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Jandl B, Dighe S, Gasche C, Makristathis A, Muttenthaler M. Intestinal biofilms: pathophysiological relevance, host defense, and therapeutic opportunities. Clin Microbiol Rev 2024; 37:e0013323. [PMID: 38995034 PMCID: PMC11391705 DOI: 10.1128/cmr.00133-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024] Open
Abstract
SUMMARYThe human intestinal tract harbors a profound variety of microorganisms that live in symbiosis with the host and each other. It is a complex and highly dynamic environment whose homeostasis directly relates to human health. Dysbiosis of the gut microbiota and polymicrobial biofilms have been associated with gastrointestinal diseases, including irritable bowel syndrome, inflammatory bowel diseases, and colorectal cancers. This review covers the molecular composition and organization of intestinal biofilms, mechanistic aspects of biofilm signaling networks for bacterial communication and behavior, and synergistic effects in polymicrobial biofilms. It further describes the clinical relevance and diseases associated with gut biofilms, the role of biofilms in antimicrobial resistance, and the intestinal host defense system and therapeutic strategies counteracting biofilms. Taken together, this review summarizes the latest knowledge and research on intestinal biofilms and their role in gut disorders and provides directions toward the development of biofilm-specific treatments.
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Affiliation(s)
- Bernhard Jandl
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Vienna, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Vienna, Austria
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Satish Dighe
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Christoph Gasche
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Medical University of Vienna, Vienna, Austria
- Loha for Life, Center for Gastroenterology and Iron Deficiency, Vienna, Austria
| | - Athanasios Makristathis
- Department of Laboratory Medicine, Division of Clinical Microbiology, Medical University of Vienna, Vienna, Austria
| | - Markus Muttenthaler
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Vienna, Austria
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
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2
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Wang J, He M, Yang M, Ai X. Gut microbiota as a key regulator of intestinal mucosal immunity. Life Sci 2024; 345:122612. [PMID: 38588949 DOI: 10.1016/j.lfs.2024.122612] [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: 02/04/2024] [Revised: 03/14/2024] [Accepted: 04/02/2024] [Indexed: 04/10/2024]
Abstract
Gut microbiota is a complex microbial community with the ability of maintaining intestinal health. Intestinal homeostasis largely depends on the mucosal immune system to defense external pathogens and promote tissue repair. In recent years, growing evidence revealed the importance of gut microbiota in shaping intestinal mucosal immunity. Therefore, according to the existing findings, this review first provided an overview of intestinal mucosal immune system before summarizing the regulatory roles of gut microbiota in intestinal innate and adaptive immunity. Specifically, this review delved into the gut microbial interactions with the cells such as intestinal epithelial cells (IECs), macrophages, dendritic cells (DCs), neutrophils, and innate lymphoid cells (ILCs) in innate immunity, and T and B lymphocytes in adaptive immunity. Furthermore, this review discussed the main effects of gut microbiota dysbiosis in intestinal diseases and offered future research prospects. The review highlighted the key regulatory roles of gut microbiota in intestinal mucosal immunity via various host-microbe interactions, providing valuable references for the development of microbial therapy in intestinal diseases.
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Affiliation(s)
- Jing Wang
- Department of Pharmacy, Affiliated Hospital of North Sichuan Medical College, Nanchong 637000, China; Department of Pharmacy, North Sichuan Medical College, Nanchong 637000, China
| | - Mei He
- Department of Pharmacy, Affiliated Hospital of North Sichuan Medical College, Nanchong 637000, China; Department of Pharmacy, North Sichuan Medical College, Nanchong 637000, China
| | - Ming Yang
- Department of Pharmacy, Affiliated Hospital of North Sichuan Medical College, Nanchong 637000, China; Department of Pharmacy, North Sichuan Medical College, Nanchong 637000, China.
| | - Xiaopeng Ai
- Department of Pharmacy, Affiliated Hospital of North Sichuan Medical College, Nanchong 637000, China; Department of Pharmacy, North Sichuan Medical College, Nanchong 637000, China.
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3
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Wang H, Wang Y, Yang L, Feng J, Tian S, Chen L, Huang W, Liu J, Wang X. Integrated 16S rRNA sequencing and metagenomics insights into microbial dysbiosis and distinct virulence factors in inflammatory bowel disease. Front Microbiol 2024; 15:1375804. [PMID: 38591039 PMCID: PMC10999624 DOI: 10.3389/fmicb.2024.1375804] [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: 01/25/2024] [Accepted: 02/26/2024] [Indexed: 04/10/2024] Open
Abstract
Introduction The escalation of urbanization correlates with rising rates of inflammatory bowel disease (IBD), necessitating research into new etiological factors. This study aims to elucidate the gut microbiota profiles in IBD patients and compare them with healthy controls in a western city of China. Methods We conducted a multicenter case-control study from the end of 2020, using 16S rRNA gene sequencing (n = 36) and metagenomic sequencing (n = 12) to analyze the gut microbiota of newly diagnosed IBD patients, including those with Crohn's disease (CD) and ulcerative colitis (UC). Results Our results demonstrated a significant enrichment of the phylum Proteobacteria, particularly the genus Escherichia-Shigella, in CD patients. Conversely, the genus Enterococcus was markedly increased in UC patients. The core gut microbiota, such as the Christensenellaceae R-7 group, Fusicatenibacter, and Holdemanella, were primarily identified in healthy subjects. Additionally, significant interactions between the microbiome and virulence factors were observed. Discussion The findings suggest that oxidative stress may play a pivotal role in the pathology of IBD. This study contributes to the growing dialogue about the impact of gut microbiota on the development of IBD and its variations across different geographies, highlighting potential avenues for further research.
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Affiliation(s)
- Haijing Wang
- Medical College of Qinghai University, Xining, China
| | - Yuanjun Wang
- Medical College of Qinghai University, Xining, China
- Qinghai University Affiliated Hospital, Xining, China
| | - Libin Yang
- Ningxia Hui Autonomous Region People's Hospital, Yinchuan, China
| | - Jiawen Feng
- Medical College of Qinghai University, Xining, China
- Qinghai Provincial Traditional Chinese Medicine Hospital, Xining, China
| | - Shou Tian
- Medical College of Qinghai University, Xining, China
- Qinghai Provincial Traditional Chinese Medicine Hospital, Xining, China
| | - Lingyan Chen
- Qinghai Provincial Traditional Chinese Medicine Hospital, Xining, China
| | - Wei Huang
- Qinghai Provincial Traditional Chinese Medicine Hospital, Xining, China
| | - Jia Liu
- Qinghai Provincial Traditional Chinese Medicine Hospital, Xining, China
| | - Xiaojin Wang
- Medical College of Qinghai University, Xining, China
- Qinghai Provincial Traditional Chinese Medicine Hospital, Xining, China
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Tong G, Qian H, Li D, Li J, Chen J, Li X, Tan Z. Intestinal Flora Imbalance Induced by Antibiotic Use in Rats. J Inflamm Res 2024; 17:1789-1804. [PMID: 38528993 PMCID: PMC10961240 DOI: 10.2147/jir.s447098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 03/14/2024] [Indexed: 03/27/2024] Open
Abstract
Aim This study aims to explore the effect of different doses of antibiotics on rats in order to observe alterations in their fecal microbiota, inflammatory changes in the colonic mucosa and four types of inflammatory markers in blood serum. Methods Our methodology involved separating 84 female Sprague Dawley rats into groups A-G, with each group consisting of 12 rats. We collected the rat feces for analysis, using a distinct medium for bacterial cultivation and counting colonies under a microscope. On the 11th and 15th days of the experiment, half of the rats from each group were euthanized and 5 mL of abdominal aortic blood and colon tissues were collected. Inflammations changes of colon were observed and assessed by pathological Hematoxylin Eosin (HE) staining. Enzyme-linked immune sorbent assay (ELISA) was adopted for detecting C-reactive protein (CRP), IL-6, IL1-β and TNF-α. Results Our findings revealed that the initial average weight of the rats did not differ between groups (p>0.05); but significant differences were observed between stool samples, water intake, food intake and weight (p=0.009, <0.001, 0.016 and 0.04, respectively) within two hours after the experiment. Additionally, there were notable differences among the groups in nine tested microbiota before and after weighting methods (all p<0.001). There were no difference in nine microbiota at day 1 (all p>0.05); at day 4 A/B (p=0.044), A/D (p<0.001), A/E (p=0.029); at day 8, all p<0.01, at day 11, only A/F exist significant difference (p<0.001); at day 14 only A/D has difference (p=0.045). Inflammation changes of colon were observed between groups A-G at days 11 and 15. Significant differences between all groups can be observed for CRP, IL-6, IL1-β and TNF-α (p<0.001). Conclusion This study suggests that antibiotics administration can disrupt the balance of bacteria in the rat gut ecosystem, resulting in an inflammatory response in their bloodstream and inducing inflammation changes of colon.
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Affiliation(s)
- Guojun Tong
- General Surgery, Huzhou Central Hospital, The Affiliated Central Hospital of Huzhou University, Huzhou, People’s Republic of China
- Central Laboratory, Huzhou Central Hospital, The Affiliated Central Hospital of Huzhou University, Huzhou, People’s Republic of China
| | - Hai Qian
- General Surgery, Huzhou Central Hospital, The Affiliated Central Hospital of Huzhou University, Huzhou, People’s Republic of China
| | - Dongli Li
- Central Laboratory, Huzhou Central Hospital, The Affiliated Central Hospital of Huzhou University, Huzhou, People’s Republic of China
| | - Jing Li
- Central Laboratory, Huzhou Central Hospital, The Affiliated Central Hospital of Huzhou University, Huzhou, People’s Republic of China
| | - Jing Chen
- Central Laboratory, Huzhou Central Hospital, The Affiliated Central Hospital of Huzhou University, Huzhou, People’s Republic of China
| | - Xiongfeng Li
- Orthopedic Surgery, Huzhou Central Hospital, The Affiliated Central Hospital of Huzhou University, Huzhou, People’s Republic of China
| | - Zhenhua Tan
- General Surgery, Huzhou Central Hospital, The Affiliated Central Hospital of Huzhou University, Huzhou, People’s Republic of China
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Joo MK, Lee JW, Woo JH, Kim HJ, Kim DH, Choi JH. Regulation of colonic neuropeptide Y expression by the gut microbiome in patients with ulcerative colitis and its association with anxiety- and depression-like behavior in mice. Gut Microbes 2024; 16:2319844. [PMID: 38404132 PMCID: PMC10900276 DOI: 10.1080/19490976.2024.2319844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 02/13/2024] [Indexed: 02/27/2024] Open
Abstract
Patients with inflammatory bowel disease (IBD), including ulcerative colitis (UC), show an increased incidence of anxiety and depression; however, the association between UC-associated psychiatric disorders and the gut microbiota is unclear. This study aimed to examine whether gut microbiota from patients with UC can alter colonic gene expression, leading to anxiety- and depression-like behavior in mice receiving fecal microbiota transplantation (FMT). RNA sequencing transcriptome analyses revealed a difference in colonic gene expression between mice receiving FMT from patients with UC (UC-FMT mice) and those receiving FMT from healthy controls (HC-FMT mice). Gene ontology analysis revealed the downregulation of neuropeptide signaling pathways, including neuropeptide Y (NPY) expression, in the colons of UC-FMT mice. The protein levels of NPY also decreased in the colon and plasma of UC-FMT mice compared to those in HC-FMT mice. The oral administration of Enterococcus mundtii (EM), a bacterium isolated from the feces of patients with UC, reduced NPY expression in the colons of mice and induced intestinal inflammation, anxiety, and depression-like behavior. Reduced NPY protein levels were also observed in the plasma and hippocampus of EM-treated mice. Intraperitoneal administration of NPY significantly alleviated anxiety- and depressive-like behaviors induced by EM in mice. Capsular polysaccharide in EM was associated with EM-induced NPY downregulation in the colon. Analysis of Gene Expression Omnibus datasets showed markedly reduced NPY expression in the inflamed colons of patients with UC compared with that in the colons of healthy controls. In summary, EM-induced reduction in the colonic expression of NPY may be associated with a decrease in hippocampal NPY and anxiety- and depression-like behavior in mice.
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Affiliation(s)
- Min-Kyung Joo
- Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul, Korea
- College of Pharmacy, Kyung Hee University, Seoul, Korea
| | - Jae-Won Lee
- Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul, Korea
- College of Pharmacy, Kyung Hee University, Seoul, Korea
| | - Jeong-Hwa Woo
- College of Pharmacy, Kyung Hee University, Seoul, Korea
| | - Hyo-Jong Kim
- Department of Internal Medicine, School of Medicine, Kyung Hee University, Seoul, Korea
| | - Dong-Hyun Kim
- Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul, Korea
- College of Pharmacy, Kyung Hee University, Seoul, Korea
| | - Jung-Hye Choi
- Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul, Korea
- College of Pharmacy, Kyung Hee University, Seoul, Korea
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Richie TG, Heeren L, Kamke A, Monk K, Pogranichniy S, Summers T, Wiechman H, Ran Q, Sarkar S, Plattner BL, Lee STM. Limitation of amino acid availability by bacterial populations during enhanced colitis in IBD mouse model. mSystems 2023; 8:e0070323. [PMID: 37909786 PMCID: PMC10746178 DOI: 10.1128/msystems.00703-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/27/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Inflammatory bowel disease is associated with an increase in Enterobacteriaceae and Enterococcus species; however, the specific mechanisms are unclear. Previous research has reported the associations between microbiota and inflammation, here we investigate potential pathways that specific bacteria populations use to drive gut inflammation. Richie et al. show that these bacterial populations utilize an alternate sulfur metabolism and are tolerant of host-derived immune-response products. These metabolic pathways drive host gut inflammation and fuel over colonization of these pathobionts in the dysbiotic colon. Cultured isolates from dysbiotic mice indicated faster growth supplemented with L-cysteine, showing these microbes can utilize essential host nutrients.
