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Sun Q, Ji YC, Ai Q, She X, Liu XC, Yan XL, Li LQ. Exogenous autoinducer-2 alleviates intestinal damage in necrotizing enterocolitis via PAR2/MMP3 signaling pathway. Int Immunopharmacol 2024; 138:112567. [PMID: 38950458 DOI: 10.1016/j.intimp.2024.112567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 06/12/2024] [Accepted: 06/24/2024] [Indexed: 07/03/2024]
Abstract
BACKGROUND Imbalanced intestinal microbiota and damage to the intestinal barrier contribute to the development of necrotizing enterocolitis (NEC). Autoinducer-2 (AI-2) plays a crucial role in repairing intestinal damage and reducing inflammation. OBJECTIVE This study aimed to investigate the impact of AI-2 on the expression of intestinal zonula occludens-1 (ZO-1) and occludin proteins in NEC. We evaluated its effects in vivo using NEC mice and in vitro using lipopolysaccharide (LPS)-stimulated intestinal cells. METHODS Pathological changes in the intestines of neonatal mice were assessed using histological staining and scoring. Cell proliferation was measured using the cell counting kit-8 (CCK-8) assay to determine the optimal conditions for LPS and AI-2 interventions. Real-time quantitative polymerase chain reaction (RT-qPCR) was used to analyze the mRNA levels of matrix metalloproteinase-3 (MMP3), protease activated receptor-2 (PAR2), interleukin-1β (IL-1β), and IL-6. Protein levels of MMP3, PAR2, ZO-1, and occludin were evaluated using western blot, immunohistochemistry, or immunofluorescence. RESULTS AI-2 alleviated NEC-induced intestinal damage (P < 0.05) and enhanced the proliferation of damaged IEC-6 cells (P < 0.05). AI-2 intervention reduced the mRNA and protein expressions of MMP3 and PAR2 in intestinal tissue and cells (P < 0.05). Additionally, it increased the protein levels of ZO-1 and occludin (P < 0.05), while reducing IL-1β and IL-6 mRNA expression (P < 0.05). CONCLUSION AI-2 intervention enhances the expression of tight junction proteins (ZO-1 and occludin), mitigates intestinal damage in NEC neonatal mice and IEC-6 cells, potentially by modulating PAR2 and MMP3 signaling. AI-2 holds promise as a protective intervention for NEC. AI-2 plays a crucial role in repairing intestinal damage and reducing inflammation.
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Affiliation(s)
- Qian Sun
- Department of Neonatology, Children's Hospital of Chongqing Medical University, Chongqing, China; National Clinical Research Center for Child Health and Disorders, Chongqing, China; Key Laboratory of Children's Development and Disorders, Ministry of Education, Chongqing, China; National International Science and Technology Cooperation Base for Development and Critical Disorders in Children, Chongqing, China; Key Laboratory of Pediatrics in Chongqing, Chongqing 400014, China
| | - Yan-Chun Ji
- Department of Neonatology, Children's Hospital of Chongqing Medical University, Chongqing, China; National Clinical Research Center for Child Health and Disorders, Chongqing, China; Key Laboratory of Children's Development and Disorders, Ministry of Education, Chongqing, China; National International Science and Technology Cooperation Base for Development and Critical Disorders in Children, Chongqing, China; Key Laboratory of Pediatrics in Chongqing, Chongqing 400014, China
| | - Qing Ai
- Department of Neonatology, Children's Hospital of Chongqing Medical University, Chongqing, China; National Clinical Research Center for Child Health and Disorders, Chongqing, China; Key Laboratory of Children's Development and Disorders, Ministry of Education, Chongqing, China; National International Science and Technology Cooperation Base for Development and Critical Disorders in Children, Chongqing, China; Key Laboratory of Pediatrics in Chongqing, Chongqing 400014, China
| | - Xiang She
- Department of Neonatology, Children's Hospital of Chongqing Medical University, Chongqing, China; National Clinical Research Center for Child Health and Disorders, Chongqing, China; Key Laboratory of Children's Development and Disorders, Ministry of Education, Chongqing, China; National International Science and Technology Cooperation Base for Development and Critical Disorders in Children, Chongqing, China; Key Laboratory of Pediatrics in Chongqing, Chongqing 400014, China
| | - Xiao-Chen Liu
- Department of Neonatology, Children's Hospital of Chongqing Medical University, Chongqing, China; National Clinical Research Center for Child Health and Disorders, Chongqing, China; Key Laboratory of Children's Development and Disorders, Ministry of Education, Chongqing, China; National International Science and Technology Cooperation Base for Development and Critical Disorders in Children, Chongqing, China; Key Laboratory of Pediatrics in Chongqing, Chongqing 400014, China
| | - Xiao-Lin Yan
- Department of Neonatology, Children's Hospital of Chongqing Medical University, Chongqing, China; National Clinical Research Center for Child Health and Disorders, Chongqing, China; Key Laboratory of Children's Development and Disorders, Ministry of Education, Chongqing, China; National International Science and Technology Cooperation Base for Development and Critical Disorders in Children, Chongqing, China; Key Laboratory of Pediatrics in Chongqing, Chongqing 400014, China
| | - Lu-Quan Li
- Department of Neonatology, Children's Hospital of Chongqing Medical University, Chongqing, China; National Clinical Research Center for Child Health and Disorders, Chongqing, China; Key Laboratory of Children's Development and Disorders, Ministry of Education, Chongqing, China; National International Science and Technology Cooperation Base for Development and Critical Disorders in Children, Chongqing, China; Key Laboratory of Pediatrics in Chongqing, Chongqing 400014, China.
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Hartmann A, Binder T, Rothballer M. Quorum sensing-related activities of beneficial and pathogenic bacteria have important implications for plant and human health. FEMS Microbiol Ecol 2024; 100:fiae076. [PMID: 38744663 PMCID: PMC11149725 DOI: 10.1093/femsec/fiae076] [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: 01/23/2024] [Revised: 03/28/2024] [Accepted: 05/13/2024] [Indexed: 05/16/2024] Open
Abstract
Eukaryotic organisms coevolved with microbes from the environment forming holobiotic meta-genomic units. Members of host-associated microbiomes have commensalic, beneficial/symbiotic, or pathogenic phenotypes. More than 100 years ago, Lorenz Hiltner, pioneer of soil microbiology, introduced the term 'Rhizosphere' to characterize the observation that a high density of saprophytic, beneficial, and pathogenic microbes are attracted by root exudates. The balance between these types of microbes decide about the health of the host. Nowadays we know, that for the interaction of microbes with all eukaryotic hosts similar principles and processes of cooperative and competitive functions are in action. Small diffusible molecules like (phyto)hormones, volatiles and quorum sensing signals are examples for mediators of interspecies and cross-kingdom interactions. Quorum sensing of bacteria is mediated by different autoinducible metabolites in a density-dependent manner. In this perspective publication, the role of QS-related activities for the health of hosts will be discussed focussing mostly on N-acyl-homoserine lactones (AHL). It is also considered that in some cases very close phylogenetic relations exist between plant beneficial and opportunistic human pathogenic bacteria. Based on a genome and system-targeted new understanding, sociomicrobiological solutions are possible for the biocontrol of diseases and the health improvement of eukaryotic hosts.
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Affiliation(s)
- Anton Hartmann
- Faculty of Biology, Microbe-Host Interactions, Ludwig-Maximilian-University Munich, Grosshaderner Str. 2, D-82152 Planegg/Martinsried, Germany
- Department of Environmental Sciences, Helmholtz Zentrum Munich, German Research Center for Health and Environment, Research Unit Microbe-Plant Interactions, Ingolstädter Landstr. 1, D-85762 Neuherberg, Germany
| | - Tatiana Binder
- Department of Environmental Sciences, Helmholtz Zentrum Munich, German Research Center for Health and Environment, Research Unit Microbe-Plant Interactions, Ingolstädter Landstr. 1, D-85762 Neuherberg, Germany
| | - Michael Rothballer
- Department of Environmental Sciences, Helmholtz Zentrum Munich, German Research Center for Health and Environment, Research Unit Microbe-Plant Interactions, Ingolstädter Landstr. 1, D-85762 Neuherberg, Germany
- Helmholtz Zentrum Munich, German Research Center for Health and Environment, Institute of Network Biology, Ingolstädter Landstr. 1 D-85762 Neuherberg, Germany
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3
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Hu R, Yang T, Ai Q, Shi Y, Ji Y, Sun Q, Tong B, Chen J, Wang Z. Autoinducer-2 promotes the colonization of Lactobacillus rhamnosus GG to improve the intestinal barrier function in a neonatal mouse model of antibiotic-induced intestinal dysbiosis. J Transl Med 2024; 22:177. [PMID: 38369503 PMCID: PMC10874557 DOI: 10.1186/s12967-024-04991-5] [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: 12/05/2023] [Accepted: 02/12/2024] [Indexed: 02/20/2024] Open
Abstract
BACKGROUND Human health is seriously threatened by antibiotic-induced intestinal disorders. Herein, we aimed to determine the effects of Autoinducer-2 (AI-2) combined with Lactobacillus rhamnosus GG (LGG) on the intestinal barrier function of antibiotic-induced intestinal dysbiosis neonatal mice. METHODS An antibiotic-induced intestinal dysbiosis neonatal mouse model was created using antibiotic cocktails, and the model mice were randomized into the control, AI-2, LGG, and LGG + AI-2 groups. Intestinal short-chain fatty acids and AI-2 concentrations were detected by mass spectrometry and chemiluminescence, respectively. The community composition of the gut microbiota was analyzed using 16S rDNA sequencing, and biofilm thickness and bacterial adhesion in the colon were assessed using scanning electron microscopy. Transcriptome RNA sequencing of intestinal tissues was performed, and the mRNA and protein levels of HCAR2 (hydroxycarboxylic acid receptor 2), claudin3, and claudin4 in intestinal tissues were determined using quantitative real-time reverse transcription PCR and western blotting. The levels of inflammatory factors in intestinal tissues were evaluated using enzyme-linked immunosorbent assays (ELISAs). D-ribose, an inhibitor of AI-2, was used to treat Caco-2 cells in vitro. RESULTS Compared with the control, AI-2, and LGG groups, the LGG + AI-2 group showed increased levels of intestinal AI-2 and proportions of Firmicutes and Lacticaseibacillus, but a reduced fraction of Proteobacteria. Specifically, the LGG + AI-2 group had considerably more biofilms and LGG on the colon surface than those of other three groups. Meanwhile, the combination of AI-2 and LGG markedly increased the concentration of butyric acid and promoted Hcar2, claudin3 and claudin4 expression levels compared with supplementation with LGG or AI-2 alone. The ELISAs revealed a significantly higher tumor necrosis factor alpha (TNF-α) level in the control group than in the LGG and LGG + AI-2 groups, whereas the interleukin 10 (IL-10) level was significantly higher in the LGG + AI-2 group than in the other three groups. In vitro, D-ribose treatment dramatically suppressed the increased levels of Hcar2, claudin3, and claudin4 in Caco-2 cells induced by AI-2 + LGG. CONCLUSIONS AI-2 promotes the colonization of LGG and biofilm formation to improve intestinal barrier function in an antibiotic-induced intestinal dysbiosis neonatal mouse model.
