciences, University of Connecticut, Storrs, Connecticut, USA
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Nagaoka K, Kawasuji H, Takegoshi Y, Murai Y, Kaneda M, Kimoto K, Tani H, Niimi H, Morinaga Y, Noguchi K, Yamamoto Y. Dominant CT Patterns and Immune Responses during the Early Infection Phases of Different SARS-CoV-2 Variants. Viruses 2023; 15:1304. [PMID: 37376606 DOI: 10.3390/v15061304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 05/30/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023] Open
Abstract
Ground-glass opacity (GGO) and organizing pneumonia (OP) are dominant pulmonary CT lesions associated with COVID-19. However, the role of different immune responses in these CT patterns remains unclear, particularly following the emergence of the Omicron variant. In this prospective observational study, we recruited patients hospitalized with COVID-19, before and after the emergence of Omicron variants. Semi-quantitative CT scores and dominant CT patterns were retrospectively determined for all patients within five days of symptom onset. Serum levels of IFN-α, IL-6, CXCL10, and VEGF were assessed using ELISA. Serum-neutralizing activity was measured using a pseudovirus assay. We enrolled 48 patients with Omicron variants and 137 with precedent variants. While the frequency of GGO patterns was similar between the two groups, the OP pattern was significantly more frequent in patients with precedent variants. In patients with precedent variants, IFN-α and CXCL10 levels were strongly correlated with GGO, whereas neutralizing activity and VEGF were correlated with OP. The correlation between IFN-α levels and CT scores was lower in patients with Omicron than in those with precedent variants. Compared to preceding variants, infection with the Omicron variant is characterized by a less frequent OP pattern and a weaker correlation between serum IFN-α and CT scores.
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Affiliation(s)
- Kentaro Nagaoka
- Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, 2630 Sugitani, Toyama 930-0194, Japan
- Clinical and Research Center for Infectious Diseases, Toyama University Hospital, 2630 Sugitani, Toyama 930-0194, Japan
| | - Hitoshi Kawasuji
- Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, 2630 Sugitani, Toyama 930-0194, Japan
| | - Yusuke Takegoshi
- Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, 2630 Sugitani, Toyama 930-0194, Japan
| | - Yushi Murai
- Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, 2630 Sugitani, Toyama 930-0194, Japan
| | - Makito Kaneda
- Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, 2630 Sugitani, Toyama 930-0194, Japan
| | - Kou Kimoto
- Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, 2630 Sugitani, Toyama 930-0194, Japan
| | - Hideki Tani
- Department of Virology, Toyama Institute of Health, 17-1 Nakataikouyama, Imizu-shi 939-0363, Japan
| | - Hideki Niimi
- Clinical and Research Center for Infectious Diseases, Toyama University Hospital, 2630 Sugitani, Toyama 930-0194, Japan
- Department of Clinical Laboratory and Molecular Pathology, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, 2630 Sugitani, Toyama 930-0194, Japan
- Center for Advanced Antibody Drug Development, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, 2630 Sugitani, Toyama 930-0194, Japan
| | - Yoshitomo Morinaga
- Clinical and Research Center for Infectious Diseases, Toyama University Hospital, 2630 Sugitani, Toyama 930-0194, Japan
- Center for Advanced Antibody Drug Development, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, 2630 Sugitani, Toyama 930-0194, Japan
- Department of Microbiology, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, 2630 Sugitani, Toyama 930-0194, Japan
| | - Kyo Noguchi
- Department of Radiology, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, 2630 Sugitani, Toyama 930-0194, Japan
| | - Yoshihiro Yamamoto
- Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, 2630 Sugitani, Toyama 930-0194, Japan
- Clinical and Research Center for Infectious Diseases, Toyama University Hospital, 2630 Sugitani, Toyama 930-0194, Japan
- Center for Advanced Antibody Drug Development, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, 2630 Sugitani, Toyama 930-0194, Japan
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228
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Segota I, Watrous JD, Kantz ED, Nallamshetty S, Tiwari S, Cheng S, Jain M, Long T. Reconstructing the landscape of gut microbial species across 29,000 diverse individuals. Nucleic Acids Res 2023; 51:4178-4190. [PMID: 37070603 PMCID: PMC10201371 DOI: 10.1093/nar/gkad249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 04/19/2023] Open
Abstract
The human gut microbiome has been linked to health and disease. Investigation of the human microbiome has largely employed 16S amplicon sequencing, with limited ability to distinguish microbes at the species level. Herein, we describe the development of Reference-based Exact Mapping (RExMap) of microbial amplicon variants that enables mapping of microbial species from standard 16S sequencing data. RExMap analysis of 16S data captures ∼75% of microbial species identified by whole-genome shotgun sequencing, despite hundreds-fold less sequencing depth. RExMap re-analysis of existing 16S data from 29,349 individuals across 16 regions from around the world reveals a detailed landscape of gut microbial species across populations and geography. Moreover, RExMap identifies a core set of fifteen gut microbes shared by humans. Core microbes are established soon after birth and closely associate with BMI across multiple independent studies. RExMap and the human microbiome dataset are presented as resources with which to explore the role of the human microbiome.
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Affiliation(s)
- Igor Segota
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jeramie D Watrous
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Edward D Kantz
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | | | - Saumya Tiwari
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Susan Cheng
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Mohit Jain
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Tao Long
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
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229
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Jati S, Mahata S, Das S, Chatterjee S, Mahata SK. Catestatin: Antimicrobial Functions and Potential Therapeutics. Pharmaceutics 2023; 15:1550. [PMID: 37242791 PMCID: PMC10220906 DOI: 10.3390/pharmaceutics15051550] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 05/09/2023] [Accepted: 05/14/2023] [Indexed: 05/28/2023] Open
Abstract
The rapid increase in drug-resistant and multidrug-resistant infections poses a serious challenge to antimicrobial therapies, and has created a global health crisis. Since antimicrobial peptides (AMPs) have escaped bacterial resistance throughout evolution, AMPs are a category of potential alternatives for antibiotic-resistant "superbugs". The Chromogranin A (CgA)-derived peptide Catestatin (CST: hCgA352-372; bCgA344-364) was initially identified in 1997 as an acute nicotinic-cholinergic antagonist. Subsequently, CST was established as a pleiotropic hormone. In 2005, it was reported that N-terminal 15 amino acids of bovine CST (bCST1-15 aka cateslytin) exert antibacterial, antifungal, and antiyeast effects without showing any hemolytic effects. In 2017, D-bCST1-15 (where L-amino acids were changed to D-amino acids) was shown to exert very effective antimicrobial effects against various bacterial strains. Beyond antimicrobial effects, D-bCST1-15 potentiated (additive/synergistic) antibacterial effects of cefotaxime, amoxicillin, and methicillin. Furthermore, D-bCST1-15 neither triggered bacterial resistance nor elicited cytokine release. The present review will highlight the antimicrobial effects of CST, bCST1-15 (aka cateslytin), D-bCST1-15, and human variants of CST (Gly364Ser-CST and Pro370Leu-CST); evolutionary conservation of CST in mammals; and their potential as a therapy for antibiotic-resistant "superbugs".