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Affiliation(s)
- Tanner G. Richie
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Leah Heeren
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Abigail Kamke
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Kourtney Monk
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | | | - Trey Summers
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Hallie Wiechman
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Qinghong Ran
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Soumyadev Sarkar
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Brandon L. Plattner
- Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, Kansas, USA
| | - Sonny T. M. Lee
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
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Amuasi GR, Dsani E, Owusu-Nyantakyi C, Owusu FA, Mohktar Q, Nilsson P, Adu B, Hendriksen RS, Egyir B. Enterococcus species: insights into antimicrobial resistance and whole-genome features of isolates recovered from livestock and raw meat in Ghana. Front Microbiol 2023; 14:1254896. [PMID: 38192291 PMCID: PMC10773571 DOI: 10.3389/fmicb.2023.1254896] [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: 07/07/2023] [Accepted: 10/25/2023] [Indexed: 01/10/2024] Open
Abstract
Introduction Enterococcus spp. have gradually evolved from commensals to causing life-threatening hospital-acquired infections globally due to their inherent antimicrobial resistance ability and virulence potential. Enterococcus spp. recovered from livestock and raw meat samples were characterized using antimicrobial susceptibility testing and whole-genome sequencing. Materials and methods Isolates were confirmed using the MALDI-ToF mass spectrometer, and antimicrobial susceptibility was determined using the Kirby-Bauer disk diffusion method. Whole genome sequencing was performed on isolates resistant to two or more antibiotics. Bioinformatics analysis was performed to determine sequence types, resistance and virulence gene content and evolutionary relationships between isolates from meat and livestock samples, and other enterococci genomes curated by PATRIC. eBURST analysis was used to assign genomes to clonal complexes. Results Enterococcus spp. were predominantly E. faecalis (96/236; 41%) and E. faecium (89/236; 38%). Overall, isolates showed resistance to erythromycin (78/236; 33%), tetracycline (71/236; 30%), ciprofloxacin (20/236; 8%), chloramphenicol (12/236; 5%), linezolid (7/236; 3%), ampicillin (4/236; 2%) and vancomycin (1/236, 0.4%). Resistance to two or more antimicrobial agents was detected among 17% (n = 40) Enterococcus spp. Resistance genes for streptogramins [lsa(A), lsa(E), msr(C)], aminoglycosides [aac(6')-Ii, aph(3')-III, ant(6)-Ia, aac(6')-aph(2″), str], amphenicol [cat], macrolides [erm(B), erm(T), msr(C)], tetracyclines [tet(M), tet(L), tet(S)] and lincosamides [lsa(A), lsa(E), lnu(B)] were detected among the isolates. Genes for biofilm formation, adhesins, sex pheromones, cytolysins, hyaluronidase, oxidative stress resistance, quorum-sensing and anti-phagocytic activity were also identified. Potential plasmids with replicon sequences (rep1, rep2, repUS43, repUS47, rep9a, rep9b) and other mobile genetic elements (Tn917, cn_5536_ISEnfa1, Tn6009, ISEnfa1, ISEfa10) were detected. Clinically relevant E. faecium ST32 and ST416 clones were identified in meat samples. Conclusion The occurrence of antimicrobial-resistant Enterococcus spp. in livestock and raw meat samples, carrying multiple resistance and virulence genes, including known clones associated with hospital-acquired infections, underscores the critical need for employing robust tools like whole genome sequencing. Such tools provide detailed data essential for ongoing surveillance efforts aimed at addressing the challenge of antimicrobial resistance with a focus on one health.
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Affiliation(s)
- Grebstad Rabbi Amuasi
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Esther Dsani
- Veterinary Services Department, Ministry of Food and Agriculture, Accra, Ghana
| | - Christian Owusu-Nyantakyi
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Felicia A. Owusu
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Quaneeta Mohktar
- Department of Immunology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Pernille Nilsson
- National Food Institute, Research Group for Global Capacity Building, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, European Union Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Bright Adu
- Department of Immunology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Rene S. Hendriksen
- National Food Institute, Research Group for Global Capacity Building, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, European Union Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Beverly Egyir
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
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Palandurkar GS, Kumar S. Biofilm's Impact on Inflammatory Bowel Diseases. Cureus 2023; 15:e45510. [PMID: 37868553 PMCID: PMC10585119 DOI: 10.7759/cureus.45510] [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: 08/18/2023] [Accepted: 09/18/2023] [Indexed: 10/24/2023] Open
Abstract
The colon has a large surface area covered with a thick mucus coating. Colon's biomass consists of about 1,012 colony-forming units per gram of feces and 500-1,000 distinct bacterial species. The term inflammatory bowel disease (IBD) indicates the collection of intestinal illnesses in which the digestive system (esophagus, large intestine, mouth, stomach, and small intestine) experiences persistent inflammation. IBD development is influenced by environmental (infections, stress, and nutrition) and genetic factors. The microbes present in gut microbiota help maintain intestinal homeostasis and support immune and epithelial cell growth, differentiation, as well as proliferation. It has been discovered that a variety of variables and microorganisms are crucial for the development of biofilms and mucosal colonization during IBD. An extracellular matrix formed by bacteria supports biofilm production in our digestive system and harms the host's immunological response. Irritable bowel syndrome (IBS) and IBD considerably affect human socioeconomic well-being and the standard of living. IBD is a serious public health issue, affecting millions of people across the globe. The gut microbiome may significantly influence IBS pathogenesis, even though few diagnostic and treatment options are available. As a result, current research focuses more on disrupting biofilm in IBD patients and stresses primarily on drugs that help improve the quality of life for human well-being. We evaluate studies on IBD and bacterial biofilm to add fresh insights into the existing state of knowledge of biofilm formation in IBD, incidence of IBD patients, molecular level of investigations, bacteria that are involved in the formation of biofilm, and present and down the line regimens and probiotics. Planning advanced ways to control and eradicate bacteria in biofilms should be the primary goal to add fresh insights into generating innovative diagnostic and alternative therapy options for IBD.
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Affiliation(s)
- Gopal S Palandurkar
- Department of Medicine, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Sunil Kumar
- Department of Medicine, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
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D'Adamo GL, Chonwerawong M, Gearing LJ, Marcelino VR, Gould JA, Rutten EL, Solari SM, Khoo PWR, Wilson TJ, Thomason T, Gulliver EL, Hertzog PJ, Giles EM, Forster SC. Bacterial clade-specific analysis identifies distinct epithelial responses in inflammatory bowel disease. Cell Rep Med 2023; 4:101124. [PMID: 37467722 PMCID: PMC10394256 DOI: 10.1016/j.xcrm.2023.101124] [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: 01/04/2023] [Revised: 03/19/2023] [Accepted: 06/21/2023] [Indexed: 07/21/2023]
Abstract
Abnormal immune responses to the resident gut microbiome can drive inflammatory bowel disease (IBD). Here, we combine high-resolution, culture-based shotgun metagenomic sequencing and analysis with matched host transcriptomics across three intestinal sites (terminal ileum, cecum, rectum) from pediatric IBD (PIBD) patients (n = 58) and matched controls (n = 42) to investigate this relationship. Combining our site-specific approach with bacterial culturing, we establish a cohort-specific bacterial culture collection, comprising 6,620 isolates (170 distinct species, 32 putative novel), cultured from 286 mucosal biopsies. Phylogeny-based, clade-specific metagenomic analysis identifies key, functionally distinct Enterococcus clades associated with either IBD or health. Strain-specific in vitro validation demonstrates differences in cell cytotoxicity and inflammatory signaling in intestinal epithelial cells, consistent with the colonic mucosa-specific response measured in patients with IBD. This demonstrates the importance of strain-specific phenotypes and consideration of anatomical sites in exploring the dysregulated host-bacterial interactions in IBD.
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Affiliation(s)
- Gemma L D'Adamo
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Michelle Chonwerawong
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Linden J Gearing
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Vanessa R Marcelino
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Jodee A Gould
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Emily L Rutten
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Sean M Solari
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Patricia W R Khoo
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia; Department of Paediatrics, Monash University, Clayton, VIC 3800, Australia
| | - Trevor J Wilson
- Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia; MHTP Medical Genomics Facility, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia
| | - Tamblyn Thomason
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Emily L Gulliver
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Paul J Hertzog
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Edward M Giles
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia; Department of Paediatrics, Monash University, Clayton, VIC 3800, Australia.
| | - Samuel C Forster
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia.
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10
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Markelova M, Senina A, Khusnutdinova D, Siniagina M, Kupriyanova E, Shakirova G, Odintsova A, Abdulkhakov R, Kolesnikova I, Shagaleeva O, Lyamina S, Abdulkhakov S, Zakharzhevskaya N, Grigoryeva T. Association between Taxonomic Composition of Gut Microbiota and Host Single Nucleotide Polymorphisms in Crohn's Disease Patients from Russia. Int J Mol Sci 2023; 24:ijms24097998. [PMID: 37175705 PMCID: PMC10178390 DOI: 10.3390/ijms24097998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
Crohn's disease (CD) is a chronic relapsing inflammatory bowel disease of unknown etiology. Genetic predisposition and dysbiotic gut microbiota are important factors in the pathogenesis of CD. In this study, we analyzed the taxonomic composition of the gut microbiota and genotypes of 24 single nucleotide polymorphisms (SNP) associated with the risk of CD. The studied cohorts included 96 CD patients and 24 healthy volunteers from Russia. Statistically significant differences were found in the allele frequencies for 8 SNPs and taxonomic composition of the gut microbiota in CD patients compared with controls. In addition, two types of gut microbiota communities were identified in CD patients. The main distinguishing driver of bacterial families for the first community type are Bacteroidaceae and unclassified members of the Clostridiales order, and the second type is characterized by increased abundance of Streptococcaceae and Enterobacteriaceae. Differences in the allele frequencies of the rs9858542 (BSN), rs3816769 (STAT3), and rs1793004 (NELL1) were also found between groups of CD patients with different types of microbiota communities. These findings confirm the complex multifactorial nature of CD.
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Affiliation(s)
- Maria Markelova
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia
| | - Anastasia Senina
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia
| | - Dilyara Khusnutdinova
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia
| | - Maria Siniagina
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia
| | - Elena Kupriyanova
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia
| | | | | | - Rustam Abdulkhakov
- Hospital Therapy Department, Kazan State Medical University, 420012 Kazan, Russia
| | - Irina Kolesnikova
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
| | - Olga Shagaleeva
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
| | - Svetlana Lyamina
- Molecular Pathology of Digestion Laboratory, A.I. Yevdokimov Moscow State University of Medicine and Dentistry, 127473 Moscow, Russia
| | - Sayar Abdulkhakov
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia
| | - Natalia Zakharzhevskaya
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
| | - Tatiana Grigoryeva
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia
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11
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Wiredu Ocansey DK, Hang S, Yuan X, Qian H, Zhou M, Valerie Olovo C, Zhang X, Mao F. The diagnostic and prognostic potential of gut bacteria in inflammatory bowel disease. Gut Microbes 2023; 15:2176118. [PMID: 36794838 PMCID: PMC9980661 DOI: 10.1080/19490976.2023.2176118] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 01/26/2023] [Indexed: 02/17/2023] Open
Abstract
The gut microbiome serves as a signaling hub that integrates environmental inputs with genetic and immune signals to influence the host's metabolism and immunity. Gut bacteria are intricately connected with human health and disease state, with specific bacteria species driving the characteristic dysbiosis found in gastrointestinal conditions such as inflammatory bowel disease (IBD); thus, gut bacteria changes could be harnessed to improve IBD diagnosis, prognosis, and treatment. The advancement in next-generation sequencing techniques such as 16S rRNA and whole-genome shotgun sequencing has allowed the exploration of the complexity of the gut microbial ecosystem with high resolution. Current microbiome data is promising and appears to perform better in some studies than the currently used fecal inflammation biomarker, calprotectin, in predicting IBD from healthy controls and irritable bowel syndrome (IBS). This study reviews current data on the differential potential of gut bacteria within IBD cohorts, and between IBD and other gastrointestinal diseases.
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Affiliation(s)
- Dickson Kofi Wiredu Ocansey
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, P.R. China
- Directorate of University Health Services, University of Cape Coast, PMB, Cape Coast, Ghana
| | - Sanhua Hang
- The People’s Hospital of Danyang, Affiliated Danyang Hospital of Nantong University, Zhenjiang, P.R. China
| | - Xinyi Yuan
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, P.R. China
| | - Hua Qian
- Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, P.R. China
| | - Mengjiao Zhou
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, P.R. China
| | - Chinasa Valerie Olovo
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, P.R. China
- Department of Microbiology, University of Nigeria, Nsukka, Nigeria
| | - Xu Zhang
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, P.R. China
| | - Fei Mao
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, P.R. China
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12
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Talapko J, Včev A, Meštrović T, Pustijanac E, Jukić M, Škrlec I. Homeostasis and Dysbiosis of the Intestinal Microbiota: Comparing Hallmarks of a Healthy State with Changes in Inflammatory Bowel Disease. Microorganisms 2022; 10:microorganisms10122405. [PMID: 36557658 PMCID: PMC9781915 DOI: 10.3390/microorganisms10122405] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
The gut microbiota, which represent a community of different microorganisms in the human intestinal tract, are crucial to preserving human health by participating in various physiological functions and acting as a metabolic organ. In physiological conditions, microbiota-host partnership exerts homeostatic stability; however, changes in intestinal microbiota composition (dysbiosis) are an important factor in the pathogenesis of inflammatory bowel disease and its two main disease entities: ulcerative colitis and Crohn's disease. The incidence and prevalence of these inflammatory conditions have increased rapidly in the last decade, becoming a significant problem for the healthcare system and a true challenge in finding novel therapeutic solutions. The issue is that, despite numerous studies, the etiopathogenesis of inflammatory bowel disease is not completely clear. Based on current knowledge, chronic intestinal inflammation occurs due to altered intestinal microbiota and environmental factors, as well as a complex interplay between the genetic predisposition of the host and an inappropriate innate and acquired immune response. It is important to note that the development of biological and immunomodulatory therapy has led to significant progress in treating inflammatory bowel disease. Certain lifestyle changes and novel approaches-including fecal microbiota transplantation and nutritional supplementation with probiotics, prebiotics, and synbiotics-have offered solutions for dysbiosis management and paved the way towards restoring a healthy microbiome, with only minimal long-term unfavorable effects.
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Affiliation(s)
- Jasminka Talapko
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, Crkvena 21, 31000 Osijek, Croatia
| | - Aleksandar Včev
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, Crkvena 21, 31000 Osijek, Croatia
| | - Tomislav Meštrović
- University Centre Varaždin, University North, 42000 Varaždin, Croatia
- Institute for Health Metrics and Evaluation and the Department of Health Metrics Sciences, University of Washington, Seattle, WA 98195, USA
- Correspondence: (T.M.); (I.Š.)
| | - Emina Pustijanac
- Faculty of Natural Sciences, Juraj Dobrila University of Pula, 52100 Pula, Croatia
| | - Melita Jukić
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, Crkvena 21, 31000 Osijek, Croatia
- General Hospital Vukovar, Županijska 35, 32000 Vukovar, Croatia
| | - Ivana Škrlec
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, Crkvena 21, 31000 Osijek, Croatia
- Correspondence: (T.M.); (I.Š.)