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Affiliation(s)
- Riqiang Hu
- Children Nutrition Research Center, Chongqing Key Laboratory of Child Neurodevelopmental and Cognitive Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Chongqing, China
| | - Ting Yang
- Children Nutrition Research Center, Chongqing Key Laboratory of Child Neurodevelopmental and Cognitive Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Chongqing, China
| | - Qing Ai
- Department of Neonatology, National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Yuan Shi
- Department of Neonatology, National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Yanchun Ji
- Department of Neonatology, National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Qian Sun
- Department of Neonatology, National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Bei Tong
- Children Nutrition Research Center, Chongqing Key Laboratory of Child Neurodevelopmental and Cognitive Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Chongqing, China
| | - Jie Chen
- Children Nutrition Research Center, Chongqing Key Laboratory of Child Neurodevelopmental and Cognitive Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Chongqing, China.
| | - Zhengli Wang
- Children Nutrition Research Center, Chongqing Key Laboratory of Child Neurodevelopmental and Cognitive Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Chongqing, China.
- Department of Neonatology, National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.
- Jiangxi Hospital Affiliated Children's Hospital of Chongqing Medical University, Chongqing, China.
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Rubas NC, Peres R, Kunihiro BP, Allan NP, Phankitnirundorn K, Wells RK, McCracken T, Lee RH, Umeda L, Conching A, Juarez R, Maunakea AK. HMGB1 mediates microbiome-immune axis dysregulation underlying reduced neutralization capacity in obesity-related post-acute sequelae of SARS-CoV-2. Sci Rep 2024; 14:355. [PMID: 38172612 PMCID: PMC10764757 DOI: 10.1038/s41598-023-50027-1] [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: 05/23/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
While obesity is a risk factor for post-acute sequelae of SARS-CoV-2 infection (PASC, "long-COVID"), the mechanism(s) underlying this phenomenon remains poorly understood. To address this gap in knowledge, we performed a 6-week longitudinal study to examine immune activity and gut microbiome dysbiosis in post-acute stage patients recovering from SARS-CoV-2 infection. Self-reported symptom frequencies and blood samples were collected weekly, with plasma assessed by ELISA and Luminex for multiple biomarkers and immune cell profiling. DNA from stool samples were collected at the early stage of recovery for baseline assessments of gut microbial composition and diversity using 16S-based metagenomic sequencing. Multiple regression analyses revealed obesity-related PASC linked to a sustained proinflammatory immune profile and reduced adaptive immunity, corresponding with reduced gut microbial diversity. In particular, enhanced signaling of the high mobility group box 1 (HMGB1) protein was found to associate with this dysregulation, with its upregulated levels in plasma associated with significantly impaired viral neutralization that was exacerbated with obesity. These findings implicate HMGB1 as a candidate biomarker of PASC, with potential applications for risk assessment and targeted therapies.
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Affiliation(s)
- Noelle C Rubas
- Department of Biochemistry, Anatomy, and Physiology, University of Hawai'i at Mānoa, Honolulu, HI, USA
- Deparment of Molecular Biosciences and Bioengineering, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Rafael Peres
- Department of Biochemistry, Anatomy, and Physiology, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Braden P Kunihiro
- Department of Biochemistry, Anatomy, and Physiology, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Nina P Allan
- Department of Biochemistry, Anatomy, and Physiology, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Krit Phankitnirundorn
- Department of Biochemistry, Anatomy, and Physiology, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Riley K Wells
- Department of Biochemistry, Anatomy, and Physiology, University of Hawai'i at Mānoa, Honolulu, HI, USA
- Deparment of Molecular Biosciences and Bioengineering, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Trevor McCracken
- Department of Biochemistry, Anatomy, and Physiology, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Rosa H Lee
- Department of Biochemistry, Anatomy, and Physiology, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Lesley Umeda
- Department of Biochemistry, Anatomy, and Physiology, University of Hawai'i at Mānoa, Honolulu, HI, USA
- Deparment of Molecular Biosciences and Bioengineering, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | | | - Ruben Juarez
- Hawai'i Integrated Analytics, Honolulu, HI, USA
- Deparment of Economics and UHERO, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | - Alika K Maunakea
- Department of Biochemistry, Anatomy, and Physiology, University of Hawai'i at Mānoa, Honolulu, HI, USA.
- Hawai'i Integrated Analytics, Honolulu, HI, USA.
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Walsh C, Owens RA, Bottacini F, Lane JA, van Sinderen D, Hickey RM. HMO-primed bifidobacteria exhibit enhanced ability to adhere to intestinal epithelial cells. Front Microbiol 2023; 14:1232173. [PMID: 38163079 PMCID: PMC10757668 DOI: 10.3389/fmicb.2023.1232173] [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: 05/31/2023] [Accepted: 11/06/2023] [Indexed: 01/03/2024] Open
Abstract
The ability of gut commensals to adhere to the intestinal epithelium can play a key role in influencing the composition of the gut microbiota. Bifidobacteria are associated with a multitude of health benefits and are one of the most widely used probiotics for humans. Enhanced bifidobacterial adhesion may increase host-microbe, microbe-nutrient, and/or microbe-microbe interactions, thereby enabling consolidated health benefits to the host. The objective of this study was to determine the ability of human milk oligosaccharides (HMOs) to enhance bifidobacterial intestinal adhesion in vitro. This study assessed the colonisation-promoting effects of HMOs on four commercial infant-associated Bifidobacterium strains (two B. longum subsp. infantis strains, B. breve and B. bifidum). HT29-MTX cells were used as an in vitro intestinal model for bacterial adhesion. Short-term exposure of four commercial infant-associated Bifidobacterium strains to HMOs derived from breastmilk substantially increased the adherence (up to 47%) of these probiotic strains. Interestingly, when strains were incubated with HMOs as a four-strain combination, the number of viable bacteria adhering to intestinal cells increased by >90%. Proteomic analysis of this multi-strain bifidobacterial mixture revealed that the increased adherence resulting from exposure to HMOs was associated with notable increases in the abundance of sortase-dependent pili and glycosyl hydrolases matched to Bifidobacterium bifidum. This study suggests that HMOs may prime infant gut-associated Bifidobacterium for colonisation to intestinal epithelial cells by influencing the expression of various colonization factors.
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Affiliation(s)
- Clodagh Walsh
- Teagasc Food Research Centre, Moorepark, Cork, Ireland
- Health and Happiness Group, H&H Research, Cork, Ireland
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
| | | | - Francesca Bottacini
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
- Biological Sciences and ADAPT Research Centre, Munster Technological University, Cork, Ireland
| | | | - Douwe van Sinderen
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
| | - Rita M. Hickey
- Teagasc Food Research Centre, Moorepark, Cork, Ireland
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
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SHIMADA M, KAWASE Y, SONOYAMA K, OGURA Y, HAYASHI T, YOKOTA A, FUKIYA S. Development of an improved colonization system for human-derived Bifidobacterium longum subsp. longum in conventional mice through the feeding of raffinose or 1-kestose. BIOSCIENCE OF MICROBIOTA, FOOD AND HEALTH 2023; 43:110-119. [PMID: 38562544 PMCID: PMC10981944 DOI: 10.12938/bmfh.2023-055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 11/05/2023] [Indexed: 04/04/2024]
Abstract
How bifidobacteria colonize and survive in the intestine is not fully understood. The administration of bifidobacteria to conventional mice can be used to evaluate their ability to colonize the intestine in the presence of endogenous gut microbiota. However, human-derived bifidobacteria do not readily colonize the intestines of conventional mice, and although colonization by Bifidobacterium breve UCC2003 has been achieved, the viability of such populations requires improvement. Therefore, we aimed to establish a colonization system with human-derived bifidobacteria of high viability in conventional mice using Bifidobacterium longum subsp. longum 105-A. Lactose, raffinose, and 1-kestose were identified as the preferred carbohydrate sources for the growth of this strain in culture. The administration of B. longum 105-A to conventional BALB/c mice fed these carbohydrates showed that diets containing 6% (w/w) raffinose or 1-kestose facilitated colonization with >108 colony-forming units/g feces for 2 weeks. The population of this strain was more stable in the raffinose-fed group than in the 1-kestose-fed group. The ingestion of these prebiotics had a greater impact on the composition of the microbiota than the administration of B. longum 105-A. The ingestion of these prebiotics also increased the fecal concentrations of organic acids, which was indicative of greater intestinal fermentation. Collectively, we established a colonization system for B. longum 105-A with high viability in conventional mice by feeding the mice raffinose or 1-kestose. This system should be useful for elucidation of the mechanisms of colonization and survival of bifidobacteria in the intestines in the presence of the endogenous gut microbiota.
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Affiliation(s)
- Mina SHIMADA
- Laboratory of Microbial Physiology, Research Faculty of
Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo, Hokkaido 060-8589,
Japan
| | - Youhei KAWASE
- Laboratory of Microbial Physiology, Research Faculty of
Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo, Hokkaido 060-8589,
Japan
| | - Kei SONOYAMA
- Laboratory of Food Biochemistry, Research Faculty of
Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo, Hokkaido 060-8589,
Japan
| | - Yoshitoshi OGURA
- Department of Bacteriology, Faculty of Medical Sciences,
Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
- Department of Infectious Medicine, Kurume University School
of Medicine, 67 Asahi-machi, Kurume-shi, Fukuoka 830-0011, Japan
| | - Tetsuya HAYASHI
- Department of Bacteriology, Faculty of Medical Sciences,
Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
| | - Atsushi YOKOTA
- Laboratory of Microbial Physiology, Research Faculty of
Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo, Hokkaido 060-8589,
Japan
| | - Satoru FUKIYA
- Laboratory of Microbial Physiology, Research Faculty of
Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo, Hokkaido 060-8589,
Japan
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Ghosh M, Raghav S, Ghosh P, Maity S, Mohela K, Jain D. Structural analysis of novel drug targets for mitigation of Pseudomonas aeruginosa biofilms. FEMS Microbiol Rev 2023; 47:fuad054. [PMID: 37771093 DOI: 10.1093/femsre/fuad054] [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: 05/30/2023] [Revised: 09/20/2023] [Accepted: 09/27/2023] [Indexed: 09/30/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen responsible for acute and chronic, hard to treat infections. Persistence of P. aeruginosa is due to its ability to develop into biofilms, which are sessile bacterial communities adhered to substratum and encapsulated in layers of self-produced exopolysaccharides. These biofilms provide enhanced protection from the host immune system and resilience towards antibiotics, which poses a challenge for treatment. Various strategies have been expended for combating biofilms, which involve inhibiting biofilm formation or promoting their dispersal. The current remediation approaches offer some hope for clinical usage, however, treatment and eradication of preformed biofilms is still a challenge. Thus, identifying novel targets and understanding the detailed mechanism of biofilm regulation becomes imperative. Structure-based drug discovery (SBDD) provides a powerful tool that exploits the knowledge of atomic resolution details of the targets to search for high affinity ligands. This review describes the available structural information on the putative target protein structures that can be utilized for high throughput in silico drug discovery against P. aeruginosa biofilms. Integrating available structural information on the target proteins in readily accessible format will accelerate the process of drug discovery.
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Affiliation(s)
- Moumita Ghosh
- Transcription Regulation Lab, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, Haryana-121001, India
| | - Shikha Raghav
- Transcription Regulation Lab, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, Haryana-121001, India
| | - Puja Ghosh
- Transcription Regulation Lab, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, Haryana-121001, India
| | - Swagatam Maity
- Transcription Regulation Lab, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, Haryana-121001, India
| | - Kavery Mohela
- Transcription Regulation Lab, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, Haryana-121001, India
| | - Deepti Jain
- Transcription Regulation Lab, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, Haryana-121001, India
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Li J, Chen X, Xie Z, Liang L, Li A, Zhao C, Wen Y, Lou Z. Screening and Metabolomic Analysis of Lactic Acid Bacteria-Antagonizing Pseudomonas aeruginosa. Foods 2023; 12:2799. [PMID: 37509891 PMCID: PMC10379379 DOI: 10.3390/foods12142799] [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: 06/03/2023] [Revised: 07/12/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Pseudomonas aeruginosa is a conditional Gram-negative pathogen that produces extracellular virulence factors that can lead to bloodstream invasion, severely harm tissues, and disseminate bacteria, ultimately leading to various diseases. In this study, lactic acid bacteria (LAB) with strong antagonistic ability against P. aeruginosa were screened, and the regulatory mechanism of LAB against P. aeruginosa was evaluated. The results showed that the three selected LAB strains had strong inhibition ability on the growth, biofilm formation, and pyocyanin expression of P. aeruginosa and a promoting effect on the expression of autoinducer-2. Among them, Lactipantibacillus plantarum (Lp. plantarum) LPyang is capable of affecting the metabolic processes of P. aeruginosa by influencing metabolic substances, such as LysoPC, oxidized glutathione, betaine, etc. These results indicate that LPyang reduces the infectivity of P. aeruginosa through inhibition of its growth, biofilm formation, pyocyanin expression, and regulation of its metabolome. This study provides new insights into the antagonistic activity of Lp. plantarum LPyang against P. aeruginosa.