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Affiliation(s)
- Suborno Jati
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA;
| | - Sumana Mahata
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA;
| | - Soumita Das
- Department of Biomedical and Nutritional Science, University of Massachusetts Lowell, Lowell, MA 01854, USA;
| | - Saurabh Chatterjee
- Department of Medicine, University of California Irvine, Irvine, CA 92697, USA;
| | - Sushil K. Mahata
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA;
- VA San Diego Healthcare System, 3350 La Jolla Village Drive, San Diego, CA 92161, USA
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230
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Bao Z, Wei R, Zheng X, Zhang T, Bi Y, Shen S, Zou P, Zhang J, Yan H, Li MD, Yang Z, Gao H. Landscapes of gut microbiome and bile acid signatures and their interaction in HBV-associated acute-on-chronic liver failure. Front Microbiol 2023; 14:1185993. [PMID: 37275140 PMCID: PMC10233926 DOI: 10.3389/fmicb.2023.1185993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 04/17/2023] [Indexed: 06/07/2023] Open
Abstract
Introduction Submassive hepatic necrosis (SMHN, defined as necrosis of 15-90% of the entire liver on explant) is a likely characteristic pathological feature of ACLF in patients with hepatitis B cirrhosis. We aimed to comprehensively explore microbiome and bile acids patterns across enterhepatic circulation and build well-performing machine learning models to predict SMHN status. Methods Based on the presence or absence of SMHN, 17 patients with HBV-related end-stage liver disease who received liver transplantation were eligible for inclusion. Serum, portal venous blood, and stool samples were collected for comparing differences of BA spectra and gut microbiome and their interactions. We adopted the random forest algorithm with recursive feature elimination (RF-RFE) to predict SMHN status. Results By comparing total BA spectrum between SMHN (-) and SMHN (+) patients, significant changes were detected only in fecal (P = 0.015). Compared with the SMHN (+) group, the SMHN (-) group showed that UDCA, 7-KLCA, 3-DHCA, 7-KDCA, ISOLCA and α-MCA in feces, r-MCA, 7-KLCA and 7-KDCA in serum, γ-MCA and 7-KLCA in portal vein were enriched, and TUDCA in feces was depleted. PCoA analysis showed significantly distinct overall microbial composition in two groups (P = 0.026). Co-abundance analysis showed that bacterial species formed strong and broad relationships with BAs. Among them, Parabacteroides distasonis had the highest node degree. We further identified a combinatorial marker panel with a high AUC of 0.92. Discussion Our study demonstrated the changes and interactions of intestinal microbiome and BAs during enterohepatic circulation in ACLF patients with SMHN. In addition, we identified a combinatorial marker panel as non-invasive biomarkers to distinguish the SMHN status with high AUC.
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Affiliation(s)
- Zhiwei Bao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Runan Wei
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoping Zheng
- Department of Infectious Diseases, ShuLan (Hangzhou) Hospital Affiliated to Zhejiang Shuren University Shulan International Medical College, Hangzhou, China
| | - Ting Zhang
- Department of Infectious Diseases, ShuLan (Hangzhou) Hospital Affiliated to Zhejiang Shuren University Shulan International Medical College, Hangzhou, China
| | - Yunjiao Bi
- The Second Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, China
| | - Sijia Shen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Pengfei Zou
- Department of Infectious Diseases, ShuLan (Hangzhou) Hospital Affiliated to Zhejiang Shuren University Shulan International Medical College, Hangzhou, China
| | - Junjie Zhang
- The Second Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, China
| | - Huadong Yan
- Department of Infectious Diseases, ShuLan (Hangzhou) Hospital Affiliated to Zhejiang Shuren University Shulan International Medical College, Hangzhou, China
| | - Ming D. Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Research Center for Air Pollution and Health, Zhejiang University, Hangzhou, China
| | - Zhongli Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hainv Gao
- Department of Infectious Diseases, ShuLan (Hangzhou) Hospital Affiliated to Zhejiang Shuren University Shulan International Medical College, Hangzhou, China
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Bender C, Stoll D, Huch M, Weinert C, Dötsch A, Dräger H, Keller J, Kulling S, Bunzel M. Time-dependent fermentation of different structural units of commercial pectins with intestinal bacteria. Carbohydr Polym 2023; 308:120642. [PMID: 36813335 DOI: 10.1016/j.carbpol.2023.120642] [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: 10/07/2022] [Revised: 01/12/2023] [Accepted: 01/27/2023] [Indexed: 02/01/2023]
Abstract
Many of the proposed health-related properties of pectins are based on their fermentability in the large intestine, but detailed structure-related studies on pectin fermentation have not been reported so far. Here, pectin fermentation kinetics were studied with a focus on structurally different pectic polymers. Therefore, six commercial pectins from citrus, apple, and sugar beet were chemically characterized and fermented in in vitro fermentation assays with human fecal samples over different periods of time (0 h, 4 h, 24 h, 48 h). Structure elucidation of intermediate cleavage products showed differences in fermentation speed and/or fermentation rate among the pectins, but the order in which specific structural pectic elements were fermented was comparable across all pectins. Neutral side chains of rhamnogalacturonan type I were fermented first (between 0 and 4 h), followed by homogalacturonan units (between 0 and 24 h) and, at last, the rhamnogalacturonan type I backbone (between 4 and 48 h). This indicates that fermentation of different pectic structural units might take place in different sections of the colon, potentially affecting their nutritional properties. For the formation of different short-chain fatty acids, mainly acetate, propionate, and butyrate, and the influence on microbiota, there was no time-dependent correlation regarding the pectic subunits. However, an increase of members of the bacterial genera Faecalibacterium, Lachnoclostridium, and Lachnospira was observed for all pectins.
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Affiliation(s)
- Caroline Bender
- Institute of Applied Biosciences, Department of Food Chemistry and Phytochemistry, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Dominic Stoll
- Federal Research Institute of Nutrition and Food, Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Karlsruhe, Germany
| | - Melanie Huch
- Federal Research Institute of Nutrition and Food, Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Karlsruhe, Germany
| | - Christoph Weinert
- Federal Research Institute of Nutrition and Food, Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Karlsruhe, Germany
| | - Andreas Dötsch
- Federal Research Institute of Nutrition and Food, Department of Physiology and Biochemistry of Nutrition, Max Rubner-Institut, Karlsruhe, Germany
| | - Hannah Dräger
- Institute of Applied Biosciences, Department of Food Chemistry and Phytochemistry, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Judith Keller
- Institute of Applied Biosciences, Department of Food Chemistry and Phytochemistry, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Sabine Kulling
- Federal Research Institute of Nutrition and Food, Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Karlsruhe, Germany
| | - Mirko Bunzel
- Institute of Applied Biosciences, Department of Food Chemistry and Phytochemistry, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany.
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Dahal RH, Kim S, Kim YK, Kim ES, Kim J. Insight into gut dysbiosis of patients with inflammatory bowel disease and ischemic colitis. Front Microbiol 2023; 14:1174832. [PMID: 37250025 PMCID: PMC10211348 DOI: 10.3389/fmicb.2023.1174832] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 04/17/2023] [Indexed: 05/31/2023] Open
Abstract
The collection of whole microbial communities (bacteria, archaea, fungi, and viruses) together constitutes the gut microbiome. Diet, age, stress, host genetics, and diseases cause increases or decreases in the relative abundance and diversity of bacterial species (dysbiosis). We aimed to investigate the gut microbial composition at different taxonomic levels of healthy controls (HCs) with active Crohn's disease (CD), ulcerative colitis (UC), and ischemic colitis (IC) using culture- and non-culture-based approaches and identify biomarkers to discriminate CD, UC, or IC. We determined the specific changes in the gut microbial profile using culture-independent (16S rRNA gene amplicon sequencing) as well as culture-based (culturomic) approaches. Biomarkers were validated using quantitative Real-Time PCR (qPCR). In both methods, bacterial diversity and species richness decreased in disease-associated conditions compared with that in HCs. Highly reduced abundance of Faecalibacterium prausnitzii and Prevotella sp. and an increased abundance of potentially pathogenic bacteria such as Enterococcus faecium, Enterococcus faecalis, and Escherichia coli in all CD, UC, or IC conditions were observed. We noted a high abundance of Latilactobacillus sakei in CD patients; Ligilactobacillus ruminis in UC patients; and Enterococcus faecium, Escherichia coli, and Enterococcus faecalis in IC patients. Highly reduced abundance of Faecalibacterium prausnitzii in all cases, and increased abundance of Latilactobacillus sakei and Enterococcus faecium in CD, Ligilactobacillus ruminis and Enterococcus faecium in UC, and Enterococcus faecium, Escherichia coli, and Enterococcus faecalis in IC could be biomarkers for CD, UC, and IC, respectively. These biomarkers may help in IBD (CD or UC) and IC diagnosis.