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13
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Wang Z, Iida N, Seishima J, Okafuji H, Yutani M, Fujinaga Y, Hashimoto Y, Tomita H, Mizukoshi E, Kaneko S. Patient-derived Enterococcus faecium with inflammatory genotypes promote colitis. J Gastroenterol 2022; 57:770-783. [PMID: 35882645 DOI: 10.1007/s00535-022-01905-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 07/07/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND Dysbiosis of gut microbiota promotes colitis in ulcerative colitis (UC). Enterococcus faecium is an important constituent of dysbiotic microbiota. However, the mechanisms underlying E. faecium-induced colitis remain unclear. METHODS Overall, 23 E. faecium strains isolated from human feces and 3 commercial strains were inoculated into Il10-/- mice. Mouse colons were histologically evaluated and analyzed using real-time PCR analysis of cytokines. Genes in 26 E. faecium strains were identified by whole-genome shotgun sequencing of genomic DNA. The production of reactive oxygen species (ROS) from each strain was measured. An antioxidant, lipoic acid, was orally administered to the colitis mouse model. RESULTS Inoculation of E. faecium derived from patients with UC resulted in colitis in Il10-/- mice. The genotypes of 26 strains were characterized by identifying 1893 known genes; clustering all the strains based on the genotypes showed two major groups-inflammatory and probiotic clusters. Additionally, linear discriminant analysis clarified that lipoic acid metabolism was a significantly abundant pathway in the probiotic cluster compared to the inflammatory cluster. Further, the production of ROS was greater in inflammatory than in probiotic strains. Administration of lipoic acid in E. faecium-inoculated mice ameliorated colitis. CONCLUSIONS Enterococcus faecium strains in the inflammatory cluster promoted colitis with higher production of ROS than the strains in the probiotic cluster.
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Affiliation(s)
- Ziyu Wang
- Department of Gastroenterology, Graduate School of Medical Sciences, Kanazawa University, 13-1 Takara-machi, Kanazawa, Ishikawa, 920-8641, Japan
| | - Noriho Iida
- Department of Gastroenterology, Graduate School of Medical Sciences, Kanazawa University, 13-1 Takara-machi, Kanazawa, Ishikawa, 920-8641, Japan
| | - Jun Seishima
- Department of Gastroenterology, Graduate School of Medical Sciences, Kanazawa University, 13-1 Takara-machi, Kanazawa, Ishikawa, 920-8641, Japan
| | - Hirofumi Okafuji
- Department of Gastroenterology, Graduate School of Medical Sciences, Kanazawa University, 13-1 Takara-machi, Kanazawa, Ishikawa, 920-8641, Japan
| | - Masahiro Yutani
- Department of Bacteriology, Graduate School of Medicinal Sciences, Kanazawa University, 13-1 Takara-machi, Kanazawa, Ishikawa, Japan
| | - Yukako Fujinaga
- Department of Bacteriology, Graduate School of Medicinal Sciences, Kanazawa University, 13-1 Takara-machi, Kanazawa, Ishikawa, Japan
| | - Yusuke Hashimoto
- Department of Bacteriology, Graduate School of Medicine, Gunma University, 3-39-15 Showa-machi, Maebashi, Gunma, Japan
| | - Haruyoshi Tomita
- Department of Bacteriology, Graduate School of Medicine, Gunma University, 3-39-15 Showa-machi, Maebashi, Gunma, Japan
| | - Eishiro Mizukoshi
- Department of Gastroenterology, Graduate School of Medical Sciences, Kanazawa University, 13-1 Takara-machi, Kanazawa, Ishikawa, 920-8641, Japan.
| | - Shuichi Kaneko
- Department of Gastroenterology, Graduate School of Medical Sciences, Kanazawa University, 13-1 Takara-machi, Kanazawa, Ishikawa, 920-8641, Japan
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14
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Piazzesi A, Putignani L. Extremely small and incredibly close: Gut microbes as modulators of inflammation and targets for therapeutic intervention. Front Microbiol 2022; 13:958346. [PMID: 36071979 PMCID: PMC9441770 DOI: 10.3389/fmicb.2022.958346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/25/2022] [Indexed: 11/15/2022] Open
Abstract
Chronic inflammation is a hallmark for a variety of disorders and is at least partially responsible for disease progression and poor patient health. In recent years, the microbiota inhabiting the human gut has been associated with not only intestinal inflammatory diseases but also those that affect the brain, liver, lungs, and joints. Despite a strong correlation between specific microbial signatures and inflammation, whether or not these microbes are disease markers or disease drivers is still a matter of debate. In this review, we discuss what is known about the molecular mechanisms by which the gut microbiota can modulate inflammation, both in the intestine and beyond. We identify the current gaps in our knowledge of biological mechanisms, discuss how these gaps have likely contributed to the uncertain outcome of fecal microbiota transplantation and probiotic clinical trials, and suggest how both mechanistic insight and -omics-based approaches can better inform study design and therapeutic intervention.
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Affiliation(s)
- Antonia Piazzesi
- Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Lorenza Putignani
- Department of Diagnostic and Laboratory Medicine, Unit of Microbiology and Diagnostic Immunology, Unit of Microbiomics and Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- *Correspondence: Lorenza Putignani,
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15
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Goya-Jorge E, Gonza I, Bondue P, Douny C, Taminiau B, Daube G, Scippo ML, Delcenserie V. Human Adult Microbiota in a Static Colon Model: AhR Transcriptional Activity at the Crossroads of Host–Microbe Interaction. Foods 2022; 11:foods11131946. [PMID: 35804761 PMCID: PMC9265634 DOI: 10.3390/foods11131946] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/21/2022] [Accepted: 06/25/2022] [Indexed: 02/01/2023] Open
Abstract
Functional symbiotic intestinal microbiota regulates immune defense and the metabolic processing of xenobiotics in the host. The aryl hydrocarbon receptor (AhR) is one of the transcription factors mediating host–microbe interaction. An in vitro static simulation of the human colon was used in this work to analyze the evolution of bacterial populations, the microbial metabolic output, and the potential induction of AhR transcriptional activity in healthy gut ecosystems. Fifteen target taxa were explored by qPCR, and the metabolic content was chromatographically profiled using SPME-GC-MS and UPLC-FLD to quantify short-chain fatty acids (SCFA) and biogenic amines, respectively. Over 72 h of fermentation, the microbiota and most produced metabolites remained stable. Fermentation supernatant induced AhR transcription in two of the three reporter gene cell lines (T47D, HepG2, HT29) evaluated. Mammary and intestinal cells were more sensitive to microbiota metabolic production, which showed greater AhR agonism than the 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) used as a positive control. Some of the SCFA and biogenic amines identified could crucially contribute to the potent AhR induction of the fermentation products. As a fundamental pathway mediating human intestinal homeostasis and as a sensor for several microbial metabolites, AhR activation might be a useful endpoint to include in studies of the gut microbiota.
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Affiliation(s)
- Elizabeth Goya-Jorge
- Laboratory of Food Quality Management, Department of Food Sciences, Faculty of Veterinary Medicine, University of Liege, Av. de Cureghem 10 (B43b), 4000 Liege, Belgium; (E.G.-J.); (I.G.)
| | - Irma Gonza
- Laboratory of Food Quality Management, Department of Food Sciences, Faculty of Veterinary Medicine, University of Liege, Av. de Cureghem 10 (B43b), 4000 Liege, Belgium; (E.G.-J.); (I.G.)
| | - Pauline Bondue
- Research & Development, ORTIS S.A., Hinter der Heck 46, 4750 Elsenborn, Belgium;
| | - Caroline Douny
- Laboratory of Food Analysis, Department of Food Sciences, Faculty of Veterinary Medicine, University of Liege, Av. de Cureghem 10 (B43b), 4000 Liege, Belgium; (C.D.); (M.-L.S.)
| | - Bernard Taminiau
- Laboratory of Microbiology, Department of Food Sciences, Faculty of Veterinary Medicine, University of Liege, Av. de Cureghem 180 (B42), 4000 Liege, Belgium; (B.T.); (G.D.)
| | - Georges Daube
- Laboratory of Microbiology, Department of Food Sciences, Faculty of Veterinary Medicine, University of Liege, Av. de Cureghem 180 (B42), 4000 Liege, Belgium; (B.T.); (G.D.)
| | - Marie-Louise Scippo
- Laboratory of Food Analysis, Department of Food Sciences, Faculty of Veterinary Medicine, University of Liege, Av. de Cureghem 10 (B43b), 4000 Liege, Belgium; (C.D.); (M.-L.S.)
| | - Véronique Delcenserie
- Laboratory of Food Quality Management, Department of Food Sciences, Faculty of Veterinary Medicine, University of Liege, Av. de Cureghem 10 (B43b), 4000 Liege, Belgium; (E.G.-J.); (I.G.)
- Correspondence: ; Tel.: +32-4-366-51-24
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16
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Making Sense of Quorum Sensing at the Intestinal Mucosal Interface. Cells 2022; 11:cells11111734. [PMID: 35681429 PMCID: PMC9179481 DOI: 10.3390/cells11111734] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 12/12/2022] Open
Abstract
The gut microbiome can produce metabolic products that exert diverse activities, including effects on the host. Short chain fatty acids and amino acid derivatives have been the focus of many studies, but given the high microbial density in the gastrointestinal tract, other bacterial products such as those released as part of quorum sensing are likely to play an important role for health and disease. In this review, we provide of an overview on quorum sensing (QS) in the gastrointestinal tract and summarise what is known regarding the role of QS molecules such as auto-inducing peptides (AIP) and acyl-homoserine lactones (AHL) from commensal, probiotic, and pathogenic bacteria in intestinal health and disease. QS regulates the expression of numerous genes including biofilm formation, bacteriocin and toxin secretion, and metabolism. QS has also been shown to play an important role in the bacteria–host interaction. We conclude that the mechanisms of action of QS at the intestinal neuro–immune interface need to be further investigated.
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17
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Tong G, Qian H, Li D, Li J, Chen J, Li X. Establishment and evaluation of a specific antibiotic-induced inflammatory bowel disease model in rats. PLoS One 2022; 17:e0264194. [PMID: 35192646 PMCID: PMC8863245 DOI: 10.1371/journal.pone.0264194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 02/06/2022] [Indexed: 12/03/2022] Open
Abstract
Physical and chemical methods for generating rat models of enteritis have been established; however, antibiotic induction has rarely been used for this purpose. The present study aimed to establish and evaluate a rat model of inflammatory bowel disease (IBD) using antibiotics. A total of 84 Sprague-Dawley (SD) rats were divided into the following groups, according to the dosage and method of administration of the antibiotics: A, control; B, low-dose clindamycin; C, medium-dose clindamycin; D, high-dose clindamycin; E, low-dose clindamycin, ampicillin and streptomycin; F, medium-dose clindamycin, ampicillin and streptomycin; and G, high-dose clindamycin, ampicillin and streptomycin. Antibiotic administration was stopped on day 7; the modeling period covered days 1-7, and the recovery period covered days 8-15. Half of the animals were dissected on day 11, with the remaining animals dissected on day 15. Food and water intake, body weight and fecal weight were recorded. Intestinal flora was analyzed via microbial culture and quantitative PCR. The content of TNF-α, IL1-β, IL-6 and C-reactive protein (CRP) was assessed in abdominal aorta blood. Colonic and rectal tissues were examined pathologically via hematoxylin-eosin staining to assess leukocyte infiltration and intestinal mucosal changes as indicators of inflammation. Rat weight, food intake, water intake and 2-h fecal weight were significantly different across the experimental groups (P = 0.040, P = 0.016, P<0.001 and P = 0.009, respectively). Microbial cultures revealed no significant differences between group A and B,C (P = 0.546,0.872) but significant differences betwenn group A and the other experimental groups (all P<0.001). Furthermore, significant differences in the levels of Bacteroides, Faecalibacterium prausnitzii and Dialister invisus on day 4 between groups A, C and F (P = 0.033, P = 0.025 and P = 0.034, respectively). Significant differences were detected in the levels of TNF-α, IL1-β, IL-6 and CRP between the groups (all P<0.001). The colonic and rectal pathological inflammation scores of the experimental groups were significantly different compared with group A (B vs. A, P = 0.002; others, all P<0.001). These findings indicated that an antibiotic-induced IBD model was successfully established in SD rats; this animal model may serve as a useful model for clinical IBD research.
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Affiliation(s)
- Guojun Tong
- Departments of General Surgery, Huzhou Central Hospital, Huzhou, Zhejiang, China
- Central Laboratory, Huzhou Central Hospital, Huzhou, Zhejiang, China
| | - Hai Qian
- Departments of General Surgery, Huzhou Central Hospital, Huzhou, Zhejiang, China
| | - Dongli Li
- Central Laboratory, Huzhou Central Hospital, Huzhou, Zhejiang, China
| | - Jing Li
- Central Laboratory, Huzhou Central Hospital, Huzhou, Zhejiang, China
| | - Jing Chen
- Central Laboratory, Huzhou Central Hospital, Huzhou, Zhejiang, China
| | - Xiongfeng Li
- Orthopedic Surgery, Huzhou Central Hospital, Huzhou, Zhejiang, China
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18
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Little M, Dutta M, Li H, Matson A, Shi X, Mascarinas G, Molla B, Weigel K, Gu H, Mani S, Cui JY. Understanding the physiological functions of the host xenobiotic-sensing nuclear receptors PXR and CAR on the gut microbiome using genetically modified mice. Acta Pharm Sin B 2022; 12:801-820. [PMID: 35256948 PMCID: PMC8897037 DOI: 10.1016/j.apsb.2021.07.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/29/2021] [Accepted: 07/09/2021] [Indexed: 12/12/2022] Open
Abstract
Pharmacological activation of the xenobiotic-sensing nuclear receptors pregnane X receptor (PXR) and constitutive androstane receptor (CAR) is well-known to increase drug metabolism and reduce inflammation. Little is known regarding their physiological functions on the gut microbiome. In this study, we discovered bivalent hormetic functions of PXR/CAR modulating the richness of the gut microbiome using genetically engineered mice. The absence of PXR or CAR increased microbial richness, and absence of both receptors synergistically increased microbial richness. PXR and CAR deficiency increased the pro-inflammatory bacteria Helicobacteraceae and Helicobacter. Deficiency in both PXR and CAR increased the relative abundance of Lactobacillus, which has bile salt hydrolase activity, corresponding to decreased primary taurine-conjugated bile acids (BAs) in feces, which may lead to higher internal burden of taurine and unconjugated BAs, both of which are linked to inflammation, oxidative stress, and cytotoxicity. The basal effect of PXR/CAR on the gut microbiome was distinct from pharmacological and toxicological activation of these receptors. Common PXR/CAR-targeted bacteria were identified, the majority of which were suppressed by these receptors. hPXR-TG mice had a distinct microbial profile as compared to wild-type mice. This study is the first to unveil the basal functions of PXR and CAR on the gut microbiome.