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Affiliation(s)
- Jianzhou Li
- College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China
- Hunan Key Laboratory for Conservation and Utilization of Biological Resources in the Nanyue Mountainous Region, College of Life Sciences, Hengyang Normal University, Hengyang 421008, China
| | - Xiaohua Chen
- Hunan Key Laboratory for Conservation and Utilization of Biological Resources in the Nanyue Mountainous Region, College of Life Sciences, Hengyang Normal University, Hengyang 421008, China
- Department of Life Sciences, Nanyue College of Hengyang Normal University, Hengyang 421008, China
| | - Ziyan Xie
- Hunan Key Laboratory for Conservation and Utilization of Biological Resources in the Nanyue Mountainous Region, College of Life Sciences, Hengyang Normal University, Hengyang 421008, China
| | - Lin Liang
- Department of Life Sciences, Nanyue College of Hengyang Normal University, Hengyang 421008, China
| | - Anping Li
- College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China
| | - Chao Zhao
- College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuxi Wen
- College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Sciences, Universidade de Vigo, 32004 Ourense, Spain
| | - Zaixiang Lou
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
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9
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Abstract
Microbial communities are shaped by positive and negative interactions ranging from competition to mutualism. In the context of the mammalian gut and its microbial inhabitants, the integrated output of the community has important impacts on host health. Cross-feeding, the sharing of metabolites between different microbes, has emergent roles in establishing communities of gut commensals that are stable, resistant to invasion, and resilient to external perturbation. In this review, we first explore the ecological and evolutionary implications of cross-feeding as a cooperative interaction. We then survey mechanisms of cross-feeding across trophic levels, from primary fermenters to H2 consumers that scavenge the final metabolic outputs of the trophic network. We extend this analysis to also include amino acid, vitamin, and cofactor cross-feeding. Throughout, we highlight evidence for the impact of these interactions on each species' fitness as well as host health. Understanding cross-feeding illuminates an important aspect of microbe-microbe and host-microbe interactions that establishes and shapes our gut communities.
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Affiliation(s)
- Elizabeth J Culp
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Andrew L Goodman
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT, USA.
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10
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Oliveira RA, Cabral V, Torcato I, Xavier KB. Deciphering the quorum-sensing lexicon of the gut microbiota. Cell Host Microbe 2023; 31:500-512. [PMID: 37054672 DOI: 10.1016/j.chom.2023.03.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
The enduring coexistence between the gut microbiota and the host has led to a symbiotic relationship that benefits both parties. In this complex, multispecies environment, bacteria can communicate through chemical molecules to sense and respond to the chemical, physical, and ecological properties of the surrounding environment. One of the best-studied cell-to-cell communication mechanisms is quorum sensing. Chemical signaling through quorum sensing is involved in regulating the bacterial group behaviors, often required for host colonization. However, most microbial-host interactions regulated by quorum sensing are studied in pathogens. Here, we will focus on the latest reports on the emerging studies of quorum sensing in the gut microbiota symbionts and on group behaviors adopted by these bacteria to colonize the mammalian gut. Moreover, we address the challenges and approaches to uncover molecule-mediated communication mechanisms, which will allow us to unravel the processes that drive the establishment of gut microbiota.
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Affiliation(s)
| | - Vitor Cabral
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Inês Torcato
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
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11
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Markus V, Paul AA, Teralı K, Özer N, Marks RS, Golberg K, Kushmaro A. Conversations in the Gut: The Role of Quorum Sensing in Normobiosis. Int J Mol Sci 2023; 24:ijms24043722. [PMID: 36835135 PMCID: PMC9963693 DOI: 10.3390/ijms24043722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/03/2023] [Accepted: 02/11/2023] [Indexed: 02/15/2023] Open
Abstract
An imbalance in gut microbiota, termed dysbiosis, has been shown to affect host health. Several factors, including dietary changes, have been reported to cause dysbiosis with its associated pathologies that include inflammatory bowel disease, cancer, obesity, depression, and autism. We recently demonstrated the inhibitory effects of artificial sweeteners on bacterial quorum sensing (QS) and proposed that QS inhibition may be one mechanism behind such dysbiosis. QS is a complex network of cell-cell communication that is mediated by small diffusible molecules known as autoinducers (AIs). Using AIs, bacteria interact with one another and coordinate their gene expression based on their population density for the benefit of the whole community or one group over another. Bacteria that cannot synthesize their own AIs secretly "listen" to the signals produced by other bacteria, a phenomenon known as "eavesdropping". AIs impact gut microbiota equilibrium by mediating intra- and interspecies interactions as well as interkingdom communication. In this review, we discuss the role of QS in normobiosis (the normal balance of bacteria in the gut) and how interference in QS causes gut microbial imbalance. First, we present a review of QS discovery and then highlight the various QS signaling molecules used by bacteria in the gut. We also explore strategies that promote gut bacterial activity via QS activation and provide prospects for the future.
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Affiliation(s)
- Victor Markus
- Department of Medical Biochemistry, Faculty of Medicine, Near East University, Nicosia 99138, Cyprus
| | - Abraham Abbey Paul
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
| | - Kerem Teralı
- Department of Medical Biochemistry, Faculty of Medicine, Cyprus International University, Nicosia 99258, Cyprus
| | - Nazmi Özer
- Department of Biochemistry, Faculty of Pharmacy, Girne American University, Kyrenia 99428, Cyprus
| | - Robert S. Marks
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
- The Ilse Katz Center for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
| | - Karina Golberg
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
- Correspondence: (K.G.); (A.K.); Tel.: +972-74-7795293 (K.G.); +972-747795291 (A.K.)
| | - Ariel Kushmaro
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
- The Ilse Katz Center for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
- School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
- Correspondence: (K.G.); (A.K.); Tel.: +972-74-7795293 (K.G.); +972-747795291 (A.K.)
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12
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Falà AK, Álvarez-Ordóñez A, Filloux A, Gahan CGM, Cotter PD. Quorum sensing in human gut and food microbiomes: Significance and potential for therapeutic targeting. Front Microbiol 2022; 13:1002185. [PMID: 36504831 PMCID: PMC9733432 DOI: 10.3389/fmicb.2022.1002185] [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: 07/24/2022] [Accepted: 10/17/2022] [Indexed: 11/27/2022] Open
Abstract
Human gut and food microbiomes interact during digestion. The outcome of these interactions influences the taxonomical composition and functional capacity of the resident human gut microbiome, with potential consequential impacts on health and disease. Microbe-microbe interactions between the resident and introduced microbiomes, which likely influence host colonisation, are orchestrated by environmental conditions, elements of the food matrix, host-associated factors as well as social cues from other microorganisms. Quorum sensing is one example of a social cue that allows bacterial communities to regulate genetic expression based on their respective population density and has emerged as an attractive target for therapeutic intervention. By interfering with bacterial quorum sensing, for instance, enzymatic degradation of signalling molecules (quorum quenching) or the application of quorum sensing inhibitory compounds, it may be possible to modulate the microbial composition of communities of interest without incurring negative effects associated with traditional antimicrobial approaches. In this review, we summarise and critically discuss the literature relating to quorum sensing from the perspective of the interactions between the food and human gut microbiome, providing a general overview of the current understanding of the prevalence and influence of quorum sensing in this context, and assessing the potential for therapeutic targeting of quorum sensing mechanisms.
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Affiliation(s)
- A. Kate Falà
- APC Microbiome Ireland, University College Cork, Cork, Ireland,School of Microbiology, University College Cork, Cork, Ireland,Food Bioscience Department, Teagasc Food Research Centre, Fermoy, Ireland
| | - Avelino Álvarez-Ordóñez
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Cormac G. M. Gahan
- APC Microbiome Ireland, University College Cork, Cork, Ireland,School of Microbiology, University College Cork, Cork, Ireland,School of Pharmacy, University College Cork, Cork, Ireland
| | - Paul D. Cotter
- APC Microbiome Ireland, University College Cork, Cork, Ireland,Food Bioscience Department, Teagasc Food Research Centre, Fermoy, Ireland,*Correspondence: Paul D. Cotter,
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13
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Deb S. Pan-genome evolution and its association with divergence of metabolic functions in Bifidobacterium genus. World J Microbiol Biotechnol 2022; 38:231. [PMID: 36205822 DOI: 10.1007/s11274-022-03430-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 09/30/2022] [Indexed: 10/10/2022]
Abstract
Previous studies were mainly focused on genomic evolution and diversity of type species of Bifidobacterium genus due to their health-promoting effect on host. However, those studies were mainly based on species-level taxonomic resolution, adaptation, and characterization of carbohydrate metabolic features of the bifidobacterial species. Here, a comprehensive analysis of the type strain genome unveils the association of pan-genome evolution with the divergence of metabolic function of the Bifidobacterium genus. This study has also demonstrated that horizontal gene transfer, as well as genome expansion and reduction events, leads to the divergence of metabolic functions in Bifidobacterium genus. Furthermore, the genome-based search of probiotic traits among all the available bifidobacterial type strains gives hints on type species, that could confer health benefits to nutrient-deficient individuals. Altogether, the present study provides insight into the developments of genomic evolution, functional divergence, and potential probiotic type species of the Bifidobacterium genus.
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Affiliation(s)
- Sushanta Deb
- Department of Molecular Biology and Bioinformatics, Tripura University, Suryamaninagar, 799022, Tripura, India. .,All India Institute of Medical Sciences (AIIMS), New Delhi, 110029, India.
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14
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Biţă A, Scorei IR, Bălşeanu TA, Ciocîlteu MV, Bejenaru C, Radu A, Bejenaru LE, Rău G, Mogoşanu GD, Neamţu J, Benner SA. New Insights into Boron Essentiality in Humans and Animals. Int J Mol Sci 2022; 23:ijms23169147. [PMID: 36012416 PMCID: PMC9409115 DOI: 10.3390/ijms23169147] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 08/12/2022] [Accepted: 08/14/2022] [Indexed: 11/19/2022] Open
Abstract
Boron (B) is considered a prebiotic chemical element with a role in both the origin and evolution of life, as well as an essential micronutrient for some bacteria, plants, fungi, and algae. B has beneficial effects on the biological functions of humans and animals, such as reproduction, growth, calcium metabolism, bone formation, energy metabolism, immunity, and brain function. Naturally organic B (NOB) species may become promising novel prebiotic candidates. NOB-containing compounds have been shown to be essential for the symbiosis between organisms from different kingdoms. New insights into the key role of NOB species in the symbiosis between human/animal hosts and their microbiota will influence the use of natural B-based colon-targeting nutraceuticals. The mechanism of action (MoA) of NOB species is related to the B signaling molecule (autoinducer-2-borate (AI-2B)) as well as the fortification of the colonic mucus gel layer with NOB species from B-rich prebiotic diets. Both the microbiota and the colonic mucus gel layer can become NOB targets. This paper reviews the evidence supporting the essentiality of the NOB species in the symbiosis between the microbiota and the human/animal hosts, with the stated aim of highlighting the MoA and targets of these species.