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Affiliation(s)
- Ram Hari Dahal
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Shukho Kim
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Yu Kyung Kim
- Department of Clinical Pathology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Eun Soo Kim
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Jungmin Kim
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
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Bleich RM, Li C, Sun S, Barlogio CJ, Broberg CA, Franks AR, Bulik-Sullivan E, Dogan B, Simpson KW, Carroll IM, Fodor AA, Arthur JC. A consortia of clinical E. coli strains with distinct in-vitro adherent/invasive properties establish their own co-colonization niche and shape the intestinal microbiota in inflammation-susceptible mice. RESEARCH SQUARE 2023:rs.3.rs-2899665. [PMID: 37214858 PMCID: PMC10197778 DOI: 10.21203/rs.3.rs-2899665/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Background Inflammatory bowel disease (IBD) patients experience recurrent episodes of intestinal inflammation and often follow an unpredictable disease course. Mucosal colonization with adherent-invasive Escherichia coli (AIEC) are believed to perpetuate intestinal inflammation. However, it remains unclear if the 24-year-old AIEC in-vitro definition fully predicts mucosal colonization in-vivo. To fill this gap, we have developed a novel molecular barcoding approach to distinguish strain variants in the gut and have integrated this approach to explore mucosal colonization of distinct patient-derived E. coli isolates in gnotobiotic mouse models of colitis. Results Germ-free inflammation-susceptible interleukin-10-deficient (Il10-/-) and inflammation-resistant WT mice were colonized with a consortia of AIEC and non-AIEC strains, then given a murine fecal transplant to provide niche competition. E. coli strains isolated from human intestinal tissue were each marked with a unique molecular barcode that permits identification and quantification by barcode-targeted sequencing. 16S rRNA sequencing was used to evaluate the microbiome response to E. coli colonization. Our data reveal that specific AIEC and non-AIEC strains reproducibly colonize the intestinal mucosa of WT and Il10-/- mice. These E. coli expand in Il10-/- mice during inflammation and induce compositional dysbiosis to the microbiome in an inflammation-dependent manner. In turn, specific microbes co-evolve in inflamed mice, potentially diversifying E. coli colonization patterns. We observed no selectivity in E. coli colonization patterns in the fecal contents, indicating minimal selective pressure in this niche from host-microbe and interbacterial interactions. Because select AIEC and non-AIEC strains colonize the mucosa, this suggests the in vitro AIEC definition may not fully predict in vivo colonization potential. Further comparison of seven E. coli genomes pinpointed unique genomic features contained only in highly colonizing strains (two AIEC and two non-AIEC). Those colonization-associated features may convey metabolic advantages (e.g., iron acquisition and carbohydrate consumption) to promote efficient mucosal colonization. Conclusions Our findings establish the in-vivo mucosal colonizer, not necessarily AIEC, as a principal dysbiosis driver through crosstalk with host and associated microbes. Furthermore, we highlight the utility of high-throughput screens to decode the in-vivo colonization dynamics of patient-derived bacteria in murine models.
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Affiliation(s)
| | - Chuang Li
- University of North Carolina at Chapel Hill
| | - Shan Sun
- University of North Carolina at Charlotte
| | | | | | | | | | - Belgin Dogan
- Cornell University College of Veterinary Medicine
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234
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Rivera FP, Medina A, Riveros M, Ochoa TJ, Pons MJ, Ruiz J. Colonizing and Virulence Factors in Enterotoxigenic Escherichia coli from Peru. Am J Trop Med Hyg 2023; 108:948-953. [PMID: 36972692 PMCID: PMC10160877 DOI: 10.4269/ajtmh.22-0677] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 01/12/2023] [Indexed: 03/29/2023] Open
Abstract
Enterotoxigenic Escherichia coli (ETEC) ranks among the most relevant diarrheagenic pathogens. Efforts to design vaccines to fight ETEC have been focused on colonizing factors (CFs) and atypical virulence factors (AVF). An effective vaccine must account for differences in the regional prevalence of these CFs and AVFs to be truly effective in a given area. In the present study, the presence of 16 CFs and 9 AVFs, as well as the heat-stable (ST) variants (STh or STp), was established by polymerase chain reaction in 205 Peruvian ETEC isolates (120 from diarrhea cases and 85 from healthy controls). Ninety-nine (48.3%) isolates were heat-labile, 63 (30.7%) ST, and 43 (21.0%) presented both toxins. Of ST isolates, 59 (28.8%) possessed STh, 30 (14.6%) STp, five (2.4%) both STh and STp, and 12 (5.8%) were not amplified for any variant tested. The presence of CFs was associated with diarrhea (P < 0.0001). The presence of eatA as well as concomitant presence of CSI, CS3, and CS21 and of C5 and C6 was statistically related to diarrhea cases. The present results suggests that, if effective, a vaccine considering CS6, CS20, and CS21, together with EtpA, would provide protection against 64.4% of the isolates analyzed, whereas the addition of CS12 and EAST1 would lead to 83.9% coverage. Large studies are needed to establish both the ideal candidates to be considered to develop a vaccine effective in the area, and continuous surveillance is needed to detect displacement of circulating isolates that may compromise future vaccines.
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Affiliation(s)
- Fulton P. Rivera
- Laboratorio de Enfermedades Entéricas, Nutrición y Resistencia Antimicrobiana, Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Facultad de Medicina, Universidad Peruana Cayetano Heredia, Lima, Peru
- Facultad de Ciencias de la Salud, Universidad Científica del Sur, Lima, Peru
| | - Anicia Medina
- Laboratorio de Enfermedades Entéricas, Nutrición y Resistencia Antimicrobiana, Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Maribel Riveros
- Laboratorio de Enfermedades Entéricas, Nutrición y Resistencia Antimicrobiana, Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Facultad de Medicina, Universidad Peruana Cayetano Heredia, Lima, Peru
- Facultad de Ciencias Naturales y Matemática, Universidad Nacional Federico Villarreal, Lima, Peru
- Laboratorio de Infectología Pediátrica, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Theresa J. Ochoa
- Laboratorio de Enfermedades Entéricas, Nutrición y Resistencia Antimicrobiana, Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Laboratorio de Infectología Pediátrica, Universidad Peruana Cayetano Heredia, Lima, Peru
- University of Texas School of Public Health, Houston, Texas
| | - Maria J. Pons
- Grupo de Enfermedades Emergentes y Reemergentes, Universidad Científica del Sur, Lima, Peru
| | - Joaquim Ruiz
- Grupo de Enfermedades Emergentes y Reemergentes, Universidad Científica del Sur, Lima, Peru
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Salerno P, Verster A, Valls R, Barrack K, Price C, Madan J, O'Toole GA, Ross BD. Persistent delay in maturation of the developing gut microbiota in infants with cystic fibrosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.02.539134. [PMID: 37205374 PMCID: PMC10187160 DOI: 10.1101/2023.05.02.539134] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The healthy human infant gut microbiome undergoes stereotypical changes in taxonomic composition between birth and maturation to an adult-like stable state. During this time, extensive communication between microbiota and the host immune system contributes to health status later in life. Although there are many reported associations between microbiota compositional alterations and disease in adults, less is known about how microbiome development is altered in pediatric diseases. One pediatric disease linked to altered gut microbiota composition is cystic fibrosis (CF), a multi-organ genetic disease involving impaired chloride secretion across epithelia and heightened inflammation both in the gut and at other body sites. Here, we use shotgun metagenomics to profile the strain-level composition and developmental dynamics of the infant fecal microbiota from several CF and non-CF longitudinal cohorts spanning from birth to greater than 36 months of life. We identify a set of keystone species whose prevalence and abundance reproducibly define microbiota development in early life in non-CF infants, but are missing or decreased in relative abundance in infants with CF. The consequences of these CF-specific differences in gut microbiota composition and dynamics are a delayed pattern of microbiota maturation, persistent entrenchment in a transitional developmental phase, and subsequent failure to attain an adult-like stable microbiota. We also detect the increased relative abundance of oral-derived bacteria and higher levels of fungi in CF, features that are associated with decreased gut bacterial density in inflammatory bowel diseases. Our results define key differences in the gut microbiota during ontogeny in CF and suggest the potential for directed therapies to overcome developmental delays in microbiota maturation.