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Key Words
- BA, bile acid
- BSH, bile salt hydrolase
- Bile acids
- CA, cholic acid
- CAR
- CAR, constitutive androstane receptor
- CDCA, chenodeoxycholic acid
- CITCO, 6-(4-chlorophenyl)imidazo[2,1-b][1,3]thiazole-5-carbaldehyde O-(3,4-dichlorobenzyl)oxime
- CV, conventional
- CYP, cytochrome P450
- DCA, deoxycholic acid
- EGF, epidermal growth factor
- Feces
- GF, germ free
- GLP-1, glucagon-like peptide-1
- GM-CSF, granulocyte-macrophage colony-stimulating factor
- Gut microbiome
- HDCA, hyodeoxycholic acid
- IBD, inflammatory bowel disease
- IFNγ, interferon-gamma
- IL, interleukin
- IS, internal standards
- Inflammation
- LCA, lithocholic acid
- LC–MS/MS, liquid chromatography–tandem mass spectrometry
- MCA, muricholic acid
- MCP-1, monocyte chemoattractant protein-1
- Mice
- NF-κB, nuclear factor kappa-light-chain-enhancer of activated B cells
- NSAID, non-steroidal anti-inflammatory drug
- Nuclear receptor
- OH, hydroxylated
- OTUs, operational taxonomy units
- PA, indole-3 propionic acid
- PBDEs, polybrominated diphenyl ethers
- PCBs, polychlorinated biphenyls
- PCoA, Principle Coordinate Analysis
- PXR
- PXR, pregnane X receptor
- PiCRUSt, Phylogenetic Investigation of Communities by Reconstruction of Observed States
- QIIME, Quantitative Insights Into Microbial Ecology
- SCFAs, short-chain fatty acids
- SNP, single-nucleotide polymorphism
- SPF, specific-pathogen-free
- T, wild type
- T-, taurine conjugated
- TCPOBOP, 1,4-bis-[2-(3,5-dichloropyridyloxy)]benzene, 3,3′,5,5′-Tetrachloro-1,4-bis(pyridyloxy)benzene
- TGR-5, Takeda G-protein-coupled receptor 5
- TLR4, toll-like receptor 4
- TNF, tumor necrosis factor
- UDCA, ursodeoxycholic acid
- YAP, yes-associated protein
- hPXR-TG, humanized PXR transgenic
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Affiliation(s)
- Mallory Little
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA 98105, USA
| | - Moumita Dutta
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA 98105, USA
| | - Hao Li
- Department of Medicine, Molecular Pharmacology and Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Adam Matson
- University of Connecticut, Hartford, CT 06106, USA
| | - Xiaojian Shi
- Arizona Metabolomics Laboratory, College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA
| | - Gabby Mascarinas
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA 98105, USA
| | - Bruk Molla
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA 98105, USA
| | - Kris Weigel
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA 98105, USA
| | - Haiwei Gu
- Arizona Metabolomics Laboratory, College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA
| | - Sridhar Mani
- Department of Medicine, Molecular Pharmacology and Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Julia Yue Cui
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA 98105, USA
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19
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Akpınar Kankaya D, Tuncer Y. Detection of Virulence Factors, Biofilm Formation and Biogenic Amine Production in
Vancomycin‐Resistant
Lactic Acid Bacteria (
VRLAB
) Isolated From Foods of Animal Origin. J FOOD PROCESS PRES 2022. [DOI: 10.1111/jfpp.16423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Didem Akpınar Kankaya
- Department of Food Technology, Gelendost Vocational School Isparta University of Applied Sciences Isparta Turkey
| | - Yasin Tuncer
- Department of Food Engineering, Faculty of Engineering Süleyman Demirel University Isparta Turkey
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20
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Kriaa A, Jablaoui A, Rhimi S, Soussou S, Mkaouar H, Mariaule V, Gruba N, Gargouri A, Maguin E, Lesner A, Rhimi M. SP-1, a Serine Protease from the Gut Microbiota, Influences Colitis and Drives Intestinal Dysbiosis in Mice. Cells 2021; 10:2658. [PMID: 34685638 PMCID: PMC8534766 DOI: 10.3390/cells10102658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/22/2021] [Accepted: 10/01/2021] [Indexed: 11/20/2022] Open
Abstract
Increased protease activity has been linked to the pathogenesis of IBD. While most studies have been focusing on host proteases in gut inflammation, it remains unclear how to address the potential contribution of their bacterial counterparts. In the present study, we report a functional characterization of a newly identified serine protease, SP-1, from the human gut microbiota. The serine protease repertoire of gut Clostridium was first explored, and the specificity of SP-1 was analyzed using a combinatorial chemistry method. Combining in vitro analyses and a mouse model of colitis, we show that oral administration of recombinant bacteria secreting SP-1 (i) compromises the epithelial barrier, (ii) alters the microbial community, and (ii) exacerbates colitis. These findings suggest that gut microbial protease activity may constitute a valuable contributor to IBD and could, therefore, represent a promising target for the treatment of the disease.
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Affiliation(s)
- Aicha Kriaa
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute-UMR1319, AgroParisTech, Université Paris-Saclay, INRAE, F-78350 Jouy-en-Josas, France; (A.K.); (A.J.); (S.R.); (S.S.); (H.M.); (V.M.); (E.M.)
| | - Amin Jablaoui
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute-UMR1319, AgroParisTech, Université Paris-Saclay, INRAE, F-78350 Jouy-en-Josas, France; (A.K.); (A.J.); (S.R.); (S.S.); (H.M.); (V.M.); (E.M.)
| | - Soufien Rhimi
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute-UMR1319, AgroParisTech, Université Paris-Saclay, INRAE, F-78350 Jouy-en-Josas, France; (A.K.); (A.J.); (S.R.); (S.S.); (H.M.); (V.M.); (E.M.)
| | - Souha Soussou
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute-UMR1319, AgroParisTech, Université Paris-Saclay, INRAE, F-78350 Jouy-en-Josas, France; (A.K.); (A.J.); (S.R.); (S.S.); (H.M.); (V.M.); (E.M.)
| | - Héla Mkaouar
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute-UMR1319, AgroParisTech, Université Paris-Saclay, INRAE, F-78350 Jouy-en-Josas, France; (A.K.); (A.J.); (S.R.); (S.S.); (H.M.); (V.M.); (E.M.)
| | - Vincent Mariaule
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute-UMR1319, AgroParisTech, Université Paris-Saclay, INRAE, F-78350 Jouy-en-Josas, France; (A.K.); (A.J.); (S.R.); (S.S.); (H.M.); (V.M.); (E.M.)
| | - Natalia Gruba
- Faculty of Chemistry, University of Gdansk, Uniwersytet Gdanski, Chemistry, Wita Stwosza 63, PL80-308 Gdansk, Poland; (N.G.); (A.L.)
| | - Ali Gargouri
- Laboratory of Molecular Biotechnology of Eukaryotes, Center of Biotechnology of Sfax, University of Sfax, Sfax Bp ‘1177’ 3018, Tunisia;
| | - Emmanuelle Maguin
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute-UMR1319, AgroParisTech, Université Paris-Saclay, INRAE, F-78350 Jouy-en-Josas, France; (A.K.); (A.J.); (S.R.); (S.S.); (H.M.); (V.M.); (E.M.)
| | - Adam Lesner
- Faculty of Chemistry, University of Gdansk, Uniwersytet Gdanski, Chemistry, Wita Stwosza 63, PL80-308 Gdansk, Poland; (N.G.); (A.L.)
| | - Moez Rhimi
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute-UMR1319, AgroParisTech, Université Paris-Saclay, INRAE, F-78350 Jouy-en-Josas, France; (A.K.); (A.J.); (S.R.); (S.S.); (H.M.); (V.M.); (E.M.)
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21
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Meza-Torres J, Auria E, Dupuy B, Tremblay YDN. Wolf in Sheep's Clothing: Clostridioides difficile Biofilm as a Reservoir for Recurrent Infections. Microorganisms 2021; 9:1922. [PMID: 34576818 PMCID: PMC8470499 DOI: 10.3390/microorganisms9091922] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/06/2021] [Accepted: 09/07/2021] [Indexed: 12/21/2022] Open
Abstract
The microbiota inhabiting the intestinal tract provide several critical functions to its host. Microorganisms found at the mucosal layer form organized three-dimensional structures which are considered to be biofilms. Their development and functions are influenced by host factors, host-microbe interactions, and microbe-microbe interactions. These structures can dictate the health of their host by strengthening the natural defenses of the gut epithelium or cause disease by exacerbating underlying conditions. Biofilm communities can also block the establishment of pathogens and prevent infectious diseases. Although these biofilms are important for colonization resistance, new data provide evidence that gut biofilms can act as a reservoir for pathogens such as Clostridioides difficile. In this review, we will look at the biofilms of the intestinal tract, their contribution to health and disease, and the factors influencing their formation. We will then focus on the factors contributing to biofilm formation in C. difficile, how these biofilms are formed, and their properties. In the last section, we will look at how the gut microbiota and the gut biofilm influence C. difficile biofilm formation, persistence, and transmission.
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Affiliation(s)
- Jazmin Meza-Torres
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, UMR-CNRS 2001, Université de Paris, 25 rue du Docteur Roux, 75724 Paris, France; (J.M.-T.); (E.A.)
| | - Emile Auria
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, UMR-CNRS 2001, Université de Paris, 25 rue du Docteur Roux, 75724 Paris, France; (J.M.-T.); (E.A.)
| | - Bruno Dupuy
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, UMR-CNRS 2001, Université de Paris, 25 rue du Docteur Roux, 75724 Paris, France; (J.M.-T.); (E.A.)
| | - Yannick D. N. Tremblay
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, UMR-CNRS 2001, Université de Paris, 25 rue du Docteur Roux, 75724 Paris, France; (J.M.-T.); (E.A.)
- Health Sciences Building, Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, SK S7N 5E5, Canada
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22
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Fecal Microbiota Transplantation for Ulcerative Colitis: The Optimum Timing and Gut Microbiota as Predictors for Long-Term Clinical Outcomes. Clin Transl Gastroenterol 2021; 11:e00224. [PMID: 32955197 PMCID: PMC7431231 DOI: 10.14309/ctg.0000000000000224] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
INTRODUCTION: The previous researches aimed to evaluate the efficacy and safety of fecal microbiota transplantation (FMT) for ulcerative colitis (UC) in a short-term observation. The present study aimed to explore the optimum timing of FMT for maintaining the long-term clinical benefits and to target the gut microbiota that may help to predict the long-term success or failure of FMT in UC. METHODS: Two hundred two patients with UC were recruited from November 2012 to September 2018. The primary endpoint of this study was the maintaining time of the first and second courses of FMT. Relapse was defined as partial Mayo score ≥2 after achieving clinical remission and an increase of partial Mayo score ≥1 after achieving clinical response. The stool samples were analyzed by 16S rRNA gene sequencing. RESULTS: The median maintaining time of the efficacy was 120 days (IQR, 45–180) and 182.5 days (IQR, 105–311.25) from the first course and second course of FMT, respectively. No FMT-related serious adverse events were observed. The differences of the relative abundance in Eggerthella, Lactobacillus, and Ruminococcus between pre-FMT and 5 days post-FMT were remarkably correlated with the long-term clinical remission (P < 0.05). DISCUSSION: This study demonstrated that patients with UC should undergo the second course of FMT within 4 months after the first course of FMT for maintaining the long-term clinical benefits. The short-term alterations of microbiota after FMT may be conducive to predicting the long-term efficacy of FMT in UC (see Visual Abstract, Supplementary Digital Content, http://links.lww.com/CTG/A363).
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23
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Motta JP, Wallace JL, Buret AG, Deraison C, Vergnolle N. Gastrointestinal biofilms in health and disease. Nat Rev Gastroenterol Hepatol 2021; 18:314-334. [PMID: 33510461 DOI: 10.1038/s41575-020-00397-y] [Citation(s) in RCA: 122] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/25/2020] [Indexed: 01/30/2023]
Abstract
Microorganisms colonize various ecological niches in the human habitat, as they do in nature. Predominant forms of multicellular communities called biofilms colonize human tissue surfaces. The gastrointestinal tract is home to a profusion of microorganisms with intertwined, but not identical, lifestyles: as isolated planktonic cells, as biofilms and in biofilm-dispersed form. It is therefore of major importance in understanding homeostatic and altered host-microorganism interactions to consider not only the planktonic lifestyle, but also biofilms and biofilm-dispersed forms. In this Review, we discuss the natural organization of microorganisms at gastrointestinal surfaces, stratification of microbiota taxonomy, biogeographical localization and trans-kingdom interactions occurring within the biofilm habitat. We also discuss existing models used to study biofilms. We assess the contribution of the host-mucosa biofilm relationship to gut homeostasis and to diseases. In addition, we describe how host factors can shape the organization, structure and composition of mucosal biofilms, and how biofilms themselves are implicated in a variety of homeostatic and pathological processes in the gut. Future studies characterizing biofilm nature, physical properties, composition and intrinsic communication could shed new light on gut physiology and lead to potential novel therapeutic options for gastrointestinal diseases.