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Affiliation(s)
- Andrei Biţă
- Department of Biochemistry, BioBoron Research Institute, S.C. Natural Research S.R.L., 31B Dunării Street, 207465 Podari, Romania
- Department of Pharmacognosy & Phytotherapy, Faculty of Pharmacy, University of Medicine and Pharmacy of Craiova, 2 Petru Rareş Street, 200349 Craiova, Romania
| | - Ion Romulus Scorei
- Department of Biochemistry, BioBoron Research Institute, S.C. Natural Research S.R.L., 31B Dunării Street, 207465 Podari, Romania
- Correspondence: ; Tel.: +40-351-407-543
| | - Tudor Adrian Bălşeanu
- Department of Physiology, Faculty of Medicine, University of Medicine and Pharmacy of Craiova, 2 Petru Rareş Street, 200349 Craiova, Romania
| | - Maria Viorica Ciocîlteu
- Department of Analytical Chemistry, Faculty of Pharmacy, University of Medicine and Pharmacy of Craiova, 2 Petru Rareş Street, 200349 Craiova, Romania
| | - Cornelia Bejenaru
- Department of Pharmaceutical Botany, Faculty of Pharmacy, University of Medicine and Pharmacy of Craiova, 2 Petru Rareş Street, 200349 Craiova, Romania
| | - Antonia Radu
- Department of Pharmaceutical Botany, Faculty of Pharmacy, University of Medicine and Pharmacy of Craiova, 2 Petru Rareş Street, 200349 Craiova, Romania
| | - Ludovic Everard Bejenaru
- Department of Pharmacognosy & Phytotherapy, Faculty of Pharmacy, University of Medicine and Pharmacy of Craiova, 2 Petru Rareş Street, 200349 Craiova, Romania
| | - Gabriela Rău
- Department of Organic Chemistry, Faculty of Pharmacy, University of Medicine and Pharmacy of Craiova, 2 Petru Rareş Street, 200349 Craiova, Romania
| | - George Dan Mogoşanu
- Department of Pharmacognosy & Phytotherapy, Faculty of Pharmacy, University of Medicine and Pharmacy of Craiova, 2 Petru Rareş Street, 200349 Craiova, Romania
| | - Johny Neamţu
- Department of Physics, Faculty of Pharmacy, University of Medicine and Pharmacy of Craiova, 2 Petru Rareş Street, 200349 Craiova, Romania
| | - Steven A. Benner
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Avenue, Room N112, Alachua, FL 32615, USA
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15
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Wang X, Zhao J, Feng Y, Feng Z, Ye Y, Liu L, Kang G, Cao X. Evolutionary Insights Into Microbiota Transplantation in Inflammatory Bowel Disease. Front Cell Infect Microbiol 2022; 12:916543. [PMID: 35811664 PMCID: PMC9257068 DOI: 10.3389/fcimb.2022.916543] [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: 04/09/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
The intestinal microbiome plays an essential role in human health and disease status. So far, microbiota transplantation is considered a potential therapeutic approach for treating some chronic diseases, including inflammatory bowel disease (IBD). The diversity of gut microbiota is critical for maintaining resilience, and therefore, transplantation with numerous genetically diverse gut microbiota with metabolic flexibility and functional redundancy can effectively improve gut health than a single probiotic strain supplement. Studies have shown that natural fecal microbiota transplantation or washing microbiota transplantation can alleviate colitis and improve intestinal dysbiosis in IBD patients. However, unexpected adverse reactions caused by the complex and unclear composition of the flora limit its wider application. The evolving strain isolation technology and modifiable pre-existing strains are driving the development of microbiota transplantation. This review summarized the updating clinical and preclinical data of IBD treatments from fecal microbiota transplantation to washing microbiota transplantation, and then to artificial consortium transplantation. In addition, the factors considered for strain combination were reviewed. Furthermore, four types of artificial consortium transplant products were collected to analyze their combination and possible compatibility principles. The perspective on individualized microbiota transplantation was also discussed ultimately.
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Affiliation(s)
- Xiaoli Wang
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Institute of Digestive Disease, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Jingwen Zhao
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Institute of Digestive Disease, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Yuanhang Feng
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Zelin Feng
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Institute of Digestive Disease, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Yulin Ye
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Institute of Digestive Disease, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Limin Liu
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Institute of Digestive Disease, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Guangbo Kang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- Institute of Shaoxing, Tianjin University, Zhejiang, China
- *Correspondence: Xiaocang Cao, ; Guangbo Kang,
| | - Xiaocang Cao
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Institute of Digestive Disease, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
- *Correspondence: Xiaocang Cao, ; Guangbo Kang,
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16
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Liu Z, Li H, Li L, Ma Q, Fang Z, Wang H, Lee Y, Zhao J, Zhang H, Chen W, Lu W. Gene-trait matching analysis reveals putative genes involved in Bifidobacterium spp. biofilm formation. Gene 2022; 826:146449. [PMID: 35337850 DOI: 10.1016/j.gene.2022.146449] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 03/07/2022] [Accepted: 03/18/2022] [Indexed: 11/04/2022]
Abstract
Biofilm formation by bacteria represents an adaptation strategy to the environment, and some special genes may lead to a strong biofilm phenotype. In this study, we attempted to find functional genes associated with bifidobacterial biofilm formation. Firstly, we evaluated the biofilm formation ability of bifidobacterial strains from six species, which showed that Bifidobacterium longum, Bifidobacterium breve, Bifidobacterium animalis, Bifidobacterium adolescentis, and Bifidobacterium pseudocatenulatum had biofilm-forming and non-biofilm-forming strains, while all Bifidobacterium bifidum strains could form strong biofilms. Then 48 strains were selected for genome sequencing and comparative analysis. The gene-trait matching analysis revealed that B. bifidum biofilm formation phenotype may associate with their unique genes, involving in stress response, quorum sensing, two components, and peptide synthesis. B. pseudocatenulatum biofilm formation was positively correlated with the eps cluster (rfbX). While no genotype related to the biofilm phenotype was found in B. longum using this analysis, but all contain autoinducer-2 (AI-2) receptor genes. Moreover, luxS, rbsB, rfbX were selected for real-time qPCR analysis, suggesting that their expression are important to biofilm formation. These results indicated that strains carrying certain genes tend to form stronger biofilms than those formed by strains without these genes.
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Affiliation(s)
- Zongmin Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Haitao Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Lingzhi Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - QingQing Ma
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - ZhiFeng Fang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Hongchao Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yuankun Lee
- Department of Microbiology & Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore; International Joint Research Laboratory for Pharmabiotics & Antibiotic Resistance, Jiangnan University, Wuxi 214122, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Wenwei Lu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; International Joint Research Laboratory for Pharmabiotics & Antibiotic Resistance, Jiangnan University, Wuxi 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China.
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17
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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: 6] [Impact Index Per Article: 3.0] [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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18
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Meng F, Zhao M, Lu Z. The LuxS/AI-2 system regulates the probiotic activities of lactic acid bacteria. Trends Food Sci Technol 2022. [DOI: 10.1016/j.tifs.2022.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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19
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Qian X, Tian P, Zhao J, Zhang H, Wang G, Chen W. Quorum Sensing of Lactic Acid Bacteria: Progress and Insights. FOOD REVIEWS INTERNATIONAL 2022. [DOI: 10.1080/87559129.2022.2062766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Xin Qian
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Peijun Tian
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou, China
- Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi, Jiangsu, China
| | - Gang Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, China
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20
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Dai Z, Wu Z, Zhu W, Wu G. Amino Acids in Microbial Metabolism and Function. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1354:127-143. [PMID: 34807440 DOI: 10.1007/978-3-030-85686-1_7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Amino acids (AAs) not only serve as building blocks for protein synthesis in microorganisms but also play important roles in their metabolism, survival, inter-species crosstalk, and virulence. Different AAs have their distinct functions in microbes of the digestive tract and this in turn has important impacts on host nutrition and physiology. Deconjugation and re-conjugation of glycine- or taurine- conjugated bile acids in the process of their enterohepatic recycling is a good example of the bacterial adaptation to harsh gut niches, inter-kingdom cross-talk with AA metabolism, and cell signaling as the critical control point. It is also a big challenge for scientists to modulate the homeostasis of the pools of AAs and their metabolites in the digestive tract with the aim to improve nutrition and regulate AA metabolism related to anti-virulence reactions. Diversity of the metabolic pathways of AAs and their multi-functions in modulating bacterial growth and survival in the digestive tract should be taken into consideration in recommending nutrient requirements for animals. Thus, the concept of functional amino acids can guide not only microbiological studies but also nutritional and physiological investigations. Cutting edge discoveries in this research area will help to better understand the mechanisms responsible for host-microbe interactions and develop new strategies for improving the nutrition, health, and well-being of both animals and humans.
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Affiliation(s)
- Zhaolai Dai
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Zhenlong Wu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Weiyun Zhu
- National Center for International Research On Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Guoyao Wu
- Department of Animal Science, Texas A&M University, College Station, 77843, TX, USA
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21
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Xiao Y, Zhao J, Zhang H, Zhai Q, Chen W. Mining genome traits that determine the different gut colonization potential of Lactobacillus and Bifidobacterium species. Microb Genom 2021; 7:000581. [PMID: 34100697 PMCID: PMC8461469 DOI: 10.1099/mgen.0.000581] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 04/12/2021] [Indexed: 12/11/2022] Open
Abstract
Although the beneficial effects of probiotics are likely to be associated with their ability to colonize the gut, little is known about the characteristics of good colonizers. In a systematic analysis of the comparative genomics, we tried to elucidate the genomic contents that account for the distinct host adaptability patterns of Lactobacillus and Bifidobacterium species. The Bifidobacterium species, with species-level phylogenetic structures affected by recombination among strains, broad mucin-foraging activity, and dietary-fibre-degrading ability, represented niche conservatism and tended to be host-adapted. The Lactobacillus species stretched across three lifestyles, namely free-living, nomadic and host-adapted, as characterized by the variations of bacterial occurrence time, guanine-cytosine (GC) content and genome size, evolution event frequency, and the presence of human-adapted bacterial genes. The numbers and activity of host-adapted factors, such as bile salt hydrolase and intestinal tissue-anchored elements, were distinctly distributed among the three lifestyles. The strains of the three lifestyles could be separated with such a collection of colonization-related genomic content (genes, genome size and GC content). Thus, our work provided valuable information for rational selection and gut engraftment prediction of probiotics. Here, we have found many interesting predictive results for bacterial gut fitness, which will be validated in vitro and in vivo.