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236
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Duncan SH, Conti E, Ricci L, Walker AW. Links between Diet, Intestinal Anaerobes, Microbial Metabolites and Health. Biomedicines 2023; 11:biomedicines11051338. [PMID: 37239009 DOI: 10.3390/biomedicines11051338] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/23/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
A dense microbial community resides in the human colon, with considerable inter-individual variability in composition, although some species are relatively dominant and widespread in healthy individuals. In disease conditions, there is often a reduction in microbial diversity and perturbations in the composition of the microbiota. Dietary complex carbohydrates that reach the large intestine are important modulators of the composition of the microbiota and their primary metabolic outputs. Specialist gut bacteria may also transform plant phenolics to form a spectrum of products possessing antioxidant and anti-inflammatory activities. Consumption of diets high in animal protein and fat may lead to the formation of potentially deleterious microbial products, including nitroso compounds, hydrogen sulphide, and trimethylamine. Gut anaerobes also form a range of secondary metabolites, including polyketides that may possess antimicrobial activity and thus contribute to microbe-microbe interactions within the colon. The overall metabolic outputs of colonic microbes are derived from an intricate network of microbial metabolic pathways and interactions; however, much still needs to be learnt about the subtleties of these complex networks. In this review we consider the multi-faceted relationships between inter-individual microbiota variation, diet, and health.
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Affiliation(s)
- Sylvia H Duncan
- Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Elena Conti
- Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Liviana Ricci
- Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Alan W Walker
- Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
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237
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Chin Fatt CR, Asbury S, Jha MK, Minhajuddin A, Sethuram S, Mayes T, Kennedy SH, Foster JA, Trivedi MH. Leveraging the microbiome to understand clinical heterogeneity in depression: findings from the T-RAD study. Transl Psychiatry 2023; 13:139. [PMID: 37117195 PMCID: PMC10147668 DOI: 10.1038/s41398-023-02416-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 01/25/2023] [Accepted: 03/24/2023] [Indexed: 04/30/2023] Open
Abstract
Alterations in the gut microbiome have been linked to a variety of mental illnesses including anxiety and depression. This study utilized advanced bioinformatics tools that integrated both the compositional and community nature of gut microbiota to investigate how gut microbiota influence clinical symptoms in a sample of participants with depression. Gut microbiota of 179 participants with major depressive disorder (MDD) in the Texas Resilience Against Depression (T-RAD) study were analyzed by 16S rRNA gene sequencing of stool samples. Severity of anxiety, depression, and anhedonia symptoms were assessed with General Anxiety Disorder - 7 item scale, Patient Health 9-item Questionnaire, and Dimensional Anhedonia Rating Scale, respectively. Using weighted correlation network analysis, a data-driven approach, three co-occurrence networks of bacterial taxa were identified. One of these co-occurrence networks was significantly associated with clinical features including depression and anxiety. The hub taxa associated with this co-occurrence module -one Ruminococcaceae family taxon, one Clostridiales vadinBB60 group family taxon, and one Christencenellaceae family taxon- were connected to several additional butyrate-producing bacteria suggesting that deficits in butyrate production may contribute to clinical symptoms. Therefore, by considering the community nature of the gut microbiome in a real world clinical sample, this study identified a gut microbial co-occurrence network that was significantly associated with clinical anxiety in a cohort of depressed individuals.
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Affiliation(s)
- Cherise R Chin Fatt
- Center for Depression Research and Clinical Care, Peter O'Donnell Jr. Brain Institute and the Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sarah Asbury
- Department of Psychiatry & Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada
| | - Manish K Jha
- Center for Depression Research and Clinical Care, Peter O'Donnell Jr. Brain Institute and the Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Abu Minhajuddin
- Center for Depression Research and Clinical Care, Peter O'Donnell Jr. Brain Institute and the Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sangita Sethuram
- Center for Depression Research and Clinical Care, Peter O'Donnell Jr. Brain Institute and the Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Taryn Mayes
- Center for Depression Research and Clinical Care, Peter O'Donnell Jr. Brain Institute and the Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sidney H Kennedy
- Department of Psychiatry, University of Toronto and Centre for Depression and Suicide Studies, Unity Health, Toronto, ON, Canada
| | - Jane A Foster
- Center for Depression Research and Clinical Care, Peter O'Donnell Jr. Brain Institute and the Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Psychiatry & Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada.
| | - Madhukar H Trivedi
- Center for Depression Research and Clinical Care, Peter O'Donnell Jr. Brain Institute and the Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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Ruiz-Malagón AJ, Hidalgo-García L, Rodríguez-Sojo MJ, Molina-Tijeras JA, García F, Diez-Echave P, Vezza T, Becerra P, Marchal JA, Redondo-Cerezo E, Hausmann M, Rogler G, Garrido-Mesa J, Rodríguez-Cabezas ME, Rodríguez-Nogales A, Gálvez J. Tigecycline reduces tumorigenesis in colorectal cancer via inhibition of cell proliferation and modulation of immune response. Biomed Pharmacother 2023; 163:114760. [PMID: 37119741 DOI: 10.1016/j.biopha.2023.114760] [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: 03/07/2023] [Revised: 04/13/2023] [Accepted: 04/20/2023] [Indexed: 05/01/2023] Open
Abstract
BACKGROUND and Purpose: Colorectal cancer (CRC) is one of the cancers with the highest incidence in which APC gene mutations occur in almost 80% of patients. This mutation leads to β-catenin aberrant accumulation and an uncontrolled proliferation. Apoptosis evasion, changes in the immune response and microbiota composition are also events that arise in CRC. Tetracyclines are drugs with proven antibiotic and immunomodulatory properties that have shown cytotoxic activity against different tumor cell lines. EXPERIMENTAL APPROACH The effect of tigecycline was evaluated in vitro in HCT116 cells and in vivo in a colitis-associated colorectal cancer (CAC) murine model. 5-fluorouracil was assayed as positive control in both studies. KEY RESULTS Tigecycline showed an antiproliferative activity targeting the Wnt/β-catenin pathway and downregulating STAT3. Moreover, tigecycline induced apoptosis through extrinsic, intrinsic and endoplasmic reticulum pathways converging on an increase of CASP7 levels. Furthermore, tigecycline modulated the immune response in CAC, reducing the cancer-associated inflammation through downregulation of cytokines expression. Additionally, tigecycline favored the cytotoxic activity of cytotoxic T lymphocytes (CTLs), one of the main immune defenses against tumor cells. Lastly, the antibiotic reestablished the gut dysbiosis in CAC mice increasing the abundance of bacterial genera and species, such as Akkermansia and Parabacteroides distasonis, that act as protectors against tumor development. These findings resulted in a reduction of the number of tumors and an amelioration of the tumorigenesis process in CAC. CONCLUSION AND IMPLICATIONS Tigecycline exerts a beneficial effect against CRC supporting the use of this antibiotic for the treatment of this disease.
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Affiliation(s)
- Antonio Jesús Ruiz-Malagón
- Department of Pharmacology, Center for Biomedical Research (CIBM), University of Granada, 18071 Granada, Spain; Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain
| | - Laura Hidalgo-García
- Department of Pharmacology, Center for Biomedical Research (CIBM), University of Granada, 18071 Granada, Spain; Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain
| | - María Jesús Rodríguez-Sojo
- Department of Pharmacology, Center for Biomedical Research (CIBM), University of Granada, 18071 Granada, Spain; Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain
| | - José Alberto Molina-Tijeras
- Department of Pharmacology, Center for Biomedical Research (CIBM), University of Granada, 18071 Granada, Spain; Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain
| | - Federico García
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain; Servicio Microbiología, Hospital Universitario Clínico San Cecilio, 18100 Granada, Spain; Ciber de Enfermedades Infecciosas, CiberInfecc, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Patricia Diez-Echave
- Department of Pharmacology, Center for Biomedical Research (CIBM), University of Granada, 18071 Granada, Spain; Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain
| | - Teresa Vezza
- Department of Pharmacology, Center for Biomedical Research (CIBM), University of Granada, 18071 Granada, Spain; Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain
| | - Patricia Becerra
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain; Servicio de Anatomía Patológica, Hospital Universitario Clínico San Cecilio, 18014 Granada, Spain
| | - Juan Antonio Marchal
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain; Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research (CIBM), University of Granada, E-18100 Granada, Spain; Department of Human Anatomy and Embryology, Faculty of Medicine, University of Granada, Granada E-18016, Spain
| | - Eduardo Redondo-Cerezo
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain; Servicio de Aparato Digestivo. Hospital Universitario Virgen de las Nieves, Granada, Spain
| | - Martin Hausmann
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Rämistrasse 100, 8091, Zurich, Switzerland
| | - Gerhard Rogler
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Rämistrasse 100, 8091, Zurich, Switzerland; Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, 8057, Zurich, Switzerland
| | - José Garrido-Mesa
- The William Harvey Research Institute, Barts and the London School of Medicine, Queen Mary University of London, London, UK.