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Affiliation(s)
- Jean-Paul Motta
- Institute of Digestive Health Research, IRSD, INSERM U1220, Toulouse, France.
| | - John L Wallace
- Department of Physiology & Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Antibe Therapeutics Inc., Toronto, ON, Canada
| | - André G Buret
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Céline Deraison
- Institute of Digestive Health Research, IRSD, INSERM U1220, Toulouse, France
| | - Nathalie Vergnolle
- Institute of Digestive Health Research, IRSD, INSERM U1220, Toulouse, France. .,Department of Physiology & Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
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24
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Stępień-Pyśniak D, Hauschild T, Dec M, Marek A, Urban-Chmiel R, Kosikowska U. Phenotypic and genotypic characterization of Enterococcus spp. from yolk sac infections in broiler chicks with a focus on virulence factors. Poult Sci 2021; 100:100985. [PMID: 33647720 PMCID: PMC7933482 DOI: 10.1016/j.psj.2021.01.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/19/2020] [Accepted: 01/01/2021] [Indexed: 11/29/2022] Open
Abstract
Bacterial infections of yolk sacs contribute to increased mortality of chicks, chronic infections during their rearing, or increased selection in the flock, which in turn leads to high economic losses in poultry production worldwide. The aim of this study was a phenotypic and genotypic characterization of enterococci isolated from yolk sac infections (YSI) of broiler chickens from Poland and the Netherlands. Biochemical, matrix-assisted laser desorption/ionization (MALDI)–time-of-flight (TOF) MS, and rpoA gene sequencing identification was performed. Moreover, phenotypic and genotypic characterization of virulence factors and analysis of the clonal relationship of isolates by MALDI-TOF MS and enterobacterial repetitive intergenic consensus—polymerase chain reaction (ERIC-PCR) were performed. The biochemical test identified 70 isolates as Enterococcus faecalis and 6 as Enterococcus mundtii. The results of MALDI-TOF MS were 100% concordant with those obtained by rpoA gene sequencing, and all 76 isolates were identified as E. faecalis. Differences were noted in the β-glucuronidase, β-glucosidase, α-galactosidase, phosphatase, melibiose, lactose, and raffinose tests that is going about the results of biochemical identification. None of the isolates were beta-hemolytic on blood agar in aerobic conditions, but all but one were gelatinase positive. Among biofilm-forming isolates (30/76; 39.5%), as many as 66.7% (20/30) were Polish E. faecalis strains. Most of the isolates carried virulence genes, that is gelE, ace, asa1, efaAfs, fsrA, fsrB, fsrC, cob, cpd, and ccf, but none had the hyl gene. Some isolates harbored cyl operon genes. One Polish strain (ST16) had all of the tested cyl genes and the esp gene, considered clinically important, and showed the highest biofilm-forming ability. Nearly 50% of the isolates showed close genetic relatedness in ERIC typing. In contrast with MALDI-TOF MS cluster analysis, ERIC-PCR results did not show a relationship with the origin of the strains. Using MALDI-TOF MS, 7 peaks were found in Polish and Dutch isolates, which may type them as species-specific biomarkers in E. faecalis from YSI.
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Affiliation(s)
- Dagmara Stępień-Pyśniak
- Department of Veterinary Prevention and Avian Diseases, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, 20-612 Lublin, Poland.
| | - Tomasz Hauschild
- Department of Microbiology and Biotechnology, Faculty of Biology, University of Bialystok, 15-245 Białystok, Poland
| | - Marta Dec
- Department of Veterinary Prevention and Avian Diseases, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, 20-612 Lublin, Poland
| | - Agnieszka Marek
- Department of Veterinary Prevention and Avian Diseases, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, 20-612 Lublin, Poland
| | - Renata Urban-Chmiel
- Department of Veterinary Prevention and Avian Diseases, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, 20-612 Lublin, Poland
| | - Urszula Kosikowska
- Department of Pharmaceutical Microbiology, Medical University in Lublin, 20-093 Lublin, Poland
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25
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Wang Y, Xiong Y, Wang Z, Zheng J, Xu G, Deng Q, Wen Z, Yu Z. Comparison of solithromycin with erythromycin in Enterococcus faecalis and Enterococcus faecium from China: antibacterial activity, clonality, resistance mechanism, and inhibition of biofilm formation. J Antibiot (Tokyo) 2020; 74:143-151. [PMID: 33077828 DOI: 10.1038/s41429-020-00374-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/16/2020] [Accepted: 08/17/2020] [Indexed: 11/09/2022]
Abstract
Solithromycin (SOL), a fourth-generation macrolide and ketolide, has been reported to have robust antibacterial activity against a wide spectrum of Gram-positive bacteria. However, the impact of SOL on planktonic growth and biofilm formation of clinical enterococcus isolates remains unclear. In this study, 276 Enterococcus faecalis isolates and 122 Enterococcus faecium were retrospectively collected from a tertiary hospital from China. SOL against clinical isolates of enterococci from China were evaluated the antimicrobial activity in comparison with erythromycin, and explore its relationship with the clonality, virulence genes and resistance mechanism of these isolates. Our data showed that the MICs of SOL against clinical E. faecalis and E. faecium isolates from China were ≤4 and ≤8 mg l-1, respectively. ST16 and ST179 were regarded as the risk factor to SOL resistance in E. faecalis. SOL could inhibit but not eradicate the biofilm formation of E. faecalis. The bactericidal effects of SOL against E. faecalis and E. faecium were demonstrated to be similar to linezolid and vancomycin using time-kill assays. In conclusion, SOL showed significantly enhanced antibacterial activity against clinical isolates of E. faecalis and E. faecium from China in comparison to erythromycin. Furthermore, SOL could inhibit the biofilm formation of E. faecalis and have the similar bactericidal ability as linezolid and vancomycin against both E. faecalis and E. faecium.
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Affiliation(s)
- Yu Wang
- Department of Infectious Diseases and the Key Lab of Endogenous Infection, The Sixth Affiliated Hospital of Shenzhen University Health Science Center, No 89, Taoyuan Road, Nanshan District, 518052, Shenzhen, China
| | - Yanpeng Xiong
- Department of Infectious Diseases and the Key Lab of Endogenous Infection, The Sixth Affiliated Hospital of Shenzhen University Health Science Center, No 89, Taoyuan Road, Nanshan District, 518052, Shenzhen, China
| | - Zhanwen Wang
- Department of Infectious Diseases and the Key Lab of Endogenous Infection, The Sixth Affiliated Hospital of Shenzhen University Health Science Center, No 89, Taoyuan Road, Nanshan District, 518052, Shenzhen, China
| | - Jinxin Zheng
- Department of Infectious Diseases and the Key Lab of Endogenous Infection, The Sixth Affiliated Hospital of Shenzhen University Health Science Center, No 89, Taoyuan Road, Nanshan District, 518052, Shenzhen, China
| | - Guangjian Xu
- Department of Infectious Diseases and the Key Lab of Endogenous Infection, The Sixth Affiliated Hospital of Shenzhen University Health Science Center, No 89, Taoyuan Road, Nanshan District, 518052, Shenzhen, China
| | - Qiwen Deng
- Department of Infectious Diseases and the Key Lab of Endogenous Infection, The Sixth Affiliated Hospital of Shenzhen University Health Science Center, No 89, Taoyuan Road, Nanshan District, 518052, Shenzhen, China
| | - Zewen Wen
- Department of Infectious Diseases and the Key Lab of Endogenous Infection, The Sixth Affiliated Hospital of Shenzhen University Health Science Center, No 89, Taoyuan Road, Nanshan District, 518052, Shenzhen, China.
| | - Zhijian Yu
- Department of Infectious Diseases and the Key Lab of Endogenous Infection, The Sixth Affiliated Hospital of Shenzhen University Health Science Center, No 89, Taoyuan Road, Nanshan District, 518052, Shenzhen, China.
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Núñez-Sánchez MA, Colom J, Walsh L, Buttimer C, Bolocan AS, Pang R, Gahan CGM, Hill C. Characterizing Phage-Host Interactions in a Simplified Human Intestinal Barrier Model. Microorganisms 2020; 8:E1374. [PMID: 32906839 PMCID: PMC7563437 DOI: 10.3390/microorganisms8091374] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 09/03/2020] [Accepted: 09/05/2020] [Indexed: 12/24/2022] Open
Abstract
An intestinal epithelium model able to produce mucus was developed to provide an environment suitable for testing the therapeutic activity of gut bacteriophages. We show that Enterococcus faecalis adheres more effectively in the presence of mucus, can invade the intestinal epithelia and is able to translocate after damaging tight junctions. Furthermore, Enterococcus phage vB_EfaM_A2 (a member of Herelleviridae that possesses virion associated immunoglobin domains) was found to translocate through the epithelium in the presence and absence of its host bacteria. Phage A2 protected eukaryotic cells by reducing mortality and maintaining the structure of the cell layer structure. We suggest the mammalian cell model utilized within this study as an adaptable in vitro model that can be employed to enable a better understanding of phage-bacteria interactions and the protective impact of phage therapy relating to the intestinal epithelium.
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Affiliation(s)
- María A. Núñez-Sánchez
- APC Microbiome Ireland, Bioscience institute, University College Cork, T12 YT20 Cork, Ireland; (M.A.N.-S.); (J.C.); (L.W.); (C.B.); (A.S.B.); (R.P.); (C.G.M.G.)
| | - Joan Colom
- APC Microbiome Ireland, Bioscience institute, University College Cork, T12 YT20 Cork, Ireland; (M.A.N.-S.); (J.C.); (L.W.); (C.B.); (A.S.B.); (R.P.); (C.G.M.G.)
| | - Lauren Walsh
- APC Microbiome Ireland, Bioscience institute, University College Cork, T12 YT20 Cork, Ireland; (M.A.N.-S.); (J.C.); (L.W.); (C.B.); (A.S.B.); (R.P.); (C.G.M.G.)
| | - Colin Buttimer
- APC Microbiome Ireland, Bioscience institute, University College Cork, T12 YT20 Cork, Ireland; (M.A.N.-S.); (J.C.); (L.W.); (C.B.); (A.S.B.); (R.P.); (C.G.M.G.)
| | - Andrei Sorin Bolocan
- APC Microbiome Ireland, Bioscience institute, University College Cork, T12 YT20 Cork, Ireland; (M.A.N.-S.); (J.C.); (L.W.); (C.B.); (A.S.B.); (R.P.); (C.G.M.G.)
| | - Rory Pang
- APC Microbiome Ireland, Bioscience institute, University College Cork, T12 YT20 Cork, Ireland; (M.A.N.-S.); (J.C.); (L.W.); (C.B.); (A.S.B.); (R.P.); (C.G.M.G.)
| | - Cormac G. M. Gahan
- APC Microbiome Ireland, Bioscience institute, University College Cork, T12 YT20 Cork, Ireland; (M.A.N.-S.); (J.C.); (L.W.); (C.B.); (A.S.B.); (R.P.); (C.G.M.G.)
- School of Microbiology, University College Cork, T12 YN60 Cork, Ireland
- School of Pharmacy, University College Cork, T12 YN60 Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, Bioscience institute, University College Cork, T12 YT20 Cork, Ireland; (M.A.N.-S.); (J.C.); (L.W.); (C.B.); (A.S.B.); (R.P.); (C.G.M.G.)
- School of Microbiology, University College Cork, T12 YN60 Cork, Ireland
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27
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Elias-Oliveira J, Leite JA, Pereira ÍS, Guimarães JB, Manso GMDC, Silva JS, Tostes RC, Carlos D. NLR and Intestinal Dysbiosis-Associated Inflammatory Illness: Drivers or Dampers? Front Immunol 2020; 11:1810. [PMID: 32903730 PMCID: PMC7438795 DOI: 10.3389/fimmu.2020.01810] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 07/07/2020] [Indexed: 12/12/2022] Open
Abstract
The intestinal microbiome maintains a close relationship with the host immunity. This connection fosters a health state by direct and indirect mechanisms. Direct influences occur mainly through the production of short-chain fatty acids (SCFAs), gastrointestinal hormones and precursors of bioactive molecules. Indirect mechanisms comprise the crosstalk between bacterial products and the host's innate immune system. Conversely, intestinal dysbiosis is a condition found in a large number of chronic intestinal inflammatory diseases, such as ulcerative colitis and Crohn's disease, as well as in diseases associated with low-grade inflammation, such as obesity, type 1 and 2 diabetes mellitus and cardiovascular diseases. NOD-Like receptors (NLRs) are cytoplasmic receptors expressed by adaptive and innate immune cells that form a multiprotein complex, termed the inflammasome, responsible for the release of mature interleukin (IL)-1β and IL-18. NLRs are also involved in the recognition of bacterial components and production of antimicrobial molecules that shape the gut microbiota and maintain the intestinal homeostasis. Recent novel findings show that NLRs may act as positive or negative regulators of inflammation by modulating NF-κB activation. This mini-review presents current and updated evidence on the interplay between NLRs and gut microbiota and their dual role, contributing to progression or conferring protection, in diabetes and other inflammatory diseases.
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Affiliation(s)
- Jefferson Elias-Oliveira
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Jefferson Antônio Leite
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Ítalo Sousa Pereira
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Jhefferson Barbosa Guimarães
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Gabriel Martins da Costa Manso
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - João Santana Silva
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Rita Cássia Tostes
- Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Daniela Carlos
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
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28
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Liu F, Sun Z, Wang F, Liu Y, Zhu Y, Du L, Wang D, Xu W. Inhibition of biofilm formation and exopolysaccharide synthesis of Enterococcus faecalis by phenyllactic acid. Food Microbiol 2020; 86:103344. [DOI: 10.1016/j.fm.2019.103344] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 07/23/2019] [Accepted: 09/27/2019] [Indexed: 12/15/2022]
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29
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Mirzaei R, Mirzaei H, Alikhani MY, Sholeh M, Arabestani MR, Saidijam M, Karampoor S, Ahmadyousefi Y, Moghadam MS, Irajian GR, Hasanvand H, Yousefimashouf R. Bacterial biofilm in colorectal cancer: What is the real mechanism of action? Microb Pathog 2020; 142:104052. [PMID: 32045645 DOI: 10.1016/j.micpath.2020.104052] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/07/2020] [Accepted: 02/07/2020] [Indexed: 02/07/2023]
Abstract
Human colorectal cancer is the third most common cancer around the world. Colorectal cancer has various risk factors, but current works have bolded a significant activity for the microbiota of the human colon in the development of this disease. Bacterial biofilm has been mediated to non-malignant pathologies like inflammatory bowel disease but has not been fully documented in the setting of colorectal cancer. The investigation has currently found that bacterial biofilm is mediated to colon cancer in the human and linked to the location of human cancer, with almost all right-sided adenomas of colon cancers possessing bacterial biofilm, whilst left-sided cancer is rarely biofilm positive. The profound comprehension of the changes in colorectal cancer can provide interesting novel concepts for anticancer treatments. In this review, we will summarize and examine the new knowledge about the links between colorectal cancer and bacterial biofilm.
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Affiliation(s)
- Rasoul Mirzaei
- Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | - Mohammad Yousef Alikhani
- Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mohammad Sholeh
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Arabestani
- Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Massoud Saidijam
- Department of Molecular Medicine and Genetics, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran; Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Hamadan University of Medical Sciences, Hamadan, Iran; Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Sajad Karampoor
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Yaghoub Ahmadyousefi
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Hamadan University of Medical Sciences, Hamadan, Iran; Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mohammad Shokri Moghadam
- Department of Microbiology, School of Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Gholam Reza Irajian
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hamze Hasanvand
- School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Rasoul Yousefimashouf
- Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran.