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Affiliation(s)
- Yue Xiao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- Yangzhou Institute of Food Biotechnology, Jiangnan University, Yangzhou, Jiangsu 225004, PR China
- Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi 214122, PR China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, PR China
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22
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Research on the role of LuxS/AI-2 quorum sensing in biofilm of Leuconostoc citreum 37 based on complete genome sequencing. 3 Biotech 2021; 11:189. [PMID: 33927980 DOI: 10.1007/s13205-021-02747-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 03/15/2021] [Indexed: 12/19/2022] Open
Abstract
Leuconostoc citreum, a type of food-grade probiotic bacteria, plays an important role in food fermentation and intestinal probiotics. Biofilms help bacteria survive under adverse conditions, and LuxS/AI-2-dependent quorum sensing (QS) plays an important role in the regulation of their biofilm-forming activities. L. citreum 37 was a biofilm-forming strain isolated from dairy products. The aim of this study was to analyze genes involved in the LuxS/AI-2 system based on genome sequencing and biofilm formation of L. citreum 37. Genome assembly yielded two contigs (one chromosome and one plasmid), and the complete genome contained 1,946,279 base pairs (bps) with a G + C content of 38.91%. The genome sequence analysis showed that there were several pathways such as the two-component system, QS, and seven other signal pathways, and 26 genes (including luxS, pfs, and 24 other genes) may participate in QS related to biofilm formation. All these results showed that the LuxS/AI-2 system is complete in the genome of L. citreum 37. The quantitative polymerase chain reaction (qPCR) of pfs, luxS genes, and AI-2 production of L. citreum 37 in planktonic state and biofilm state showed that the expression of pfs and luxS genes was consistent with the production of AI-2 and was positively correlated with biofilm formation. After luxS of L. citreum 37 expressed in Escherichia coli BL21, AI-2 production was detected, suggesting that the luxS gene played an important role in AI-2 synthesis, Therefore, luxS may regulate the biofilm formation of L. citreum 37 by participating in AI-2 synthesis. It is projected that results of this study could help facilitate further understanding and application of L. citreum 37. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02747-2.
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Xiao Y, Zhai Q, Zhang H, Chen W, Hill C. Gut Colonization Mechanisms of Lactobacillus and Bifidobacterium: An Argument for Personalized Designs. Annu Rev Food Sci Technol 2021; 12:213-233. [DOI: 10.1146/annurev-food-061120-014739] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Lactobacillus and Bifidobacterium spp. are best understood for their applications as probiotics, which are often transient, but as commensals it is probable that stable colonization in the gut is important for their beneficial roles. Recent research suggests that the establishment and persistence of strains of Lactobacillus and Bifidobacterium in the gut are species- and strain-specific and affected by natural history, genomic adaptability, and metabolic interactions of the bacteria and the microbiome and immune aspects of the host but also regulated by diet. This provides new perspectives on the underlying molecular mechanisms. With an emphasis on host–microbe interaction, this review outlines how the characteristics of individual Lactobacillus and Bifidobacterium bacteria, the host genotype and microbiome structure,diet, and host–microbe coadaptation during bacterial gut transition determine and influence the colonization process. The diet-tuned and personally tailored colonization can be achieved via a machine learning prediction model proposed here.
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Affiliation(s)
- Yue Xiao
- State Key Laboratory of Food Science and Technology and School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China;, , ,
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology and School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China;, , ,
- International Joint Research Laboratory for Probiotics, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology and School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China;, , ,
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China
- Institute of Food Biotechnology, Jiangnan University, Yangzhou, Jiangsu 225004, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology and School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China;, , ,
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China
- Beijing Advanced Innovation Center of Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China
| | - Colin Hill
- School of Microbiology and APC Microbiome Institute, University College Cork, Cork T12 YN60, Ireland
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24
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Alessandri G, van Sinderen D, Ventura M. The genus bifidobacterium: From genomics to functionality of an important component of the mammalian gut microbiota running title: Bifidobacterial adaptation to and interaction with the host. Comput Struct Biotechnol J 2021; 19:1472-1487. [PMID: 33777340 PMCID: PMC7979991 DOI: 10.1016/j.csbj.2021.03.006] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/03/2021] [Accepted: 03/03/2021] [Indexed: 02/07/2023] Open
Abstract
Members of the genus Bifidobacterium are dominant and symbiotic inhabitants of the mammalian gastrointestinal tract. Being vertically transmitted, bifidobacterial host colonization commences immediately after birth and leads to a phase of host infancy during which bifidobacteria are highly prevalent and abundant to then transit to a reduced, yet stable abundance phase during host adulthood. However, in order to reach and stably colonize their elective niche, i.e. the large intestine, bifidobacteria have to cope with a multitude of oxidative, osmotic and bile salt/acid stress challenges that occur along the gastrointestinal tract (GIT). Concurrently, bifidobacteria not only have to compete with the myriad of other gut commensals for nutrient acquisition, but they also require protection against bacterial viruses. In this context, Next-Generation Sequencing (NGS) techniques, allowing large-scale comparative and functional genome analyses have helped to identify the genetic strategies that bifidobacteria have developed in order to colonize, survive and adopt to the highly competitive mammalian gastrointestinal environment. The current review is aimed at providing a comprehensive overview concerning the molecular strategies on which bifidobacteria rely to stably and successfully colonize the mammalian gut.
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Affiliation(s)
- Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Ireland and School of Microbiology, University College Cork, Western Road, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.,Microbiome Research Hub, University of Parma, Parma, Italy
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25
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A Resource for Cloning and Expression Vectors Designed for Bifidobacteria: Overview of Available Tools and Biotechnological Applications. Methods Mol Biol 2021. [PMID: 33649956 DOI: 10.1007/978-1-0716-1274-3_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2023]
Abstract
Bifidobacteria represent an important group of (mostly) commensal microorganisms, which have enjoyed increasing scientific and industrial attention due to their purported health-promoting attributes. For the latter reason, several species have been granted "generally recognized as safe" (GRAS) and "qualified presumption of safety" (QPS) status by the Food and Drugs Administration (FDA) and European Food Safety Authority (EFSA) organizations. Increasing scientific evidence supports their potential as oral delivery vectors to produce bioactive and therapeutic molecules at intestinal level. In order to achieve an efficient utilization of bifidobacterial strains as health-promoting (food) ingredients, it is necessary to provide evidence on the molecular mechanisms behind their purported beneficial and probiotic traits, and precise mechanisms of interaction with their human (or other mammalian) host. In this context, developing appropriate molecular tools to generate and investigate recombinant strains is necessary. While bifidobacteria have long remained recalcitrant to genetic manipulation, a wide array of Bifidobacterium-specific replicating vectors and genetic modification procedures have been described in literature. The current chapter intends to provide an updated overview on the vectors used to genetically modify and manipulate bifidobacteria, including their general characteristics, reviewing examples of their use to successfully generate recombinant bifidobacterial strains for specific purposes, and providing a general workflow and cautions to design and conduct heterologous expression in bifidobacteria. Knowledge gaps and fields of research that may help to widen the molecular toolbox to improve the functional and technological potential of bifidobacteria are also discussed.
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26
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Transcriptome Analysis Reveals the Genes Involved in Bifidobacterium Longum FGSZY16M3 Biofilm Formation. Microorganisms 2021; 9:microorganisms9020385. [PMID: 33672820 PMCID: PMC7917626 DOI: 10.3390/microorganisms9020385] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 01/29/2021] [Accepted: 02/08/2021] [Indexed: 12/11/2022] Open
Abstract
Biofilm formation has evolved as an adaptive strategy for bacteria to cope with harsh environmental conditions. Currently, little is known about the molecular mechanisms of biofilm formation in bifidobacteria. A time series transcriptome sequencing analysis of both biofilm and planktonic cells of Bifidobacterium longum FGSZY16M3 was performed to identify candidate genes involved in biofilm formation. Protein–protein interaction network analysis of 1296 differentially expressed genes during biofilm formation yielded 15 clusters of highly interconnected nodes, indicating that genes related to the SOS response (dnaK, groS, guaB, ruvA, recA, radA, recN, recF, pstA, and sufD) associated with the early stage of biofilm formation. Genes involved in extracellular polymeric substances were upregulated (epsH, epsK, efp, frr, pheT, rfbA, rfbJ, rfbP, rpmF, secY and yidC) in the stage of biofilm maturation. To further investigate the genes related to biofilm formation, weighted gene co-expression network analysis (WGCNA) was performed with 2032 transcript genes, leading to the identification of nine WGCNA modules and 133 genes associated with response to stress, regulation of gene expression, quorum sensing, and two-component system. These results indicate that biofilm formation in B. longum is a multifactorial process, involving stress response, structural development, and regulatory processes.
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27
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Wu L, Luo Y. Bacterial Quorum-Sensing Systems and Their Role in Intestinal Bacteria-Host Crosstalk. Front Microbiol 2021; 12:611413. [PMID: 33584614 PMCID: PMC7876071 DOI: 10.3389/fmicb.2021.611413] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 01/12/2021] [Indexed: 02/05/2023] Open
Abstract
Quorum-sensing (QS) system is a rapidly developing field in which we are gradually expanding our understanding about how bacteria communicate with each other and regulate their activities in bacterial sociality. In addition to collectively modifying bacterial behavior, QS-related autoinducers may also be embedded in the crosstalk between host and parasitic microbes. In this review, we summarize current studies on QS in the intestinal microbiome field and its potential role in maintaining homeostasis under physiological conditions. Additionally, we outline the canonical autoinducers and their related QS signal-response systems by which several pathogens interact with the host under pathological conditions, with the goal of better understanding intestinal bacterial sociality and facilitating novel antimicrobial therapeutic strategies.
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Affiliation(s)
- Liang Wu
- Department of Rheumatology and Immunology, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Institute of Immunology and Inflammation, Sichuan University, Chengdu, China
| | - Yubin Luo
- Department of Rheumatology and Immunology, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Institute of Immunology and Inflammation, Sichuan University, Chengdu, China
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28
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Haque M, Islam S, Sheikh MA, Dhingra S, Uwambaye P, Labricciosa FM, Iskandar K, Charan J, Abukabda AB, Jahan D. Quorum sensing: a new prospect for the management of antimicrobial-resistant infectious diseases. Expert Rev Anti Infect Ther 2020; 19:571-586. [PMID: 33131352 DOI: 10.1080/14787210.2021.1843427] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Quorum-sensing (QS) is a microbial cell-to-cell communication system that utilizes small signaling molecules to mediates interactions between cross-kingdom microorganisms, including Gram-positive and -negative microbes. QS molecules include N-acyl-homoserine-lactones (AHLs), furanosyl borate, hydroxyl-palmitic acid methylester, and methyl-dodecanoic acid. These signaling molecules maintain the symbiotic relationship between a host and the healthy microbial flora and also control various microbial virulence factors. This manuscript has been developed based on published scientific papers. AREAS COVERED Furanones, glycosylated chemicals, heavy metals, and nanomaterials are considered QS inhibitors (QSIs) and are therefore capable of inhibiting the microbial QS system. QSIs are currently being considered as antimicrobial therapeutic options. Currently, the low speed at which new antimicrobial agents are being developed impairs the treatment of drug-resistant infections. Therefore, QSIs are currently being studied as potential interventions targeting QS-signaling molecules and quorum quenching (QQ) enzymes to reduce microbial virulence. EXPERT OPINION QSIs represent a novel opportunity to combat antimicrobial resistance (AMR). However, no clinical trials have been conducted thus far assessing their efficacy. With the recent advancements in technology and the development of well-designed clinical trials aimed at targeting various components of the, QS system, these agents will undoubtedly provide a useful alternative to treat infectious diseases.