| | - María Elena Rodríguez-Cabezas
- Department of Pharmacology, Center for Biomedical Research (CIBM), University of Granada, 18071 Granada, Spain; Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain.
| | - Alba Rodríguez-Nogales
- Department of Pharmacology, Center for Biomedical Research (CIBM), University of Granada, 18071 Granada, Spain; Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain
| | - Julio Gálvez
- Department of Pharmacology, Center for Biomedical Research (CIBM), University of Granada, 18071 Granada, Spain; Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III, 28029 Madrid, Spain
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Aldubayan MA, Mao X, Laursen MF, Pigsborg K, Christensen LH, Roager HM, Nielsen DS, Hjorth MF, Magkos F. Supplementation with inulin-type fructans affects gut microbiota and attenuates some of the cardiometabolic benefits of a plant-based diet in individuals with overweight or obesity. Front Nutr 2023; 10:1108088. [PMID: 37181156 PMCID: PMC10167298 DOI: 10.3389/fnut.2023.1108088] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 03/30/2023] [Indexed: 05/16/2023] Open
Abstract
Background The gut microbiota has emerged as a potential therapeutic target to improve the management of obesity and its comorbidities. Objective We investigated the impact of a high fiber (∼38 g/d) plant-based diet, consumed ad libitum, with or without added inulin-type fructans (ITF), on the gut microbiota composition and cardiometabolic outcomes in subjects with obesity. We also tested if baseline Prevotella/Bacteroides (P/B) ratio predicts weight loss outcomes. Methods This is a secondary exploratory analysis from the PREVENTOMICS study, in which 100 subjects (82 completers) aged 18-65 years with body mass index 27-40 kg/m2 were randomized to 10 weeks of double-blinded treatment with a personalized or a generic plant-based diet. Changes from baseline to end-of-trial in gut microbiota composition (16S rRNA gene amplicon sequencing), body composition, cardiometabolic health and inflammatory markers were evaluated in the whole cohort (n = 82), and also compared in the subgroup of subjects who were supplemented with an additional 20 g/d ITF-prebiotics (n = 21) or their controls (n = 22). Results In response to the plant-based diet, all subjects lost weight (-3.2 [95% CI -3.9, -2.5] kg) and experienced significant improvements in body composition and cardiometabolic health indices. Addition of ITF to the plant-based diet reduced microbial diversity (Shannon index) and selectively increased Bifidobacterium and Faecalibacterium (q < 0.05). The change in the latter was significantly associated with higher values of insulin and HOMA-IR and lower HDL cholesterol. In addition, the LDL:HDL ratio and the concentrations of IL-10, MCP-1 and TNFα were significantly elevated in the ITF-subgroup. There was no relationship between baseline P/B ratio and changes in body weight (r = -0.07, p = 0.53). Conclusion A plant-based diet consumed ad libitum modestly decreases body weight and has multiple health benefits in individuals with obesity. Addition of ITF-prebiotics on top this naturally fiber-rich background selectively changes gut microbiota composition and attenuates some of the realized cardiometabolic benefits. Clinical trial registration [https://clinicaltrials.gov/ct2/show/NCT04590989], identifier [NCT04590989].
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Affiliation(s)
- Mona Adnan Aldubayan
- Department of Clinical Nutrition, College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Xiaotian Mao
- Department of Food Science, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | | | - Kristina Pigsborg
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Lars H. Christensen
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Henrik M. Roager
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Dennis S. Nielsen
- Department of Food Science, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Mads Fiil Hjorth
- Obesity and Nutritional Sciences, Novo Nordisk Foundation, Tuborg Havnevej, Hellerup, Denmark
| | - Faidon Magkos
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
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240
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Nantambi H, Sembera J, Ankunda V, Ssali I, Kalyebi AW, Oluka GK, Kato L, Ubaldo B, Kibengo F, Katende JS, Gombe B, Baine C, Odoch G, Mugaba S, Sande OJ, Kaleebu P, Serwanga J. Pre-pandemic SARS-CoV-2-specific IFN-γ and antibody responses were low in Ugandan samples and significantly reduced in HIV-positive specimens. Front Immunol 2023; 14:1148877. [PMID: 37153598 PMCID: PMC10154590 DOI: 10.3389/fimmu.2023.1148877] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/04/2023] [Indexed: 05/09/2023] Open
Abstract
Introduction We investigated whether prior SARS-CoV-2-specific IFN-γ and antibody responses in Ugandan COVID-19 pre-pandemic specimens aligned to this population's low disease severity. Methods We used nucleoprotein (N), spike (S), NTD, RBD, envelope, membrane, SD1/2-directed IFN-γ ELISpots, and an S- and N-IgG antibody ELISA to screen for SARS-CoV-2-specific cross-reactivity. Results HCoV-OC43-, HCoV-229E-, and SARS-CoV-2-specific IFN-γ occurred in 23, 15, and 17 of 104 specimens, respectively. Cross-reactive IgG was more common against the nucleoprotein (7/110, 15.5%; p = 0.0016, Fishers' Exact) than the spike (3/110, 2.72%). Specimens lacking anti-HuCoV antibodies had higher rates of pre-epidemic SARS-CoV-2-specific IFN-γ cross-reactivity (p-value = 0.00001, Fishers' exact test), suggesting that exposure to additional factors not examined here might play a role. SARS-CoV-2-specific cross-reactive antibodies were significantly less common in HIV-positive specimens (p=0.017; Fishers' Exact test). Correlations between SARS-CoV-2- and HuCoV-specific IFN-γ responses were consistently weak in both HIV negative and positive specimens. Discussion These findings support the existence of pre-epidemic SARS-CoV-2-specific cellular and humoral cross-reactivity in this population. The data do not establish that these virus-specific IFN-γ and antibody responses are entirely specific to SARS-CoV-2. Inability of the antibodies to neutralise SARS-CoV-2 implies that prior exposure did not result in immunity. Correlations between SARS-CoV-2 and HuCoV-specific responses were consistently weak, suggesting that additional variables likely contributed to the pre-epidemic cross-reactivity patterns. The data suggests that surveillance efforts based on the nucleoprotein might overestimate the exposure to SARS-CoV-2 compared to inclusion of additional targets, like the spike protein. This study, while limited in scope, suggests that HIV-positive people are less likely than HIV-negative people to produce protective antibodies against SARS-CoV-2.
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Affiliation(s)
- Hellen Nantambi
- Medical Research Council (MRC), Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM), Uganda Research Unit, Entebbe, Uganda
- Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Jackson Sembera
- Medical Research Council (MRC), Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM), Uganda Research Unit, Entebbe, Uganda
- Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Violet Ankunda
- Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Ivan Ssali
- Medical Research Council (MRC), Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM), Uganda Research Unit, Entebbe, Uganda
| | - Arthur Watelo Kalyebi
- Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Gerald Kevin Oluka
- Medical Research Council (MRC), Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM), Uganda Research Unit, Entebbe, Uganda
- Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Laban Kato
- Medical Research Council (MRC), Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM), Uganda Research Unit, Entebbe, Uganda
| | - Bahemuka Ubaldo
- Medical Research Council (MRC), Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM), Uganda Research Unit, Entebbe, Uganda
| | - Freddie Kibengo
- Medical Research Council (MRC), Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM), Uganda Research Unit, Entebbe, Uganda
| | - Joseph Ssebwana Katende
- Medical Research Council (MRC), Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM), Uganda Research Unit, Entebbe, Uganda
- Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Ben Gombe
- Medical Research Council (MRC), Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM), Uganda Research Unit, Entebbe, Uganda
| | - Claire Baine
- Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Geoffrey Odoch
- Medical Research Council (MRC), Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM), Uganda Research Unit, Entebbe, Uganda
| | - Susan Mugaba
- Medical Research Council (MRC), Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM), Uganda Research Unit, Entebbe, Uganda
| | - Obondo James Sande
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - The COVID-19 Immunoprofiling Team
- Medical Research Council (MRC), Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM), Uganda Research Unit, Entebbe, Uganda
- Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Pontiano Kaleebu
- Medical Research Council (MRC), Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM), Uganda Research Unit, Entebbe, Uganda
- Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Jennifer Serwanga
- Medical Research Council (MRC), Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM), Uganda Research Unit, Entebbe, Uganda
- Department of Immunology, Uganda Virus Research Institute, Entebbe, Uganda
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Krawczyk A, Salamon D, Kowalska-Duplaga K, Zapała B, Książek T, Drażniuk-Warchoł M, Gosiewski T. Changes in the gut mycobiome in pediatric patients in relation to the clinical activity of Crohn's disease. World J Gastroenterol 2023; 29:2172-2187. [PMID: 37122605 PMCID: PMC10130967 DOI: 10.3748/wjg.v29.i14.2172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/13/2023] [Accepted: 03/13/2023] [Indexed: 04/13/2023] Open
Abstract
BACKGROUND Numerous studies have shown that in Crohn’s disease (CD), the gut microbiota is of great importance in the induction and maintenance of inflammation in the gastrointestinal tract. Until recently, studies have focused almost exclusively on bacteria in the gut. Lately, more attention has been paid to the role of intestinal fungi.