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30
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Dos Santos BA, de Oliveira JDS, Parmanhani-da-Silva BM, Ribeiro RL, Teixeira LM, Neves FPG. CRISPR elements and their association with antimicrobial resistance and virulence genes among vancomycin-resistant and vancomycin-susceptible enterococci recovered from human and food sources. INFECTION GENETICS AND EVOLUTION 2020; 80:104183. [PMID: 31923727 DOI: 10.1016/j.meegid.2020.104183] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 12/23/2019] [Accepted: 01/06/2020] [Indexed: 11/26/2022]
Abstract
We aimed to investigate the occurrence of CRISPR elements in the genomes of vancomycin-resistant (VRE) and vancomycin-susceptible (VSE) enterococci and their association with the presence of antimicrobial resistance and virulence genes. We analyzed 180 isolates, including 91 VRE and 89 VSE. Isolates were identified by PCR or MALDI-TOF. Antimicrobial susceptibility and MICs for vancomycin were determined by the disk-diffusion method and E-test®, respectively. The presence of resistance and virulence genes, as well as CRISPR elements, was investigated by PCR. We identified 95 (53%) E. faecalis, 78 (43%) E. faecium, five (2.8%) E. gallinarum, and one (0.6% each) E. casseliflavus and E. durans. The highest and the lowest non-susceptibility frequencies were observed for erythromycin (n = 152; 84.4%) and fosfomycin (n = 5; 2.8%), respectively. Most erythromycin-resistant isolates had the erm(B) gene (106/152; 69.7%). Of 118 (65.6%) isolates with high-level resistance to aminoglycoside, 69 (58.5%) had at least one aminoglycoside resistance gene, mostly ant(6)-Ia and aac(6')-Ie + aph(2″)-Ia. We found at least one virulence gene among 135 (75%) isolates, mostly gelE (79/180; 43.9%). Ninety-two (51.1%) isolates had at least one CRISPR element, especially CRISPR3 (62/92; 67.4%). CRISPR elements were more common among E. faecalis, in which we observed a relationship between the absence of CRISPR and the presence of the vanA resistance gene, and the hyl and esp virulence genes. Among VRE. faecium, a relationship was found between the absence of CRISPR and the hyl gene. In conclusion, we found evident associations between the lack of CRISPR elements with species, multidrug resistance, and major resistance- and virulence-associated genes.
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Affiliation(s)
- Barbara Araújo Dos Santos
- Instituto Biomédico, Universidade Federal Fluminense. Rua Professor Hernani Melo, 101. São Domingos, Niterói, RJ 24210-130, Brazil
| | - Jessica da Silva de Oliveira
- Instituto Biomédico, Universidade Federal Fluminense. Rua Professor Hernani Melo, 101. São Domingos, Niterói, RJ 24210-130, Brazil
| | | | - Rachel Leite Ribeiro
- Hospital Universitário Antônio Pedro, Universidade Federal Fluminense, Av. Marquês do Paraná, 303. Centro, Niterói, RJ 24033-900, Brazil.
| | - Lúcia Martins Teixeira
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373. Cidade Universitária, Rio de Janeiro, RJ 21941-902, Brazil.
| | - Felipe Piedade Gonçalves Neves
- Instituto Biomédico, Universidade Federal Fluminense. Rua Professor Hernani Melo, 101. São Domingos, Niterói, RJ 24210-130, Brazil.
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31
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Weis S, Schwiertz A, Unger MM, Becker A, Faßbender K, Ratering S, Kohl M, Schnell S, Schäfer KH, Egert M. Effect of Parkinson's disease and related medications on the composition of the fecal bacterial microbiota. NPJ Parkinsons Dis 2019; 5:28. [PMID: 31815177 PMCID: PMC6884491 DOI: 10.1038/s41531-019-0100-x] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 10/29/2019] [Indexed: 02/07/2023] Open
Abstract
Parkinson's disease (PD) is one of the most common neurodegenerative disorders. PD patients suffer from gastrointestinal dysfunctions and alterations of the autonomous nervous system, especially its part in the gut wall, i.e., the enteric nervous system (ENS). Such alterations and functional gastrointestinal deficits often occur years before the classical clinical symptoms of PD appear. Until now, only little is known about PD-associated changes in gut microbiota composition and their potential implication in PD development. In order to increase knowledge in this field, fecal samples of 34 PD patients and 25 healthy, age-matched control persons were investigated. Here, the V4 and V5 hypervariable region of bacterial 16S rRNA genes was PCR-amplified and sequenced using an Ion Torrent PGM platform. Within the PD group, we observed a relative decrease in bacterial taxa which are linked to health-promoting, anti-inflammatory, neuroprotective or other beneficial effects on the epithelial barrier, such as Faecalibacterium and Fusicatenibacter. Both taxa were lowered in PD patients with elevated levels of the fecal inflammation marker calprotectin. In addition, we observed an increase in shares of the Clostridiales family XI and their affiliated members in these samples. Finally, we found that the relative abundances of the bacterial genera Peptoniphilus, Finegoldia, Faecalibacterium Fusicatenibacter, Anaerococcus, Bifidobacterium, Enterococcus, and Ruminococcus were significantly influenced by medication with L-dopa and entacapone, respectively. Our data confirm previously reported effects of COMT inhibitors on the fecal microbiota of PD patients and suggest a possible effect of L-dopa medication on the relative abundance of several bacterial genera.
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Affiliation(s)
- Severin Weis
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Villingen-Schwenningen, Germany
| | | | - Marcus M. Unger
- Department of Neurology, Saarland University, Homburg, Germany
| | - Anouck Becker
- Department of Neurology, Saarland University, Homburg, Germany
| | - Klaus Faßbender
- Department of Neurology, Saarland University, Homburg, Germany
| | - Stefan Ratering
- Institute of Applied Microbiology, Justus-Liebig-University, Giessen, Germany
| | - Matthias Kohl
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Group for Statistics in Biology and Medicine, Furtwangen University, Villingen-Schwenningen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Justus-Liebig-University, Giessen, Germany
| | - Karl-Herbert Schäfer
- Department of Biotechnology, ENS Working Group, University of Applied Sciences Kaiserslautern, Zweibrücken, Germany
| | - Markus Egert
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Villingen-Schwenningen, Germany
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Chandra N, Srivastava A, Kumar S. Bacterial biofilms in human gastrointestinal tract: An intricate balance between health and inflammatory bowel diseases. World J Pharmacol 2019; 8:26-40. [DOI: 10.5497/wjp.v8.i3.26] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 07/05/2019] [Accepted: 07/16/2019] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel disease (IBD) has been a worldwide health problem. It is characterized by severe intestinal inflammation due to immune responses against the gut microbes in genetically susceptible individuals. The understanding of gut microbiota for its composition and complex interaction in normal and diseased conditions has been assisted by the use of molecular, metagenomics and meta transcriptomics studies. The alteration of intestinal microbiota is the key determinant in the degree of inflammation caused and the prolonged course of disease. The relationship between luminal gut bacteria and innate immunity is also of prime significance. Such developments have further led to the search of specific (including bacteria and fungi) as a causative agent of IBD. Although detailed research has been done for the role of gut microbiota in IBD, molecular mechanisms and related gene expression are still not well understood in this disease, which hampers the generation of effective therapeutic agents for IBD. This paper assessed various factors contributing to IBD, genetic dysbiosis and pathogenic influence in the gut microbiota, interactions such as microbiome-host immune system interaction and microbe-microbe interactions involved in IBD, currently available IBD therapies, followed by a detailed review on bacterial infections that might be involved in IBD, globally and specifically in India.
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Affiliation(s)
- Niharika Chandra
- Faculty of Biotechnology, Institute of Bio-Sciences and Technology, Shri Ramswaroop Memorial University, Uttar Pradesh 225003, India
| | - Ankita Srivastava
- Faculty of Bio-Sciences, Institute of Bio-Sciences and Technology, Shri Ramswaroop Memorial University, Uttar Pradesh 225003, India
| | - Sunil Kumar
- Faculty of Bio-Sciences, Institute of Bio-Sciences and Technology, Shri Ramswaroop Memorial University, Uttar Pradesh 225003, India
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Lengfelder I, Sava IG, Hansen JJ, Kleigrewe K, Herzog J, Neuhaus K, Hofmann T, Sartor RB, Haller D. Complex Bacterial Consortia Reprogram the Colitogenic Activity of Enterococcus faecalis in a Gnotobiotic Mouse Model of Chronic, Immune-Mediated Colitis. Front Immunol 2019; 10:1420. [PMID: 31281321 PMCID: PMC6596359 DOI: 10.3389/fimmu.2019.01420] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 06/05/2019] [Indexed: 12/17/2022] Open
Abstract
Inflammatory bowel diseases (IBD) are associated with compositional and functional changes of the intestinal microbiota, but specific contributions of individual bacteria to chronic intestinal inflammation remain unclear. Enterococcus faecalis is a resident member of the human intestinal core microbiota that has been linked to the pathogenesis of IBD and induces chronic colitis in susceptible monoassociated IL-10-deficient (IL-10−/−) mice. In this study, we characterized the colitogenic activity of E. faecalis as part of a simplified human microbial consortium based on seven enteric bacterial strains (SIHUMI). RNA sequencing analysis of E. faecalis isolated from monoassociated wild type and IL-10−/− mice identified 408 genes including 14 genes of the ethanolamine utilization (eut) locus that were significantly up-regulated in response to inflammation. Despite considerable up-regulation of eut genes, deletion of ethanolamine utilization (ΔeutVW) had no impact on E. faecalis colitogenic activity in monoassociated IL-10−/− mice. However, replacement of the E. faecalis wild type bacteria by a ΔeutVW mutant in SIHUMI-colonized IL-10−/− mice resulted in exacerbated colitis, suggesting protective functions of E. faecalis ethanolamine utilization in complex bacterial communities. To better understand E. faecalis gene response in the presence of other microbes, we purified wild type E. faecalis cells from the colon content of SIHUMI-colonized wild type and IL-10−/− mice using immuno-magnetic separation and performed RNA sequencing. Transcriptional profiling revealed that the bacterial environment reprograms E. faecalis gene expression in response to inflammation, with the majority of differentially expressed genes not being shared between monocolonized and SIHUMI conditions. While in E. faecalis monoassociation a general bacterial stress response could be observed, expression of E. faecalis genes in SIHUMI-colonized mice was characterized by up-regulation of genes involved in growth and replication. Interestingly, in mice colonized with SIHUMI lacking E. faecalis enhanced inflammation was observed in comparison to SIHUMI-colonized mice, supporting the hypothesis that E. faecalis ethanolamine metabolism protects against colitis in complex consortia. In conclusion, this study demonstrates that complex bacterial consortia interactions reprogram the gene expression profile and colitogenic activity of the opportunistic pathogen E. faecalis toward a protective function.
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Affiliation(s)
- Isabella Lengfelder
- Chair of Nutrition and Immunology, Technische Universität München, Freising, Germany
| | - Irina G Sava
- Chair of Nutrition and Immunology, Technische Universität München, Freising, Germany
| | - Jonathan J Hansen
- Division of Gastroenterology and Hepatology, University of North Carolina, Chapel Hill, NC, United States
| | - Karin Kleigrewe
- Bavarian Center for Biomolecular Mass Spectrometry, Technische Universität München, Freising, Germany
| | - Jeremy Herzog
- Division of Gastroenterology and Hepatology, University of North Carolina, Chapel Hill, NC, United States
| | - Klaus Neuhaus
- ZIEL - Institute for Food & Health, Technische Universität München, Freising, Germany.,ZIEL Core Facility Microbiome, Technische Universität München, Freising, Germany
| | - Thomas Hofmann
- Bavarian Center for Biomolecular Mass Spectrometry, Technische Universität München, Freising, Germany.,ZIEL - Institute for Food & Health, Technische Universität München, Freising, Germany
| | - R Balfour Sartor
- Division of Gastroenterology and Hepatology, University of North Carolina, Chapel Hill, NC, United States
| | - Dirk Haller
- Chair of Nutrition and Immunology, Technische Universität München, Freising, Germany.,ZIEL - Institute for Food & Health, Technische Universität München, Freising, Germany
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34
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Rehman MA, Yin X, Zaheer R, Goji N, Amoako KK, McAllister T, Pritchard J, Topp E, Diarra MS. Genotypes and Phenotypes of Enterococci Isolated From Broiler Chickens. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2018. [DOI: 10.3389/fsufs.2018.00083] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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35
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Yu LCH. Microbiota dysbiosis and barrier dysfunction in inflammatory bowel disease and colorectal cancers: exploring a common ground hypothesis. J Biomed Sci 2018; 25:79. [PMID: 30413188 PMCID: PMC6234774 DOI: 10.1186/s12929-018-0483-8] [Citation(s) in RCA: 237] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 10/29/2018] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a multifactorial disease which arises as a result of the interaction of genetic, environmental, barrier and microbial factors leading to chronic inflammation in the intestine. Patients with IBD had a higher risk of developing colorectal carcinoma (CRC), of which the subset was classified as colitis-associated cancers. Genetic polymorphism of innate immune receptors had long been considered a major risk factor for IBD, and the mutations were also recently observed in CRC. Altered microbial composition (termed microbiota dybiosis) and dysfunctional gut barrier manifested by epithelial hyperpermeability and high amount of mucosa-associated bacteria were observed in IBD and CRC patients. The findings suggested that aberrant immune responses to penetrating commensal microbes may play key roles in fueling disease progression. Accumulative evidence demonstrated that mucosa-associated bacteria harbored colitogenic and protumoral properties in experimental models, supporting an active role of bacteria as pathobionts (commensal-derived opportunistic pathogens). Nevertheless, the host factors involved in bacterial dysbiosis and conversion mechanisms from lumen-dwelling commensals to mucosal pathobionts remain unclear. Based on the observation of gut leakiness in patients and the evidence of epithelial hyperpermeability prior to the onset of mucosal histopathology in colitic animals, it was postulated that the epithelial barrier dysfunction associated with mucosal enrichment of specific bacterial strains may predispose the shift to disease-associated microbiota. The speculation of leaky gut as an initiating factor for microbiota dysbiosis that eventually led to pathological consequences was proposed as the "common ground hypothesis", which will be highlighted in this review. Overall, the understanding of the core interplay between gut microbiota and epithelial barriers at early subclinical phases will shed light to novel therapeutic strategies to manage chronic inflammatory disorders and colitis-associated cancers.
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Affiliation(s)
- Linda Chia-Hui Yu
- Graduate Institute of Physiology, National Taiwan University College of Medicine, Suite 1020, #1 Jen-Ai Rd. Sec. 1, Taipei, 100, Taiwan, Republic of China.