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Affiliation(s)
- Mainul Haque
- Faculty of Medicine and Defence Health, Universiti Pertahanan Nasional Malaysia (National Defence University of Malaysia), Kuala Lumpur, Malaysia
| | - Salequl Islam
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | | | - Sameer Dhingra
- School of Pharmacy, Faculty of Medical Sciences, The University of the West Indies, St. Augustine Campus, Eric Williams Medical Sciences Complex, Trinidad & Tobago
| | - Peace Uwambaye
- Department of Preventive & Community Dentistry, University of Rwanda College of Medicine and Health Sciences, School of Dentistry, Kigali, Rwanda
| | | | - Katia Iskandar
- Department of Mathématiques Informatique et Télécommunications, Université Toulouse III, Paul Sabatier, INSERM, UMR 1027, F-31000 Toulouse, France.,INSPECT-LB: Institut National de Santé Publique, d'Épidémiologie Clinique et de Toxicologie-Liban, Beirut 6573-14, Lebanon.,Faculty of Pharmacy, Lebanese University, Beirut 1106, Lebanon
| | - Jaykaran Charan
- Department of Pharmacology, All India Institute of Medical Sciences, Jodhpur, Rajasthan, India
| | | | - Dilshad Jahan
- Department of Hematology, Asgar Ali Hospital, Dhaka, Bangladesh
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29
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Competitors versus Collaborators: Micronutrient Processing by Pathogenic and Commensal Human-Associated Gut Bacteria. Mol Cell 2020; 78:570-576. [PMID: 32442503 DOI: 10.1016/j.molcel.2020.03.032] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 03/24/2020] [Accepted: 03/25/2020] [Indexed: 12/18/2022]
Abstract
Co-evolution of gut commensal bacteria and humans has ensured that the micronutrient needs of both parties are met. This minireview summarizes the known molecular mechanisms of iron, zinc, and B vitamin processing by human-associated bacteria, comparing gut pathogens and commensals, and highlights the tension between their roles as competitors versus collaborators with the human host.
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30
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Ishikawa KH, Mita D, Kawamoto D, Nicoli JR, Albuquerque-Souza E, Lorenzetti Simionato MR, Mayer MPA. Probiotics alter biofilm formation and the transcription of Porphyromonas gingivalis virulence-associated genes. J Oral Microbiol 2020; 12:1805553. [PMID: 32944156 PMCID: PMC7482675 DOI: 10.1080/20002297.2020.1805553] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Background and Objective The potential of probiotics on the prevention and control of periodontitis and other chronic inflammatory conditions has been suggested. Lactobacillus and Bifidobacterium species influence P. gingivalis interaction with gingival epithelial cells (GECs) but may not act in a unique way. In order to select the most appropriate probiotic against P. gingivalis, we aimed to evaluate the effect of several strains on Porphyromonas gingivalis biofilm formation and transcription virulence-associated factors (PgVAFs). Methods Cell-free pH neutralized supernatants (CFS) and living Lactobacillus spp. and Bifidobacterium spp. were tested against P. gingivalis ATCC 33277 and W83, in mono- and multi-species (with Streptococcus oralis and S. gordonii) biofilms. Relative transcription of P. gingivalis genes (fimA, mfa1, kgp, rgp, ftsH and luxS) was determined in biofilms and under GECs co-infection. Results Probiotics CFS reduced P. gingivalis ATCC 33277 levels in mono-species biofilms and living probiotics reduced P. gingivalis abundance in multi-species biofilms. L. acidophilus LA5 down-regulated transcription of most PgVAFs in biofilms and GECs. Conclusions Probiotics affect P. gingivalis biofilm formation by down-regulating overall PgVAFs with the most pronounced effect observed for L. acidophilus LA5.
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Affiliation(s)
- Karin Hitomi Ishikawa
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Daniela Mita
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Dione Kawamoto
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Jacques Robert Nicoli
- Department of Microbiology, Biological Science Institute, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Emmanuel Albuquerque-Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Division of Periodontics, Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | | | - Marcia Pinto Alves Mayer
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Division of Periodontics, Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo, Brazil
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31
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Microbiota Changes Due to Grape Seed Extract Diet Improved Intestinal Homeostasis and Decreased Fatness in Parental Broiler Hens. Microorganisms 2020; 8:microorganisms8081141. [PMID: 32731511 PMCID: PMC7465624 DOI: 10.3390/microorganisms8081141] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/25/2020] [Accepted: 07/27/2020] [Indexed: 11/16/2022] Open
Abstract
In poultry, the selection of broilers for growth performance has induced a deterioration in the health of the parental hens associated with poor reproductive efficiency. To improve these parameters, we administered to laying parental broiler hens a regular diet supplemented or not (Control) with a moderate (1%) or a high level (2%) of grape seed extract (GSE). The 1% GSE diet was administered from a young age (from 4 to 40 weeks of age) and the high level of 2% GSE was administered only during a 2-week period (from 38 to 40 weeks of age) in the laying period. The analysis of 40-week-old hens showed that 2% GSE displayed a reduction in the fat tissue and an improvement in fertility with heavier and more resistant eggs. Seven monomer phenolic metabolites of GSE were significantly measured in the plasma of the 2% GSE hens. GSE supplementation increased the relative abundance of the following bacteria populations: Bifidobacteriaceae, Lactobacilliaceae and Lachnospiraceae. In conclusion, a supplementation period of only 2 weeks with 2% GSE is sufficient to improve the metabolic and laying parameters of breeder hens through a modification in the microbiota.
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32
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Bulgart HR, Neczypor EW, Wold LE, Mackos AR. Microbial involvement in Alzheimer disease development and progression. Mol Neurodegener 2020; 15:42. [PMID: 32709243 PMCID: PMC7382139 DOI: 10.1186/s13024-020-00378-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 04/29/2020] [Indexed: 02/08/2023] Open
Abstract
Alzheimer disease (AD) is the most prominent form of dementia and the 5th leading cause of death in individuals over 65. AD is a complex disease stemming from genetic, environmental, and lifestyle factors. It is known that AD patients have increased levels of senile plaques, neurofibrillary tangles, and neuroinflammation; however, the mechanism(s) by which the plaques, tangles, and neuroinflammation manifest remain elusive. A recent hypothesis has emerged that resident bacterial populations contribute to the development and progression of AD by contributing to neuroinflammation, senile plaque formation, and potentially neurofibrillary tangle accumulation (Fig. 1). This review will highlight recent studies involved in elucidating microbial involvement in AD development and progression.
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Affiliation(s)
- Hannah R. Bulgart
- Biomedical Sciences Graduate Program, College of Medicine, The Ohio State University, Columbus, OH USA
| | - Evan W. Neczypor
- Dorothy M. Davis Heart and Lung Research Institute, College of Medicine, The Ohio State University, Columbus, OH USA
- College of Nursing, The Ohio State University, 1585 Neil Ave, Columbus, OH 43210 USA
| | - Loren E. Wold
- Dorothy M. Davis Heart and Lung Research Institute, College of Medicine, The Ohio State University, Columbus, OH USA
- College of Nursing, The Ohio State University, 1585 Neil Ave, Columbus, OH 43210 USA
- Department of Physiology and Cell Biology, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH USA
| | - Amy R. Mackos
- College of Nursing, The Ohio State University, 1585 Neil Ave, Columbus, OH 43210 USA
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33
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Kelly SM, Lanigan N, O'Neill IJ, Bottacini F, Lugli GA, Viappiani A, Turroni F, Ventura M, van Sinderen D. Bifidobacterial biofilm formation is a multifactorial adaptive phenomenon in response to bile exposure. Sci Rep 2020; 10:11598. [PMID: 32665665 PMCID: PMC7360559 DOI: 10.1038/s41598-020-68179-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 05/28/2020] [Indexed: 12/20/2022] Open
Abstract
In the current study, we show that biofilm formation by various strains and species belonging to Bifidobacterium, a genus that includes gut commensals with reported health-promoting activities, is induced by high concentrations of bile (0.5% (w/v) or higher) and individual bile salts (20 mM or higher), rather than by acid or osmotic stress. The transcriptomic response of a bifidobacterial prototype Bifidobacterium breve UCC2003 to such high bile concentrations was investigated and a random transposon bank of B. breve UCC2003 was screened for mutants that affect biofilm formation in order to identify genes involved in this adaptive process. Eleven mutants affected in their ability to form a biofilm were identified, while biofilm formation capacity of an insertional mutation in luxS and an exopolysaccharide (EPS) negative B. breve UCC2003 was also studied. Reduced capacity to form biofilm also caused reduced viability when exposed to porcine bile. We propose that bifidobacterial biofilm formation is an adaptive response to high concentrations of bile in order to avoid bactericidal effects of high bile concentrations in the gastrointestinal environment. Biofilm formation appears to be a multi-factorial process involving EPS production, proteins and extracellular DNA release, representing a crucial strategy in response to bile stress in order to enhance fitness in the gut environment.
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Affiliation(s)
- Sandra M Kelly
- School of Microbiology, University College Cork, Western Road, Cork, Ireland.,APC Microbiome Ireland, University College Cork, Western Road, Cork, Ireland
| | - Noreen Lanigan
- School of Microbiology, University College Cork, Western Road, Cork, Ireland.,APC Microbiome Ireland, University College Cork, Western Road, Cork, Ireland
| | - Ian J O'Neill
- APC Microbiome Ireland, University College Cork, Western Road, Cork, Ireland
| | - Francesca Bottacini
- APC Microbiome Ireland, University College Cork, Western Road, Cork, Ireland
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.,Microbiome Research Hub, University of Parma, Parma, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.,Microbiome Research Hub, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, Western Road, Cork, Ireland. .,APC Microbiome Ireland, University College Cork, Western Road, Cork, Ireland.
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34
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Fu CY, Li LQ, Yang T, She X, Ai Q, Wang ZL. Autoinducer-2 May Be a New Biomarker for Monitoring Neonatal Necrotizing Enterocolitis. Front Cell Infect Microbiol 2020; 10:140. [PMID: 32373545 PMCID: PMC7179697 DOI: 10.3389/fcimb.2020.00140] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 03/18/2020] [Indexed: 12/19/2022] Open
Abstract
Autoinducer-2 (AI-2) has a widely accepted role in bacterial intra- and interspecies communication. Little is known about the relationships between AI-2 and NEC. This study found that AI-2 levels in patients and in a NEC mouse model were detected using the Vibrio harveyi BB170 assay system. Bacterial communities of the newborns' stool microbiota (NEC acute group, NEC recovery group, control group, and antibiotics-free group) and of the NEC mouse model (NEC group and control group) were detected by high-throughput sequencing. Intestinal histopathological changes were observed after HE staining. The AI-2 level in the NEC acute group (44.75 [40.17~65.52]) was significantly lower than that in the control group, NEC recovery group and antibiotics-free group. The overall microbiota compositions of each group at the phylum level were not significantly different. The proportions of Enterococcus, Clostridium_sensu_stricto_1, Peptoclostridium, and Veillonella had significant differences among the 4 groups at the genus level. In animal experiments, the AI-2 level in feces of NEC mice (56.89 ± 11.87) was significantly lower than that in the feces of control group mice (102.70 ± 22.97). The microbiota compositions of NEC and control group mice at the phylum level were not significantly different. At the genus level, Klebsiella, Clostridium_sensu_stricto_1, and Peptoclostridium abundances in the NEC group increased significantly compared with those in the control group (P < 0.05). In addition, Lactobacillus, Pasteurella, and Parabacteroides abundances in the NEC group decreased significantly compared with those in the normal control group (P < 0.05), while Lactobacillus, Pasteurella, and Parabacteroides abundances had the opposite trend. The AI-2 concentration decreased significantly in the acute phase of NEC and increased gradually in the convalescent phase. We conclude that the concentration of AI-2 was correlated with intestinal flora disorder and different stages of disease. AI-2 may be a new biomarker for the diagnosis and monitoring of NEC. Trial Registry: ClinicalTrials.gov; ChiCTR-ROC-17013746; URL: www.clinicaltrials.gov.