AIM To study the gut mycobiome analysis of pediatric patients with CD (in different stages of disease activity) compared to healthy children.
METHODS Fecal samples were collected from patients: With active, newly diagnosed CD (n = 50); active but previously diagnosed and treated CD (n = 16); non-active CD and who were in clinical remission (n = 39) and from healthy volunteers (n = 40). Fungal DNA was isolated from the samples. Next, next generation sequencing (MiSeq, Illumina) was performed. The composition of mycobiota was correlated with clinical and blood parameters.
RESULTS Candida spp. were overrepresented in CD patients, while in the control group, the most abundant genus was Saccharomyces. In CD patients, the percentage of Malassezia was almost twice that of the control (P < 0.05). In active CD patients, we documented a higher abundance of Debaryomyces hansenii (D. hansenii) compared to the non-active CD and control (P < 0.05) groups. Moreover, statistically significant changes in the abundance of Mycosphaerella, Rhodotorula, and Microidium were observed. The analyses at the species level and linear discriminant analysis showed that in each group it was possible to distinguish a specific species characteristic of a given patient population. Moreover, we have documented statistically significant correlations between: D. hansenii and patient age (negative); C. zeylanoides and patient age (positive); C. dubliniensis and calprotectin (positive); C. sake and calprotectin (positive); and C. tropicalis and pediatric CD activity index (PCDAI) (positive).
CONCLUSION Mycobiome changes in CD patients, and the positive correlation of some species with calprotectin or PCDAI, give strong evidence that fungi may be of key importance in the development of CD.
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Affiliation(s)
- Agnieszka Krawczyk
- Department of Microbiology, Division of Molecular Medical Microbiology, Jagiellonian University Medical College, Cracow 31-121, Poland
| | - Dominika Salamon
- Department of Microbiology, Division of Molecular Medical Microbiology, Jagiellonian University Medical College, Cracow 31-121, Poland
| | - Kinga Kowalska-Duplaga
- Department of Pediatrics, Gastroenterology and Nutrition, Jagiellonian University Medical College, Cracow 30-663, Poland
| | - Barbara Zapała
- Department of Clinical Biochemistry, Jagiellonian University Medical College, Cracow 31-066, Poland
| | - Teofila Książek
- Department of Medical Genetics, Jagiellonian University Medical College, Cracow 30-663, Poland
| | - Marta Drażniuk-Warchoł
- Department of Pediatrics, Gastroenterology and Nutrition, University Children's Hospital, Cracow 30-663, Poland
| | - Tomasz Gosiewski
- Department of Microbiology, Division of Molecular Medical Microbiology, Jagiellonian University Medical College, Cracow 31-121, Poland
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Oliveira ECSD, Quaglio AEV, Magro DO, Di Stasi LC, Sassaki LY. Intestinal Microbiota and miRNA in IBD: A Narrative Review about Discoveries and Perspectives for the Future. Int J Mol Sci 2023; 24:ijms24087176. [PMID: 37108339 PMCID: PMC10138604 DOI: 10.3390/ijms24087176] [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: 02/27/2023] [Revised: 04/04/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
Inflammatory bowel disease (IBD) includes Crohn's disease (CD) and ulcerative colitis (UC) and comprises a chronic gastrointestinal tract disorder characterized by hyperactive and dysregulated immune responses to environmental factors, including gut microbiota and dietary components. An imbalance of the intestinal microbiota may contribute to the development and/or worsening of the inflammatory process. MicroRNAs (miRNAs) have been associated with various physiological processes, such as cell development and proliferation, apoptosis, and cancer. In addition, they play an important role in inflammatory processes, acting in the regulation of pro- and anti-inflammatory pathways. Differences in the profiles of miRNAs may represent a useful tool in the diagnosis of UC and CD and as a prognostic marker in both diseases. The relationship between miRNAs and the intestinal microbiota is not completely elucidated, but recently this topic has gained prominence and has become the target of several studies that demonstrate the role of miRNAs in the modulation of the intestinal microbiota and induction of dysbiosis; the microbiota, in turn, can regulate the expression of miRNAs and, consequently, alter the intestinal homeostasis. Therefore, this review aims to describe the interaction between the intestinal microbiota and miRNAs in IBD, recent discoveries, and perspectives for the future.
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Affiliation(s)
- Ellen Cristina Souza de Oliveira
- Department of Internal Medicine, Medical School, Sao Paulo State University (UNESP), Campus Botucatu, Sao Paulo CEP 18618-970, Brazil
| | - Ana Elisa Valencise Quaglio
- Laboratory of Phytomedicines, Pharmacology and Biotechnology (PhytoPharmaTec), Department of Biophysics and Pharmacology, Institute of Biosciences, Sao Paulo State University (UNESP), Campus Botucatu, Sao Paulo CEP 18618-689, Brazil
| | - Daniéla Oliveira Magro
- Department of Surgery, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Sao Paulo CEP 13083-970, Brazil
| | - Luiz Claudio Di Stasi
- Laboratory of Phytomedicines, Pharmacology and Biotechnology (PhytoPharmaTec), Department of Biophysics and Pharmacology, Institute of Biosciences, Sao Paulo State University (UNESP), Campus Botucatu, Sao Paulo CEP 18618-689, Brazil
| | - Ligia Yukie Sassaki
- Department of Internal Medicine, Medical School, Sao Paulo State University (UNESP), Campus Botucatu, Sao Paulo CEP 18618-970, Brazil
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Sawaswong V, Chanchaem P, Kemthong T, Warit S, Chaiprasert A, Malaivijitnond S, Payungporn S. Alteration of gut microbiota in wild-borne long-tailed macaques after 1-year being housed in hygienic captivity. Sci Rep 2023; 13:5842. [PMID: 37037869 PMCID: PMC10085984 DOI: 10.1038/s41598-023-33163-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 04/07/2023] [Indexed: 04/12/2023] Open
Abstract
The wild-born long-tailed macaques (Macaca fascicularis) were recently recruited and used as breeders for the National Primate Research Center of Thailand, Chulalongkorn University (NPRCT-CU), and changes in their in-depth gut microbiota profiles were investigated. The Oxford Nanopore Technology (ONT) was used to explore full-length 16S rDNA sequences of gut microbiota in animals once captured in their natural habitat and 1-year following translocation and housing in a hygienic environment at NPRCT-CU. Our findings show that the gut microbiota of macaques after 1 year of hygienic housing and programmed diets feeding was altered and reshaped. The prevalent gut bacteria such as Prevotella copri and Faecalibacterium prausnitzii were enriched after translocation, causing the lower alpha diversity. The correlation analysis revealed that Prevotella copri, Phascolarctobacterium succinatutens, and Prevotella stercorea, showed a positive correlation with each other. Significantly enriched pathways in the macaques after translocation included biosynthesis of essential amino acids, fatty acids, polyamine and butanoate. The effects of microbiota change could help macaques to harvest the energy from programmed diets and adapt their gut metabolism. The novel probiotics and microbiota engineering approach could be further developed based on the current findings and should be helpful for captive animal health care management.