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36
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Wang F, Wu H, Jin P, Sun Z, Liu F, Du L, Wang D, Xu W. Antimicrobial Activity of Phenyllactic Acid AgainstEnterococcus faecalisand Its Effect on Cell Membrane. Foodborne Pathog Dis 2018; 15:645-652. [DOI: 10.1089/fpd.2018.2470] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Fengting Wang
- Institute of Agro-Product Processing, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Haihong Wu
- Institute of Agro-Product Processing, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Panpan Jin
- Institute of Agro-Product Processing, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Zhilan Sun
- Institute of Agro-Product Processing, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Fang Liu
- Institute of Agro-Product Processing, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Lihui Du
- Key Laboratory of Grains and Oils Quality Control and Processing, College of Food Science and Engineering, Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing University of Finance and Economics, Nanjing, China
| | - Daoying Wang
- Institute of Agro-Product Processing, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Weimin Xu
- Institute of Agro-Product Processing, Jiangsu Academy of Agricultural Sciences, Nanjing, China
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37
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Aristimuño Ficoseco C, Mansilla FI, Maldonado NC, Miranda H, Fátima Nader-Macias ME, Vignolo GM. Safety and Growth Optimization of Lactic Acid Bacteria Isolated From Feedlot Cattle for Probiotic Formula Design. Front Microbiol 2018; 9:2220. [PMID: 30323790 PMCID: PMC6172481 DOI: 10.3389/fmicb.2018.02220] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 08/30/2018] [Indexed: 01/08/2023] Open
Abstract
In order to eliminate the widespread use of antibiotics in livestock production, the research for alternatives has increased lately. This study examined the safety of 40 lactic acid bacteria (LAB) isolated from bovine feedlot environment and previously selected as potential probiotics. A high sensitivity prevalence to ampicillin (AMP, 100%), gentamicin (GEN, 96.3%), kanamycin (KAN, 96.3%), clindamycin (CLI, 85.2%), chloramphenicol (CHL, 92.6%) and streptomycin (STR, 88.9%) while moderate and high resistance against erythromycin (ERY, 48%) and tetracycline (TET, 79%) respectively, were determined. Feedlot enterococci and pediococci displayed high resistance to CLI, ERY, GEN and TET (73, 100, 54.5, and 73%, respectively). Among fifteen resistance genes investigated, seven were identified in lactobacilli; their presence not always was correlated with phenotypic resistance. STR resistance genes, aadA and ant(6) were observed in 7.4 and 3.7% of isolates, respectively; genes responsible for aminoglycosides resistance, such as bla (7.4%), and aph(3”)-III (3.7%) were also recognized. In addition, resistance cat and tetS genes (3.7 and 7.4%, respectively) were harbored by feedlot lactobacilli strains. The presence of ermB gene in 22.3% of isolates, including two of the six strains phenotypically resistant to ERY, exhibited the highest prevalence among the assessed antibiotics. None of the feedlot lactobacilli harbored virulence factors genes, while positive PCR amplification for ace, agg, fsrA, and atpA genes was found for enterococci. With the objective of producing large cell biomass for probiotic delivery, growth media without peptone but containing glucose and skim milk powder (Mgl and Mlac) were selected as optimal. Lactobacillus acidophilus CRL2074, L. amylovorus CRL2115, L. mucosae CRL2069, and L. rhamnosus CRL2084 were strains selected as free of antibiotic resistance and virulence determinants, able to reach high cell numbers in non-expensive culture media and being compatible among them.
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Affiliation(s)
- Cecilia Aristimuño Ficoseco
- Centro de Referencia para Lactobacilos, Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucuman, Argentina
| | - Flavia I Mansilla
- Centro de Referencia para Lactobacilos, Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucuman, Argentina
| | - Natalia C Maldonado
- Centro de Referencia para Lactobacilos, Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucuman, Argentina
| | - Hortencia Miranda
- Centro de Referencia para Lactobacilos, Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucuman, Argentina
| | - María E Fátima Nader-Macias
- Centro de Referencia para Lactobacilos, Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucuman, Argentina
| | - Graciela M Vignolo
- Centro de Referencia para Lactobacilos, Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucuman, Argentina
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38
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Filler Nodules: Inflammatory or Infectious? A Review of Biofilms and Their Implications on Clinical Practice. Dermatol Surg 2018; 44:53-60. [PMID: 28538034 DOI: 10.1097/dss.0000000000001202] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
BACKGROUND The numbers of minimally invasive cosmetic procedures performed in the United States have steadily increased each year. Concurrently, the rates of filler complications have also increased. Delayed filler reactions and granulomas have recently been attributed to biofilm infections. OBJECTIVE The biology and pathogenesis of biofilms, and their diagnosis, treatment, and prevention will be discussed. METHODS The relevant and recent literature on delayed filler reactions and biofilms was reviewed. RESULTS Increasing evidence implicates biofilm infections in the pathogenesis of delayed filler reactions. Therapeutic and preventative measures can be taken to minimize the occurrence of these potentially devastating consequences of dermal fillers. CONCLUSION Awareness of biofilm infections is key in the assessment of filler reactions in order to ensure timely and accurate diagnosis and treatment.
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Roche-Lima A, Carrasquillo-Carrión K, Gómez-Moreno R, Cruz JM, Velázquez-Morales DM, Rogozin IB, Baerga-Ortiz A. The Presence of Genotoxic and/or Pro-inflammatory Bacterial Genes in Gut Metagenomic Databases and Their Possible Link With Inflammatory Bowel Diseases. Front Genet 2018; 9:116. [PMID: 29692798 PMCID: PMC5902703 DOI: 10.3389/fgene.2018.00116] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 03/22/2018] [Indexed: 01/19/2023] Open
Abstract
Background: The human gut microbiota is a dynamic community of microorganisms that mediate important biochemical processes. Differences in the gut microbial composition have been associated with inflammatory bowel diseases (IBD) and other intestinal disorders. In this study, we quantified and compared the frequencies of eight genotoxic and/or pro-inflammatory bacterial genes found in metagenomic Whole Genome Sequences (mWGSs) of samples from individuals with IBD vs. a cohort of healthy human subjects. Methods: The eight selected gene sequences were clbN, clbB, cif, cnf-1, usp, tcpC from Escherichia coli, gelE from Enterococcus faecalis and murB from Akkermansia muciniphila. We also included the sequences for the conserved murB genes from E. coli and E. faecalis as markers for the presence of Enterobacteriaceae or Enterococci in the samples. The gene sequences were chosen based on their previously reported ability to disrupt normal cellular processes to either promote inflammation or to cause DNA damage in cultured cells or animal models, which could be linked to a role in IBD. The selected sequences were searched in three different mWGS datasets accessed through the Human Microbiome Project (HMP): a healthy cohort (N = 251), a Crohn's disease cohort (N = 60) and an ulcerative colitis cohort (N = 17). Results: Firstly, the sequences for the murB housekeeping genes from Enterobacteriaceae and Enterococci were more frequently found in the IBD cohorts (32% E. coli in IBD vs. 12% in healthy; 13% E. faecalis in IBD vs. 3% in healthy) than in the healthy cohort, confirming earlier reports of a higher presence of both of these taxa in IBD. For some of the sequences in our study, especially usp and gelE, their frequency was even more sharply increased in the IBD cohorts than in the healthy cohort, suggesting an association with IBD that is not easily explained by the increased presence of E. coli or E. faecalis in those samples. Conclusion: Our results suggest a significant association between the presence of some of these genotoxic or pro-inflammatory gene sequences and IBDs. In addition, these results illustrate the power and limitations of the HMP database in the detection of possible clinical correlations for individual bacterial genes.
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Affiliation(s)
- Abiel Roche-Lima
- Center for Collaborative Research in Health Disparities - RCMI Program, Medical Sciences Campus, University of Puerto Rico, San Juan, Puerto Rico
| | - Kelvin Carrasquillo-Carrión
- Center for Collaborative Research in Health Disparities - RCMI Program, Medical Sciences Campus, University of Puerto Rico, San Juan, Puerto Rico
| | - Ramón Gómez-Moreno
- Department of Biochemistry, Medical Sciences Campus, University of Puerto Rico, San Juan, Puerto Rico.,Molecular Sciences Research Center, University of Puerto Rico, San Juan, Puerto Rico
| | - Juan M Cruz
- Department of Biochemistry, Medical Sciences Campus, University of Puerto Rico, San Juan, Puerto Rico
| | - Dayanara M Velázquez-Morales
- Center for Collaborative Research in Health Disparities - RCMI Program, Medical Sciences Campus, University of Puerto Rico, San Juan, Puerto Rico
| | - Igor B Rogozin
- National Center for Biotechnology Information, U.S. National Library of Medicine, Bethesda, MD, United States
| | - Abel Baerga-Ortiz
- Department of Biochemistry, Medical Sciences Campus, University of Puerto Rico, San Juan, Puerto Rico.,Molecular Sciences Research Center, University of Puerto Rico, San Juan, Puerto Rico
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40
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Wang Y, Gao X, Ghozlane A, Hu H, Li X, Xiao Y, Li D, Yu G, Zhang T. Characteristics of Faecal Microbiota in Paediatric Crohn's Disease and Their Dynamic Changes During Infliximab Therapy. J Crohns Colitis 2018; 12:337-346. [PMID: 29194468 DOI: 10.1093/ecco-jcc/jjx153] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 11/27/2017] [Indexed: 12/12/2022]
Abstract
BACKGROUND Crohn's disease [CD] is known to be associated with gut microbial dysbiosis. Infliximab [IFX] is increasingly used to treat paediatric CD; however, it is not clear how the gut microbiota is modified during IFX treatment. The aim of this study was to characterise the faecal microbiota community composition in paediatric CD patients and to assess its dynamic changes during IFX therapy. METHODS A 16S rRNA sequencing approach was applied to determine the compositions of microbial communities in faecal samples. The composition and function of the faecal microbiota were compared between CD patients and healthy controls. RESULTS Characteristics of faecal microbiome composition in paediatric CD patients before IFX treatment were represented by a lower biodiversity, a gain in Enterococcus, and a significant loss in multiple short-chain fatty acid [SCFA]-producing bacteria, including Anaerostipes, Blautia, Coprococcus, Faecalibacterium, Lachnospira, Odoribacter, Roseburia, Ruminococcus, and Sutterella. Additionally, alterations were observed in metabolic functions of the gut microbial community in CD. IFX treatment increased the biodiversity of gut microbiota and shifted its composition as well as its functional capabilities in the paediatric CD patients toward a healthy status. However, multiple SCFA-producing taxa were not significantly expanded. The sustained response of paediatric CD patients to IFX was associated with abundance of SCFA-producing bacteria. CONCLUSIONS A lower biodiversity with alterations in the composition and function of faecal microbial community, characterising gut microbial dysbiosis, was observed in Chinese paediatric CD patients. IFX diminished the CD-associated gut microbial dysbiosis but was deficient in increasing certain SCFA-producing taxa.
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Affiliation(s)
- Yizhong Wang
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xuefeng Gao
- Shenzhen HRK Bio-tech Co., Shenzhen, Guangdong, China
| | - Amine Ghozlane
- Bioinformatics and Biostatistics Hub-Centre de Bioinformatique, Biostatistique et Biologie Intégrative, Institut Pasteur-Centre National de la Recherche Scientifique, Paris, France
| | - Hui Hu
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaolu Li
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yongmei Xiao
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Dan Li
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Guangjun Yu
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Ting Zhang
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
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Cieśla J, Stępień-Pyśniak D, Nawrocka A, Łukowska M, Hauschild T, Wernicki A, Bieganowski A. Surface properties of Enterococcus faecalis cells isolated from chicken hearts determine their low ability to form biofilms. BIOFOULING 2018; 34:149-161. [PMID: 29319345 DOI: 10.1080/08927014.2017.1416105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 12/05/2017] [Indexed: 06/07/2023]
Abstract
Enterococcus faecalis is one of the most significant bacterial pathogens associated with the first-week mortality of chickens. Here, the surface properties of bacterial cells and the selected virulence factors of E. faecalis strains isolated from the hearts of clinically healthy broiler chickens were studied. Investigations were carried out on live and autoclaved cells. E. faecalis (ATCC 29212) was used as a reference strain. The bacterial cells revealed different haemolytic activities. Their surface free energy was dominated by the hydrophobic component. The cell walls of the bird isolates showed slightly weaker acidic characteristics than those of E. faecalis (ATCC 29212). Moreover, the bacterial cells from the chicken hearts showed higher electrophoretic mobility and surface electrical charge than the reference strain, and consequently demonstrated a low ability to form biofilms.
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Affiliation(s)
- Jolanta Cieśla
- a Institute of Agrophysics , Polish Academy of Sciences , Lublin , Poland
| | | | - Agnieszka Nawrocka
- a Institute of Agrophysics , Polish Academy of Sciences , Lublin , Poland
| | | | - Tomasz Hauschild
- c Department of Microbiology, Institute of Biology , University of Bialystok , Bialystok , Poland
| | - Andrzej Wernicki
- b Faculty of Veterinary Medicine , University of Life Sciences , Lublin , Poland
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Kalenyak K, Isaiah A, Heilmann RM, Suchodolski JS, Burgener IA. Comparison of the intestinal mucosal microbiota in dogs diagnosed with idiopathic inflammatory bowel disease and dogs with food-responsive diarrhea before and after treatment. FEMS Microbiol Ecol 2017; 94:4705888. [DOI: 10.1093/femsec/fix173] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 12/01/2017] [Indexed: 12/19/2022] Open
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43
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Santos BA, Oliveira JS, Cardoso NT, Barbosa AV, Superti SV, Teixeira LM, Neves FP. Major globally disseminated clonal complexes of antimicrobial resistant enterococci associated with infections in cancer patients in Brazil. INFECTION GENETICS AND EVOLUTION 2017; 55:56-62. [DOI: 10.1016/j.meegid.2017.08.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 08/15/2017] [Accepted: 08/27/2017] [Indexed: 11/30/2022]
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44
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Ali L, Goraya MU, Arafat Y, Ajmal M, Chen JL, Yu D. Molecular Mechanism of Quorum-Sensing in Enterococcus faecalis: Its Role in Virulence and Therapeutic Approaches. Int J Mol Sci 2017; 18:ijms18050960. [PMID: 28467378 PMCID: PMC5454873 DOI: 10.3390/ijms18050960] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Accepted: 04/26/2017] [Indexed: 12/22/2022] Open
Abstract
Quorum-sensing systems control major virulence determinants in Enterococcusfaecalis, which causes nosocomial infections. The E. faecalis quorum-sensing systems include several virulence factors that are regulated by the cytolysin operon, which encodes the cytolysin toxin. In addition, the E. faecalis Fsr regulator system controls the expression of gelatinase, serine protease, and enterocin O16. The cytolysin and Fsr virulence factor systems are linked to enterococcal diseases that affect the health of humans and other host models. Therefore, there is substantial interest in understanding and targeting these regulatory pathways to develop novel therapies for enterococcal infection control. Quorum-sensing inhibitors could be potential therapeutic agents for attenuating the pathogenic effects of E. faecalis. Here, we discuss the regulation of cytolysin, the LuxS system, and the Fsr system, their role in E. faecalis-mediated infections, and possible therapeutic approaches to prevent E. faecalis infection.