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Affiliation(s)
- Chun-Yan Fu
- Department of Neonatal Diagnosis and Treatment Center, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China.,National Clinical Research Center for Child Health and Disorders, Chongqing, China.,China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing, China.,Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Chongqing, China
| | - Lu-Quan Li
- Department of Neonatal Diagnosis and Treatment Center, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China.,National Clinical Research Center for Child Health and Disorders, Chongqing, China.,China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing, China.,Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Chongqing, China
| | - Ting Yang
- Department of Neonatal Diagnosis and Treatment Center, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China.,National Clinical Research Center for Child Health and Disorders, Chongqing, China.,China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing, China.,Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Chongqing, China
| | - Xiang She
- Department of Neonatal Diagnosis and Treatment Center, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China.,National Clinical Research Center for Child Health and Disorders, Chongqing, China.,China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing, China.,Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Chongqing, China
| | - Qing Ai
- Department of Neonatal Diagnosis and Treatment Center, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China.,National Clinical Research Center for Child Health and Disorders, Chongqing, China.,China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing, China.,Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Chongqing, China
| | - Zheng-Li Wang
- Department of Neonatal Diagnosis and Treatment Center, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China.,National Clinical Research Center for Child Health and Disorders, Chongqing, China.,China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing, China.,Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Chongqing, China
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35
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Gu Y, Wu J, Tian J, Li L, Zhang B, Zhang Y, He Y. Effects of Exogenous Synthetic Autoinducer-2 on Physiological Behaviors and Proteome of Lactic Acid Bacteria. ACS OMEGA 2020; 5:1326-1335. [PMID: 32010802 PMCID: PMC6990425 DOI: 10.1021/acsomega.9b01021] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 01/03/2020] [Indexed: 06/10/2023]
Abstract
Bacterial populations use a cell-to-cell communication system to coordinate community-wide regulation processes, which is termed quorum sensing (QS). Autoinducer-2 (AI-2) is a universal signal molecule that mediates inter- and intraspecies QS systems among different bacteria. In this study, the effects of exogenous addition of AI-2 synthesized in vitro on physiological behaviors and proteome were investigated in lactic acid bacteria strains. Exogenous AI-2 had a concentration-dependent effect on the Enterococcus faecium 8-3 cell density. There was no significant influence on biofilm formation and individual morphology of cells upon 60 μM AI-2 addition in E. faecium 8-3 and Lactobacillus fermentum 2-1. However, it improved the acid and alkali resistance of E. faecium 8-3. With the addition of AI-2, 15 differentially expressed proteins were identified in E. faecium 8-3, which participate in RNA transport signaling, RNA polymerase, ribosome, oxidative phosphorylation, cysteine and methionine metabolism, pyrimidine metabolism, ATP-binding cassette (ABC) transporters, purine metabolism, biosynthesis of the amino acid pathway, etc. Among them, the expression of 5-methylthioadenosine/S-adenosylhomocysteine nucleosidase, which is known to be involved in AI-2 synthesis and cysteine and amino acid metabolism, was upregulated. These findings will lay the foundation to clarify the mechanism of cell-to-cell communication and bacterial physiological behaviors mediated by AI-2.
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36
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Yi J, Zhang D, Cheng Y, Tan J, Luo Y. The impact of Paenibacillus polymyxa HY96-2 luxS on biofilm formation and control of tomato bacterial wilt. Appl Microbiol Biotechnol 2019; 103:9643-9657. [PMID: 31686149 PMCID: PMC6867978 DOI: 10.1007/s00253-019-10162-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 08/27/2019] [Accepted: 09/28/2019] [Indexed: 12/24/2022]
Abstract
The focus of this study was to investigate the effects of luxS, a key regulatory gene of the autoinducer-2 (AI-2) quorum sensing (QS) system, on the biofilm formation and biocontrol efficacy against Ralstonia solanacearum by Paenibacillus polymyxa HY96-2. luxS mutants were constructed and assayed for biofilm formation of the wild-type (WT) strain and luxS mutants of P. polymyxa HY96-2 in vitro and in vivo. The results showed that luxS positively regulated the biofilm formation of HY96-2. Greenhouse experiments of tomato bacterial wilt found that from the early stage to late stage postinoculation, the biocontrol efficacy of the luxS deletion strain was the lowest with 50.70 ± 1.39% in the late stage. However, the luxS overexpression strain had the highest biocontrol efficacy with 75.66 ± 1.94% in the late stage. The complementation of luxS could restore the biocontrol efficacy of the luxS deletion strain with 69.84 ± 1.09% in the late stage, which was higher than that of the WT strain with 65.94 ± 2.73%. Therefore, we deduced that luxS could promote the biofilm formation of P. polymyxa HY96-2 and further promoted its biocontrol efficacy against R. solanacearum.
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Affiliation(s)
- Jincui Yi
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Daojing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Yuejuan Cheng
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Jingjing Tan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Yuanchan Luo
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
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Krzyżek P. Challenges and Limitations of Anti-quorum Sensing Therapies. Front Microbiol 2019; 10:2473. [PMID: 31736912 PMCID: PMC6834643 DOI: 10.3389/fmicb.2019.02473] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 10/15/2019] [Indexed: 12/15/2022] Open
Abstract
Quorum sensing (QS) is a mechanism allowing microorganisms to sense population density and synchronously control genes expression. It has been shown that QS supervises the activity of many processes important for microbial pathogenicity, e.g., sporulation, biofilm formation, and secretion of enzymes or membrane vesicles. This contributed to the concept of anti-QS therapy [also called quorum quenching (QQ)] and the opportunity of its application in fighting against various types of pathogens. In recent years, many published articles reported promising results indicating the possibility of reducing pathogenicity of tested microorganisms and their easier eradication when co-treated with antibiotics. The aim of the present article is to point to the opposite, negative side of the QQ therapy, with particular emphasis on three fundamental properties attributed to anti-QS substances: the selectivity, virulence reduction, and lack of resistance against QQ. This point of view may highlight new directions of research, which should be taken into account in the future before the widespread introduction of QQ therapies in the treatment of people.
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Affiliation(s)
- Paweł Krzyżek
- Department of Microbiology, Wroclaw Medical University, Wrocław, Poland
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38
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Caenorhabditis Elegans and Probiotics Interactions from a Prolongevity Perspective. Int J Mol Sci 2019; 20:ijms20205020. [PMID: 31658751 PMCID: PMC6834311 DOI: 10.3390/ijms20205020] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/09/2019] [Accepted: 10/10/2019] [Indexed: 02/08/2023] Open
Abstract
Probiotics exert beneficial effects on host health through different mechanisms of action, such as production of antimicrobial substances, competition with pathogens, enhancement of host mucosal barrier integrity and immunomodulation. In the context of ageing, which is characterized by several physiological alterations leading to a low grade inflammatory status called inflammageing, evidences suggest a potential prolongevity role of probiotics. Unraveling the mechanisms underlying anti-ageing effects requires the use of simple model systems. To this respect, the nematode Caenorhabditis elegans represents a suitable model organism for the study of both host-microbe interactions and for ageing studies, because of conserved signaling pathways and host defense mechanisms involved in the regulation of its lifespan. Therefore, this review analyses the impact of probiotics on C. elegans age-related parameters, with particular emphasis on oxidative stress, immunity, inflammation and protection from pathogen infections. The picture emerging from our analysis highlights that several probiotic strains are able to exert anti-ageing effects in nematodes by acting on common molecular pathways, such as insulin/insulin-like growth factor-1 (IIS) and p38 mitogen-activated protein kinase (p38 MAPK). In this perspective, C. elegans appears to be advantageous for shedding light on key mechanisms involved in host prolongevity in response to probiotics supplementation.
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39
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Mining Lactobacillus and Bifidobacterium for organisms with long-term gut colonization potential. Clin Nutr 2019; 39:1315-1323. [PMID: 31174942 DOI: 10.1016/j.clnu.2019.05.014] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/01/2019] [Accepted: 05/17/2019] [Indexed: 11/20/2022]
Abstract
Probiotics administered orally endure one of two fates: some merely pass through, but others colonize the gut permanently. Although probiotics that can stably engraft in the gut are believed to exert beneficial effects on the host in terms of increasing the efficiency of metabolic activity and enabling durable modulation of the indigenous microbiota, the strains of long-term gut colonizers are poorly delineated. This review summarizes the gut colonization modes of Lactobacillus and Bifidobacterium in the context of their natural niches and engraftment metadata in an attempt to identify organisms with long-term gut colonization potential. Advances in colonization evaluation methods are identified, and the effects of dietary components and metabolic interactions among ingested strains on bacterial colonization are discussed.
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40
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Cerdó T, Ruiz A, Acuña I, Jáuregui R, Jehmlich N, Haange SB, von Bergen M, Suárez A, Campoy C. Gut microbial functional maturation and succession during human early life. Environ Microbiol 2018; 20:2160-2177. [PMID: 29687552 DOI: 10.1111/1462-2920.14235] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 04/08/2018] [Indexed: 12/20/2022]
Abstract
The evolutional trajectory of gut microbial colonization from birth has been shown to prime for health later in life. Here, we combined cultivation-independent 16S rRNA gene sequencing and metaproteomics to investigate the functional maturation of gut microbiota in faecal samples from full-term healthy infants collected at 6 and 18 months of age. Phylogenetic analysis of the metaproteomes showed that Bifidobacterium provided the highest number of distinct protein groups. Considerable divergences between taxa abundance and protein phylogeny were observed at all taxonomic ranks. Age had a profound effect on early microbiota where compositional and functional diversity of less dissimilar communities increased with time. Comparisons of the relative abundances of proteins revealed the transition of taxon-associated saccharolytic and fermentation strategies from milk and mucin-derived monosaccharide catabolism feeding acetate/propanoate synthesis to complex food-derived hexoses fuelling butanoate production. Furthermore, co-occurrence network analysis uncovered two anti-correlated modules of functional taxa. A low-connected Bifidobacteriaceae-centred guild of facultative anaerobes was succeeded by a rich club of obligate anaerobes densely interconnected around Lachnospiraceae, underpinning their pivotal roles in microbial ecosystem assemblies. Our findings establish a framework to visualize whole microbial community metabolism and ecosystem succession dynamics, proposing opportunities for microbiota-targeted health-promoting strategies early in life.
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Affiliation(s)
- Tomás Cerdó
- Department of Paediatrics, School of Medicine, University of Granada, Granada, Spain.,EURISTIKOS Excellence Centre for Paediatric Research, Biomedical Research Centre, University of Granada, Granada, Spain
| | - Alicia Ruiz
- EURISTIKOS Excellence Centre for Paediatric Research, Biomedical Research Centre, University of Granada, Granada, Spain.,Department of Biochemistry and Molecular Biology 2, Biomedical Research Centre, University of Granada, Spain
| | - Inmaculada Acuña
- Department of Biochemistry and Molecular Biology 2, Biomedical Research Centre, University of Granada, Spain
| | - Ruy Jáuregui
- AgResearch Grasslands, Tennent Drive, Private Bag 11008, Palmerston North, New Zealand
| | - Nico Jehmlich
- Department of Molecular System Biology, Helmholtz Centre for Environmental Research- UFZ, Permoserstraße 15, Leipzig, Germany
| | - Sven-Bastian Haange
- Department of Molecular System Biology, Helmholtz Centre for Environmental Research- UFZ, Permoserstraße 15, Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular System Biology, Helmholtz Centre for Environmental Research- UFZ, Permoserstraße 15, Leipzig, Germany
| | - Antonio Suárez
- Department of Biochemistry and Molecular Biology 2, Biomedical Research Centre, University of Granada, Spain
| | - Cristina Campoy
- Department of Paediatrics, School of Medicine, University of Granada, Granada, Spain.,EURISTIKOS Excellence Centre for Paediatric Research, Biomedical Research Centre, University of Granada, Granada, Spain.,Spanish Network of Biomedical Research in Epidemiology and Public Health (CIBERESP), Carlos III Institute, Granada node, Spain
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41
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Song J, Qin Q, Li T, Ren F, Zhang H, Xie Y, Jin J. Impact of carbohydrates on autoinducer-2 secretion of Bifidobacterium longum subsp. longum BBMN68. Lett Appl Microbiol 2018; 66:340-346. [PMID: 29356014 DOI: 10.1111/lam.12854] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 11/27/2017] [Accepted: 01/16/2018] [Indexed: 01/27/2023]
Abstract
In this study, the regularity of autoinducer-2 (AI-2) secretion during growth and the effect of the addition of various carbohydrates on AI-2 secretion in Bifidobacterium longum subsp. longum BBMN68 were investigated. The results indicated that the AI-2 concentration reached its highest level (2536·60 nmol l-1 ) at the early stationary growth phase, and then decreased to 1263·72 nmol l-1 at the late stationary growth phase in Bifidobacterium cultures. When the density of the cultures which mannose, fructose, sucrose and lactose had been added to reached an OD600 nm of 1·0, the AI-2 concentrations in the cultures were 1953·84, 1637·34, 1200·99 and 1077·60 nmol l-1 , respectively. These concentrations were all significantly higher than that of the control culture (1031·33 nmol l-1 ). Similarly, the addition of fructooligosaccharide significantly increased the AI-2 concentrations to 2094·29 nmol l-1 . This study provides the advanced evidence that certain carbohydrates promote the secretion of AI-2, and that this occurs at the single cell level and is therefore unaffected by cell density. SIGNIFICANCE AND IMPACT OF THE STUDY This study provided the advanced data of the regularity of autoinducer-2 (AI-2) secretion during growth and the promotion on AI-2 secretion of different added carbohydrates in Bifidobacterium, which may be a new potential strategy to improve the acid resistance of Bifidobacterium applied in the food industry.