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Affiliation(s)
- Vorthon Sawaswong
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, 10330, Thailand
- Center of Excellence in Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, 1873 Rama IV Road, Patumwan, Bangkok, 10330, Thailand
- Nucleic Acid Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Prangwalai Chanchaem
- Center of Excellence in Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, 1873 Rama IV Road, Patumwan, Bangkok, 10330, Thailand
| | - Taratorn Kemthong
- National Primate Research Center of Thailand, Chulalongkorn University, Saraburi, 18110, Thailand
| | - Saradee Warit
- Industrial Tuberculosis Team, Industrial Medical Molecular Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Angkana Chaiprasert
- Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Suchinda Malaivijitnond
- National Primate Research Center of Thailand, Chulalongkorn University, Saraburi, 18110, Thailand
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Sunchai Payungporn
- Center of Excellence in Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, 1873 Rama IV Road, Patumwan, Bangkok, 10330, Thailand.
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Wang D, Tang G, Zhao L, Wang M, Chen L, Zhao C, Liang Z, Chen J, Cao Y, Yao J. Potential roles of the rectum keystone microbiota in modulating the microbial community and growth performance in goat model. J Anim Sci Biotechnol 2023; 14:55. [PMID: 37029437 PMCID: PMC10080759 DOI: 10.1186/s40104-023-00850-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 02/05/2023] [Indexed: 04/09/2023] Open
Abstract
BACKGROUND Ruminal microbiota in early life plays critical roles in the life-time health and productivity of ruminant animals. However, understanding of the relationship between gut microbiota and ruminant phenotypes is very limited. Here, the relationship between the rectum microbiota, their primary metabolites, and growth rate of a total of 76 young dairy goats (6-month-old) were analyzed, and then 10 goats with the highest or lowest growth rates respectively were further compared for the differences in the rectum microbiota, metabolites, and animal's immune parameters, to investigate the potential mechanisms by which the rectum microbiota contributes to the health and growth rate. RESULTS The analysis of Spearman correlation and microbial co-occurrence network indicated that some keystone rectum microbiota, including unclassified Prevotellaceae, Faecalibacterium and Succinivibrio, were the key modulators to shape the rectum microbiota and closely correlated with the rectum SCFA production and serum IgG, which contribute to the health and growth rate of young goats. In addition, random forest machine learning analysis suggested that six bacterial taxa in feces could be used as potential biomarkers for differentiating high or low growth rate goats, with 98.3% accuracy of prediction. Moreover, the rectum microbiota played more important roles in gut fermentation in early life (6-month-old) than in adulthood stage (19-month-old) of goats. CONCLUSION We concluded that the rectum microbiota was associated with the health and growth rate of young goats, and can be a focus on the design of the early-life gut microbial intervention.
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Affiliation(s)
- Dangdang Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Guangfu Tang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Lichao Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Mengya Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Luyu Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Congcong Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Ziqi Liang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jie Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yangchun Cao
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Junhu Yao
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Vallianou NG, Kounatidis D, Tsilingiris D, Panagopoulos F, Christodoulatos GS, Evangelopoulos A, Karampela I, Dalamaga M. The Role of Next-Generation Probiotics in Obesity and Obesity-Associated Disorders: Current Knowledge and Future Perspectives. Int J Mol Sci 2023; 24:ijms24076755. [PMID: 37047729 PMCID: PMC10095285 DOI: 10.3390/ijms24076755] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 03/31/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023] Open
Abstract
Obesity and obesity-associated disorders pose a major public health issue worldwide. Apart from conventional weight loss drugs, next-generation probiotics (NGPs) seem to be very promising as potential preventive and therapeutic agents against obesity. Candidate NGPs such as Akkermansia muciniphila, Faecalibacterium prausnitzii, Anaerobutyricum hallii, Bacteroides uniformis, Bacteroides coprocola, Parabacteroides distasonis, Parabacteroides goldsteinii, Hafnia alvei, Odoribacter laneus and Christensenella minuta have shown promise in preclinical models of obesity and obesity-associated disorders. Proposed mechanisms include the modulation of gut flora and amelioration of intestinal dysbiosis, improvement of intestinal barrier function, reduction in chronic low-grade inflammation and modulation of gut peptide secretion. Akkermansia muciniphila and Hafnia alvei have already been administered in overweight/obese patients with encouraging results. However, safety issues and strict regulations should be constantly implemented and updated. In this review, we aim to explore (1) current knowledge regarding NGPs; (2) their utility in obesity and obesity-associated disorders; (3) their safety profile; and (4) their therapeutic potential in individuals with overweight/obesity. More large-scale, multicentric and longitudinal studies are mandatory to explore their preventive and therapeutic potential against obesity and its related disorders.
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Affiliation(s)
- Natalia G. Vallianou
- Department of Internal Medicine, Evangelismos General Hospital, 45-47 Ipsilantou Street, 10676 Athens, Greece
| | - Dimitris Kounatidis
- Department of Internal Medicine, Evangelismos General Hospital, 45-47 Ipsilantou Street, 10676 Athens, Greece
| | - Dimitrios Tsilingiris
- First Department of Internal Medicine, University Hospital of Alexandroupolis, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Fotis Panagopoulos
- Department of Internal Medicine, Evangelismos General Hospital, 45-47 Ipsilantou Street, 10676 Athens, Greece
| | - Gerasimos Socrates Christodoulatos
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 11527 Athens, Greece
- Department of Microbiology, Sismanogleio General Hospital, 1 Sismanogleiou Street, 15126 Athens, Greece
| | - Angelos Evangelopoulos
- Roche Hellas Diagnostics S.A., 18-20 Amarousiou-Chalandriou Street, 15125 Athens, Greece
| | - Irene Karampela
- 2nd Department of Critical Care, Medical School, University of Athens, Attikon General University Hospital, 1 Rimini Street, 12462 Athens, Greece
| | - Maria Dalamaga
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 11527 Athens, Greece
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Harris C, Czaja K. Can Circadian Eating Pattern Adjustments Reduce Risk or Prevent Development of T2D? Nutrients 2023; 15:nu15071762. [PMID: 37049602 PMCID: PMC10096926 DOI: 10.3390/nu15071762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/30/2023] [Accepted: 04/01/2023] [Indexed: 04/07/2023] Open
Abstract
Type 2 diabetes (T2D) is a chronic condition that occurs in insulin-resistant people with reduced glucose uptake. It is contributed to and exacerbated by a poor diet that results in accumulation of adipose tissue, high blood sugar, and other metabolic issues. Because humans have undergone food scarcity throughout history, our species has adapted a fat reserve genotype. This adaptation is no longer beneficial, as eating at a higher frequency than that of our ancestors has had a significant effect on T2D development. Eating at high frequencies disrupts the circadian clock, the circadian rhythm, and the composition of the gut microbiome, as well as hormone secretion and sensitivity. The current literature suggests an improved diet requires meal consistency, avoiding late-night eating, low meal frequency, and fasting to increase metabolic health. In addition, fasting as a treatment for T2D must be used correctly for beneficial results. Early time-restricted eating (TRE) provides many benefits such as improving insulin resistance, cognitive function, and glycemic control. Alternate-day fasting (ADF), 5:2 fasting, and long-term fasting all have benefits; however, they may be less advantageous than early TRE. Therefore, eating pattern adjustments can be used to reduce T2D if used correctly.
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Affiliation(s)
- Carlee Harris
- Department of Biomedical Sciences, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - Krzysztof Czaja
- Department of Biomedical Sciences, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
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HUGHES RILEYL, PINDUS DOMINIKAM, KHAN NAIMANA, BURD NICHOLASA, HOLSCHER HANNAHD. Associations between Accelerometer-Measured Physical Activity and Fecal Microbiota in Adults with Overweight and Obesity. Med Sci Sports Exerc 2023; 55:680-689. [PMID: 36728974 PMCID: PMC9997628 DOI: 10.1249/mss.0000000000003096] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
PURPOSE We aimed to assess whether total daily physical activity (PA), PA intensities, sedentary time (ST), and prolonged ST are associated with differences in the gut microbiota composition or short-chain fatty acid (SCFA) profile of adults with overweight or obesity. METHODS Cross-sectional associations between total daily PA (counts per minute), PA intensities (light and moderate-to-vigorous (MVPA)), ST, prolonged ST, and fecal microbiota composition were assessed in adults ( n = 124) between 25 and 45 yr of age with body mass index ≥25 kg·m -2 . Fecal microbiota composition was assessed with 16S rRNA gene sequencing. Daily PA and ST were measured with a hip-worn ActiGraph wGT3X-BT accelerometer. RESULTS Daily PA volume and intensity were positively associated with relative abundance of Faecalibacterium ( P = 0.04) and negatively associated with the abundances of Alistipes , Parabacteroides , and Gemmiger ( P = 0.003-0.04) as well as the concentrations of acetate, butyrate, and total SCFA (all P = 0.04). Conversely, ST was negatively associated with abundance of Faecalibacterium but positively associated with the abundances of taxa, including Ruminococcaceae, Parabacteroides , Alistipes , and Gemmiger . Clustering of participants based on whether they met PA recommendations suggested that SCFA profiles differed between individuals who did and did not meet PA recommendations. K-means clustering based on percent of time spent in MVPA and ST also identified differences in fecal microbiota composition between cluster 1 (lower MVPA, higher ST) and cluster 2 (higher MVPA, lower ST), including a higher abundance of Alistipes in cluster 1. CONCLUSIONS The current analysis suggests a beneficial association of daily PA on the fecal microbiota and a negative association of ST, particularly with respect to the associations of these variables with the genera Faecalibacterium , a butyrate-producing taxon.