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Affiliation(s)
- Liaqat Ali
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad 45550, Pakistan.
| | - Mohsan Ullah Goraya
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Yasir Arafat
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Muhammad Ajmal
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad 45550, Pakistan.
| | - Ji-Long Chen
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China.
| | - Daojin Yu
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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45
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Lim JS, Lim MY, Choi Y, Ko G. Modeling environmental risk factors of autism in mice induces IBD-related gut microbial dysbiosis and hyperserotonemia. Mol Brain 2017; 10:14. [PMID: 28427452 PMCID: PMC5399341 DOI: 10.1186/s13041-017-0292-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 04/04/2017] [Indexed: 02/07/2023] Open
Abstract
Autism spectrum disorder (ASD) is a range of neurodevelopmental conditions that are sharply increasing in prevalence worldwide. Intriguingly, ASD is often accompanied by an array of systemic aberrations including (1) increased serotonin, (2) various modes of gastrointestinal disorders, and (3) inflammatory bowel disease (IBD), albeit the underlying cause for such comorbidities remains uncertain. Also, accumulating number of studies report that the gut microbial composition is significantly altered in children with ASD or patients with IBD. Surprisingly, when we analyzed the gut microbiota of poly I:C and VPA-induced mouse models of ASD, we found a distinct pattern of microbial dysbiosis that highly recapitulated those reported in clinical cases of ASD and IBD. Moreover, we report that such microbial dysbiosis led to notable perturbations in microbial metabolic pathways that are known to negatively affect the host, especially with regards to the pathogenesis of ASD and IBD. Lastly, we found that serum level of serotonin is significantly increased in both poly I:C and VPA mice, and that it correlates with increases of a bacterial genus and a metabolic pathway that are implicated in stimulation of host serotonin production. Our results using animal model identify prenatal environmental risk factors of autism as possible causative agents of IBD-related gut microbial dysbiosis in ASD, and suggest a multifaceted role of gut microbiota in the systemic pathogenesis of ASD and hyperserotonemia.
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Affiliation(s)
- Joon Seo Lim
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea.,Institute of Health and Environment, Seoul National University, Seoul, Republic of Korea
| | - Mi Young Lim
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea.,Institute of Health and Environment, Seoul National University, Seoul, Republic of Korea.,Research Group of Gut Microbiome, Korea Food Research Institute, Seongnam, Gyeonggi-do, Republic of Korea
| | - Yongbin Choi
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - GwangPyo Ko
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea. .,Center for Human and Environmental Microbiome, Seoul National University, Seoul, Republic of Korea. .,N-Bio, Seoul National University, Seoul, Republic of Korea. .,KoBioLabs, Inc., 1-Gwanak-ro, Gwanak-gu, Bldg 220, Rm 630, Seoul, 151-746, Republic of Korea.
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46
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Bacterial Biofilms in Colorectal Cancer Initiation and Progression. Trends Mol Med 2016; 23:18-30. [PMID: 27986421 DOI: 10.1016/j.molmed.2016.11.004] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 11/15/2016] [Accepted: 11/16/2016] [Indexed: 02/06/2023]
Abstract
Intestinal microbiota have emerged as an important factor in colorectal cancer (CRC) initiation and progression. The currently prominent view on bacterial tumorigenesis is that CRC initiation is triggered by local mucosal colonization with specific pathogens (drivers), and that subsequent changes in the peritumoral environment allow colonization by opportunistic (passenger) microbes, further facilitating disease progression. Screening for CRC 'driver-passenger' microorganisms might thus allow early CRC diagnosis or preventive intervention. Such efforts are now being revolutionized by the notion that CRC initiation and progression require organization of bacterial communities into higher-order structures termed biofilms. We explore here the concept that a polymicrobial biofilm promotes pro-carcinogenic activities that may partially underlie progression along the adenoma-CRC axis.
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47
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Turroni S, Rampelli S, Centanni M, Schnorr SL, Consolandi C, Severgnini M, Peano C, Soverini M, Falconi M, Crittenden AN, Henry AG, Brigidi P, Candela M. Enterocyte-Associated Microbiome of the Hadza Hunter-Gatherers. Front Microbiol 2016; 7:865. [PMID: 27375586 PMCID: PMC4893497 DOI: 10.3389/fmicb.2016.00865] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 05/23/2016] [Indexed: 12/15/2022] Open
Abstract
By means of a recently developed non-invasive ex vivo minimal model based on the interaction of the human enterocyte-like HT29 cell line and fecal slurries, we explored the enterocyte-associated microbiome of 21 Hadza hunter-gatherers and nine urban living Italians. Though reductionist, this model allows inferring the microbiota structural and functional arrangement as it interacts with enterocytes. Microbial suspensions obtained from Hadza or Italian stools were first evaluated for structural integrity by high resolution-scanning electron microscopy and co-incubated with HT29 cell monolayers. The enterocyte adherent microbiota fraction was then characterized by 16S rRNA gene sequencing and predictive functional profiling using PICRUSt. Compared to Italians, the Hadza enterocyte-associated microbiome was characterized by a greater amount of adhesive microorganisms with pathogenic potential, such as Proteobacteria, Erysipelotrichaceae, Enterococcus, Clostridium and Sarcina. These compositional characteristics were reflected in a functional enrichment in membrane transport, signal transduction, signaling molecules and interaction. Our results depict a new interesting mutualistic configuration of the enterocyte-associated microbiome in Hadza, stressing the importance of microbe-host interaction at the mucosal surface along the course of human evolution.
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Affiliation(s)
- Silvia Turroni
- Microbial Ecology of Health Unit, Department of Pharmacy and Biotechnology, University of Bologna Bologna, Italy
| | - Simone Rampelli
- Microbial Ecology of Health Unit, Department of Pharmacy and Biotechnology, University of Bologna Bologna, Italy
| | - Manuela Centanni
- Microbial Ecology of Health Unit, Department of Pharmacy and Biotechnology, University of Bologna Bologna, Italy
| | - Stephanie L Schnorr
- Max Planck Research Group on Plant Foods in Hominin Dietary Ecology, Max Planck Institute for Evolutionary Anthropology Leipzig, Germany
| | - Clarissa Consolandi
- Institute of Biomedical Technologies, Italian National Research Council Segrate, Italy
| | - Marco Severgnini
- Institute of Biomedical Technologies, Italian National Research Council Segrate, Italy
| | - Clelia Peano
- Institute of Biomedical Technologies, Italian National Research Council Segrate, Italy
| | - Matteo Soverini
- Microbial Ecology of Health Unit, Department of Pharmacy and Biotechnology, University of Bologna Bologna, Italy
| | - Mirella Falconi
- Department of Biomedical and Neuromotor Sciences, University of Bologna Bologna, Italy
| | - Alyssa N Crittenden
- Metabolism, Anthropometry, and Nutrition Laboratory, Department of Anthropology, University of Nevada, Las Vegas NV, USA
| | - Amanda G Henry
- Max Planck Research Group on Plant Foods in Hominin Dietary Ecology, Max Planck Institute for Evolutionary Anthropology Leipzig, Germany
| | - Patrizia Brigidi
- Microbial Ecology of Health Unit, Department of Pharmacy and Biotechnology, University of Bologna Bologna, Italy
| | - Marco Candela
- Microbial Ecology of Health Unit, Department of Pharmacy and Biotechnology, University of Bologna Bologna, Italy
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48
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Topological distortion and reorganized modular structure of gut microbial co-occurrence networks in inflammatory bowel disease. Sci Rep 2016; 6:26087. [PMID: 27188829 PMCID: PMC4870640 DOI: 10.1038/srep26087] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 04/27/2016] [Indexed: 12/24/2022] Open
Abstract
The gut microbiome plays a key role in human health, and alterations of the normal gut flora are associated with a variety of distinct disease states. Yet, the natural dependencies between microbes in healthy and diseased individuals remain far from understood. Here we use a network-based approach to characterize microbial co-occurrence in individuals with inflammatory bowel disease (IBD) and healthy (non-IBD control) individuals. We find that microbial networks in patients with IBD differ in both global structure and local connectivity patterns. While a “core” microbiome is preserved, network topology of other densely interconnected microbe modules is distorted, with potent inflammation-mediating organisms assuming roles as integrative and highly connected inter-modular hubs. We show that while both networks display a rich-club organization, in which a small set of microbes commonly co-occur, the healthy network is more easily disrupted by elimination of a small number of key species. Further investigation of network alterations in disease might offer mechanistic insights into the specific pathogens responsible for microbiome-mediated inflammation in IBD.
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49
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Golińska E, van der Linden M, Więcek G, Mikołajczyk D, Machul A, Samet A, Piórkowska A, Dorycka M, Heczko PB, Strus M. Virulence factors of Streptococcus pyogenes strains from women in peri-labor with invasive infections. Eur J Clin Microbiol Infect Dis 2016; 35:747-54. [PMID: 26873375 PMCID: PMC4840219 DOI: 10.1007/s10096-016-2593-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 01/19/2016] [Indexed: 10/24/2022]
Abstract
Invasive group A streptococcal (GAS) infections constitute an important epidemiological problem. Many cases occur in women during the postnatal period. The objective of this study was to evaluate the presence of the genes responsible for production of iron-chelating protein (perR) and superantigens (speA, speB, speC, speF, speG, speH, speI, speJ, speK, speL, speM, smeZ, and ssa) in S. pyogenes strains isolated from invasive infections in women after delivery. Furthermore, this study sought to verify whether S. pyogenes strains show special phenotypic and genotypic (sla, spy1325) characteristics that may play a decisive role in adherence to the genital tract epithelium. Moreover, the emm-types and antibiotic susceptibility were determined. We tested 30 invasive S. pyogenes strains isolated from postpartum invasive infection and 37 GAS control strains isolated from the genital tracts of asymptomatic multiparous women. The majority of the tested strains were shown to express two types of emm genes (1 and 28), though emm -12, -28, -75 and -89 were uniquely expressed in the group of strains isolated from invasive infections. A significantly higher prevalence of perR in the strains from puerperal fever was shown. Significant differences were also found between the two groups with respect to the incidence of the genes related to adherence; GAS strains originating from women with sepsis/puerperal fever showed presence of these genes less frequently than those of the control group. Although differences in frequencies of the gene coding for various superantigens were noted between the compared groups of GAS strains, they were not significant.
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Affiliation(s)
- E Golińska
- Jagiellonian University Medical College, 18 Czysta Str., 31-121, Kracow, Poland
| | - M van der Linden
- Institute of Microbiology, RWTH Aachen University, Faculty of Medicine and University Hospital, Aachen, Germany
| | - G Więcek
- Jagiellonian University Medical College, 18 Czysta Str., 31-121, Kracow, Poland
| | - D Mikołajczyk
- Jagiellonian University Medical College, 18 Czysta Str., 31-121, Kracow, Poland
| | - A Machul
- Jagiellonian University Medical College, 18 Czysta Str., 31-121, Kracow, Poland
| | - A Samet
- Department of Clinical Microbiology, University Clinical Center in Gdansk, 7 Debinki Str., 80-952, Gdansk, Poland
| | - A Piórkowska
- Department of Clinical Microbiology, University Clinical Center in Gdansk, 7 Debinki Str., 80-952, Gdansk, Poland
| | - M Dorycka
- Microbiological Laboratory, Diagnostics Inc., Kracow Branch, Na Skarpie 66 axis, 31-913, Kracow, Poland
| | - P B Heczko
- Jagiellonian University Medical College, 18 Czysta Str., 31-121, Kracow, Poland
| | - M Strus
- Jagiellonian University Medical College, 18 Czysta Str., 31-121, Kracow, Poland.
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50
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Du L, Liu L, Liu F, Ju X, Yuan J. Phenotypic and Genotypic Alterations of Durancin GL-Resistant Enterococcus durans Strains. Foodborne Pathog Dis 2016; 13:325-32. [PMID: 27096434 DOI: 10.1089/fpd.2015.2094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The emergence and spread of bacteriocin-resistant bacteria threaten the efficiency of bacteriocin usage as food preservatives. In this experiment, 19 selected Enterococcus durans strains acquired resistance after exposure to durancin GL, and the mutants had similar intermediate levels of resistance. One wild-type E. durans KLDS 6.0603 and its two resistant mutants, E. durans KLDS 6.0603-2 and E. durans KLDS 6.0603-3, were used to characterize phenotypic and genotypic differences. Approximately 100 μg/mL of durancin GL can penetrate the cytoplasmic membrane of E. durans KLDS 6.0603, causing damage to bacterial cells, but cannot penetrate E. durans KLDS 6.0603-2 and KLDS 6.0603-3 membranes. Unsaturated fatty acid content in resistant strains was significantly increased compared with wild-type strains, indicating that the former has more fluidity of cell membrane than the latter. Decreased mannose phosphotransferase system gene expression (mptD) was observed in the two resistant strains. Results showed that the factors, including the increased unsaturated fatty acid and decreased mptD expression, could contribute to durancin GL resistance.
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Affiliation(s)
- Lihui Du
- 1 College of Food Science and Engineering, Collaborative Innovation Center for Modern Grain Circulation and Safety, Key Laboratory of Grains and Oils Quality Control and Processing, Nanjing University of Finance and Economics , Nanjing, China
| | - Lingping Liu
- 1 College of Food Science and Engineering, Collaborative Innovation Center for Modern Grain Circulation and Safety, Key Laboratory of Grains and Oils Quality Control and Processing, Nanjing University of Finance and Economics , Nanjing, China
| | - Fang Liu
- 2 Institute of Agricultural Products Processing , Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xingrong Ju
- 1 College of Food Science and Engineering, Collaborative Innovation Center for Modern Grain Circulation and Safety, Key Laboratory of Grains and Oils Quality Control and Processing, Nanjing University of Finance and Economics , Nanjing, China
| | - Jian Yuan
- 1 College of Food Science and Engineering, Collaborative Innovation Center for Modern Grain Circulation and Safety, Key Laboratory of Grains and Oils Quality Control and Processing, Nanjing University of Finance and Economics , Nanjing, China
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