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Affiliation(s)
- RILEY L. HUGHES
- Department of Food Science and Human Nutrition, University of Illinois at Urbana–Champaign, Urbana, IL
| | - DOMINIKA M. PINDUS
- Department of Kinesiology and Community Health, University of Illinois at Urbana–Champaign, Urbana, IL
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana–Champaign, Urbana, IL
- Neuroscience Program, University of Illinois at Urbana–Champaign, Urbana, IL
| | - NAIMAN A. KHAN
- Department of Kinesiology and Community Health, University of Illinois at Urbana–Champaign, Urbana, IL
- Neuroscience Program, University of Illinois at Urbana–Champaign, Urbana, IL
- Division of Nutrition Sciences, University of Illinois at Urbana–Champaign, Urbana, IL
| | - NICHOLAS A. BURD
- Department of Kinesiology and Community Health, University of Illinois at Urbana–Champaign, Urbana, IL
- Division of Nutrition Sciences, University of Illinois at Urbana–Champaign, Urbana, IL
| | - HANNAH D. HOLSCHER
- Department of Kinesiology and Community Health, University of Illinois at Urbana–Champaign, Urbana, IL
- Division of Nutrition Sciences, University of Illinois at Urbana–Champaign, Urbana, IL
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Vatlin AA, Bekker OB, Shur KV, Ilyasov RA, Shatrov PA, Maslov DA, Danilenko VN. Kanamycin and Ofloxacin Activate the Intrinsic Resistance to Multiple Antibiotics in Mycobacterium smegmatis. BIOLOGY 2023; 12:biology12040506. [PMID: 37106707 PMCID: PMC10135989 DOI: 10.3390/biology12040506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/16/2023] [Accepted: 03/25/2023] [Indexed: 03/30/2023]
Abstract
Drug resistance (DR) in Mycobacterium tuberculosis is the main problem in fighting tuberculosis (TB). This pathogenic bacterium has several types of DR implementation: acquired and intrinsic DR. Recent studies have shown that exposure to various antibiotics activates multiple genes, including genes responsible for intrinsic DR. To date, there is evidence of the acquisition of resistance at concentrations well below the standard MICs. In this study, we aimed to investigate the mechanism of intrinsic drug cross-resistance induction by subinhibitory concentrations of antibiotics. We showed that pretreatment of M. smegmatis with low doses of antibiotics (kanamycin and ofloxacin) induced drug resistance. This effect may be caused by a change in the expression of transcriptional regulators of the mycobacterial resistome, in particular the main transcriptional regulator whiB7.
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Khelaifia S, Virginie P, Belkacemi S, Tassery H, Terrer E, Aboudharam G. Culturing the Human Oral Microbiota, Updating Methodologies and Cultivation Techniques. Microorganisms 2023; 11:microorganisms11040836. [PMID: 37110259 PMCID: PMC10143722 DOI: 10.3390/microorganisms11040836] [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: 01/24/2023] [Revised: 03/16/2023] [Accepted: 03/23/2023] [Indexed: 04/29/2023] Open
Abstract
Recent years have been marked by a paradigm shift in the study of the human microbiota, with a re-emergence of culture-dependent approaches. Numerous studies have been devoted to the human microbiota, while studies on the oral microbiota still remain limited. Indeed, various techniques described in the literature may enable an exhaustive study of the microbial composition of a complex ecosystem. In this article, we report different methodologies and culture media described in the literature that can be applied to study the oral microbiota by culture. We report on specific methodologies for targeted culture and specific culture techniques and selection methodologies for cultivating members of the three kingdoms of life commonly found in the human oral cavity, namely, eukaryota, bacteria and archaea. This bibliographic review aims to bring together the various techniques described in the literature, enabling a comprehensive study of the oral microbiota in order to demonstrate its involvement in oral health and diseases.
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Affiliation(s)
- Saber Khelaifia
- Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Univ, IRD, MEPHI, AP-HM, 19-21 Boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
- Ecole de Médecine Dentaire, 27 Boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
| | - Pilliol Virginie
- Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Univ, IRD, MEPHI, AP-HM, 19-21 Boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
- Ecole de Médecine Dentaire, 27 Boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
| | - Souad Belkacemi
- Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Univ, IRD, MEPHI, AP-HM, 19-21 Boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
| | - Herve Tassery
- Ecole de Médecine Dentaire, 27 Boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
| | - Elodie Terrer
- Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Univ, IRD, MEPHI, AP-HM, 19-21 Boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
- Ecole de Médecine Dentaire, 27 Boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
| | - Gérard Aboudharam
- Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Univ, IRD, MEPHI, AP-HM, 19-21 Boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
- Ecole de Médecine Dentaire, 27 Boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
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Ballini A, Charitos IA, Cantore S, Topi S, Bottalico L, Santacroce L. About Functional Foods: The Probiotics and Prebiotics State of Art. Antibiotics (Basel) 2023; 12:antibiotics12040635. [PMID: 37106999 PMCID: PMC10135203 DOI: 10.3390/antibiotics12040635] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/18/2023] [Accepted: 03/21/2023] [Indexed: 04/29/2023] Open
Abstract
Poor diet, obesity and a sedentary lifestyle have a significant impact on natural microbiota disorders; specifically, the intestinal one. This in turn can lead to a multitude of organ dysfunctions. The gut microbiota contains more than 500 species of bacteria and constitutes 95% of the total number of cells in the human body, thus contributing significantly to the host's resistance to infectious diseases. Nowadays, consumers have turned to purchased foods, especially those containing probiotic bacteria or prebiotics, that constitute some of the functional food market, which is constantly expanding. Indeed, there are many products available that incorporate probiotics, such as yogurt, cheese, juices, jams, cookies, salami sausages, mayonnaise, nutritional supplements, etc. The probiotics are microorganisms that, when taken in sufficient amounts, contribute positively to the health of the host and are the focus of interest for both scientific studies and commercial companies. Thus, in the last decade, the introduction of DNA sequencing technologies with subsequent bioinformatics processing contributes to the in-depth characterization of the vast biodiversity of the gut microbiota, their composition, their connection with the physiological function-known as homeostasis-of the human organism, and their involvement in several diseases. Therefore, in this study, we highlighted the extensive investigation of current scientific research for the association of those types of functional foods containing probiotics and prebiotics in the diet and the composition of the intestinal microbiota. As a result, this study can form the foundation for a new research path based on reliable data from the literature, acting a guide in the continuous effort to monitor the rapid developments in this field.
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Affiliation(s)
- Andrea Ballini
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Ioannis Alexandros Charitos
- National Poisoning Center, Emergency/Urgent Department, Riuniti University Hospital of Foggia, 71122 Foggia, Italy
| | - Stefania Cantore
- Independent Researcher, Regional Dental Community Service "Sorriso & Benessere-Ricerca e Clinica", 70129 Bari, Italy
| | - Skender Topi
- Department of Clinical Disciplines, University of Elbasan, 3001 Elbasan, Albania
| | - Lucrezia Bottalico
- Department of Clinical Disciplines, University of Elbasan, 3001 Elbasan, Albania
| | - Luigi Santacroce
- Microbiology and Virology Unit, Department of Interdisciplinary Medicine, University of Bari "Aldo Moro", 70124 Bari, Italy
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