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Affiliation(s)
- J Song
- Food Science and Engineering College, Beijing University of Agriculture, Beijing Laboratory of Food Quality and Safety, Beijing Key Laboratory of Detection and Control of Spoilage Organisms and Pesticide Residues in Agricultural Products, Beijing, China
| | - Q Qin
- China Youth University for Political Sciences, Beijing, China
| | - T Li
- Food Science and Engineering College, Beijing University of Agriculture, Beijing Laboratory of Food Quality and Safety, Beijing Key Laboratory of Detection and Control of Spoilage Organisms and Pesticide Residues in Agricultural Products, Beijing, China
| | - F Ren
- The Innovation Centre of Food Nutrition and Human Health (Beijing), Beijing Higher Institution Engineering Research Centre of Animal Product, College of Food Science and Nutritional Engineering, China Agriculture University, Beijing, China
| | - H Zhang
- Food Science and Engineering College, Beijing University of Agriculture, Beijing Laboratory of Food Quality and Safety, Beijing Key Laboratory of Detection and Control of Spoilage Organisms and Pesticide Residues in Agricultural Products, Beijing, China
| | - Y Xie
- Food Science and Engineering College, Beijing University of Agriculture, Beijing Laboratory of Food Quality and Safety, Beijing Key Laboratory of Detection and Control of Spoilage Organisms and Pesticide Residues in Agricultural Products, Beijing, China
| | - J Jin
- Food Science and Engineering College, Beijing University of Agriculture, Beijing Laboratory of Food Quality and Safety, Beijing Key Laboratory of Detection and Control of Spoilage Organisms and Pesticide Residues in Agricultural Products, Beijing, China
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42
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Rios-Covian D, Nogacka A, Salazar N, Hernández-Barranco AM, Cuesta I, Gueimonde M, de Los Reyes Gavilán CG. Bifidobacterium breve IPLA20005 affects in vitro the expression of hly and luxS genes, related to the virulence of Listeria monocytogenes Lm23. Can J Microbiol 2018; 64:215-221. [PMID: 29298396 DOI: 10.1139/cjm-2017-0625] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mechanistic features that characterize the interaction and inhibition of the food-borne pathogen Listeria monocytogenes by members of the genus Bifidobacterium still remain unclear. In the present work, we tried to shed light on the influence that co-cultivation of L. monocytogenes with Bifidobacterium breve may exert on both microorganisms and on virulence of the pathogen. Production of acetate and lactate was measured by gas chromatography and high-performance liquid chromatography, respectively; bacterial counts were obtained by plate count; gene expression was determined by RT-qPCR; and haemolytic activity was analyzed against goat erythrocytes. We found slightly but significantly lower final counts of Listeria and Bifidobacterium (p < 0.05) and lower haemolytic efficiency in L. monocytogenes cells from cocultures than in those from monocultures. In contrast, the hly and luxS genes, which code for the cytolysin listeriolysin O and participate in biofilm formation, respectively, were overexpressed when L. monocytogenes was grown in coculture. This indicates that the presence of Bifidobacterium is able to modify the gene expression and haemolytic activity of L. monocytogenes when both microorganisms grow together.
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Affiliation(s)
- David Rios-Covian
- a Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas, Villaviciosa, Asturias, Spain
| | - Alicja Nogacka
- a Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas, Villaviciosa, Asturias, Spain.,b Diet, Microbiota and Health group, Instituto de Investigación Sanitaria del Principado de Asturias, Asturias, Spain
| | - Nuria Salazar
- a Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas, Villaviciosa, Asturias, Spain.,b Diet, Microbiota and Health group, Instituto de Investigación Sanitaria del Principado de Asturias, Asturias, Spain
| | - A M Hernández-Barranco
- c Scientific and Technical Facilities, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas, Villaviciosa, Asturias, Spain
| | - Isabel Cuesta
- c Scientific and Technical Facilities, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas, Villaviciosa, Asturias, Spain
| | - Miguel Gueimonde
- a Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas, Villaviciosa, Asturias, Spain.,b Diet, Microbiota and Health group, Instituto de Investigación Sanitaria del Principado de Asturias, Asturias, Spain
| | - Clara G de Los Reyes Gavilán
- a Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas, Villaviciosa, Asturias, Spain.,b Diet, Microbiota and Health group, Instituto de Investigación Sanitaria del Principado de Asturias, Asturias, Spain
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43
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Song XD, Liu CJ, Huang SH, Li XR, Yang E, Luo YY. Cloning, expression and characterization of two S-ribosylhomocysteine lyases from Lactobacillus plantarum YM-4-3: Implication of conserved and divergent roles in quorum sensing. Protein Expr Purif 2018; 145:32-38. [PMID: 29305177 DOI: 10.1016/j.pep.2017.12.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 11/03/2017] [Accepted: 12/27/2017] [Indexed: 12/31/2022]
Abstract
Quorum sensing (QS) is a means of cell-to-cell communication that regulates, via small signalling molecules, expression of a series of genes and controls multicellular behaviour in many bacterial species. The enzyme S-ribosylhomocysteine lyase (LuxS) transforms S-ribosylhomocysteine (SRH) into 4, 5-dihydroxy-2, 3-pentanedione (DPD), the precursor of the interspecies QS signalling molecule autoinducer-2 (AI-2). In this study, two LuxS-coding genes, luxS1 and luxS2, with 70% sequence identity were isolated from Lactobacillus plantarum YM-4-3, and overexpressed in Escherichia coli BL21 (DE3), and the protein products were purified successfully. After incubation of LuxS1 or LuxS2 with SRH, the reaction products were able to induce Vibrio harveyi BB170 bioluminescence, clearly demonstrating that both LuxS1 and LuxS2 synthesize AI-2 from SRH in vitro. Ellman's assay results revealed optimal temperatures for LuxS1 and LuxS2 of 45 and 37 °C, respectively, and their activities were stimulated or inhibited by several metal ions and chemical reagents. In addition, enzyme kinetics data showed that Km, Vmax and Kcat value of LuxS1 for the substrate (SRH) were higher than that of LuxS2. These results suggest that LuxS1 and LuxS2 mediate QS in a temperature-dependent manner and may play conserved roles in AI-2 synthesis but exhibit different activities in response to external environmental stress. To our knowledge, this paper is the first report of two luxS genes present in one bacterial genome and the subsequent comparative elucidation of their functions in AI-2 production. Collectively, our study provides a solid basis for future research concerning the AI-2/LuxS QS system in L. plantarum YM-4-3.
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Affiliation(s)
- Xiao-Dong Song
- Laboratory of Applied Microbiology, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, PR China
| | - Chen-Jian Liu
- Laboratory of Applied Microbiology, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, PR China
| | - Shi-Hao Huang
- Laboratory of Applied Microbiology, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, PR China
| | - Xiao-Ran Li
- Laboratory of Applied Microbiology, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, PR China
| | - En Yang
- Laboratory of Applied Microbiology, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, PR China
| | - Yi-Yong Luo
- Laboratory of Applied Microbiology, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, PR China.
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44
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Turroni F, Milani C, Duranti S, Ferrario C, Lugli GA, Mancabelli L, van Sinderen D, Ventura M. Bifidobacteria and the infant gut: an example of co-evolution and natural selection. Cell Mol Life Sci 2018; 75:103-118. [PMID: 28983638 PMCID: PMC11105234 DOI: 10.1007/s00018-017-2672-0] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 09/29/2017] [Indexed: 12/16/2022]
Abstract
Throughout the human life, the gut microbiota interacts with us in a number of different ways, thereby influencing our health status. The acquisition of such an interactive gut microbiota commences at birth. Medical and environmental factors including diet, antibiotic exposure and mode of delivery are major factors that shape the composition of the microbial communities in the infant gut. Among the most abundant members of the infant microbiota are species belonging to the Bifidobacterium genus, which are believed to confer beneficial effects upon their host. Bifidobacteria may be acquired directly from the mother by vertical transmission and their persistence in the infant gut is associated with their saccharolytic activity toward glycans that are abundant in the infant gut. Here, we discuss the establishment of the infant gut microbiota and the contribution of bifidobacteria to this early life microbial consortium.
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Affiliation(s)
- Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Chiara Ferrario
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.
- Microbiome Research Hub, University of Parma, Parma, Italy.
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Milani C, Duranti S, Bottacini F, Casey E, Turroni F, Mahony J, Belzer C, Delgado Palacio S, Arboleya Montes S, Mancabelli L, Lugli GA, Rodriguez JM, Bode L, de Vos W, Gueimonde M, Margolles A, van Sinderen D, Ventura M. The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota. Microbiol Mol Biol Rev 2017; 81:e00036-17. [PMID: 29118049 PMCID: PMC5706746 DOI: 10.1128/mmbr.00036-17] [Citation(s) in RCA: 947] [Impact Index Per Article: 135.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The human gut microbiota is engaged in multiple interactions affecting host health during the host's entire life span. Microbes colonize the neonatal gut immediately following birth. The establishment and interactive development of this early gut microbiota are believed to be (at least partially) driven and modulated by specific compounds present in human milk. It has been shown that certain genomes of infant gut commensals, in particular those of bifidobacterial species, are genetically adapted to utilize specific glycans of this human secretory fluid, thus representing a very intriguing example of host-microbe coevolution, where both partners are believed to benefit. In recent years, various metagenomic studies have tried to dissect the composition and functionality of the infant gut microbiome and to explore the distribution across the different ecological niches of the infant gut biogeography of the corresponding microbial consortia, including those corresponding to bacteria and viruses, in healthy and ill subjects. Such analyses have linked certain features of the microbiota/microbiome, such as reduced diversity or aberrant composition, to intestinal illnesses in infants or disease states that are manifested at later stages of life, including asthma, inflammatory bowel disease, and metabolic disorders. Thus, a growing number of studies have reported on how the early human gut microbiota composition/development may affect risk factors related to adult health conditions. This concept has fueled the development of strategies to shape the infant microbiota composition based on various functional food products. In this review, we describe the infant microbiota, the mechanisms that drive its establishment and composition, and how microbial consortia may be molded by natural or artificial interventions. Finally, we discuss the relevance of key microbial players of the infant gut microbiota, in particular bifidobacteria, with respect to their role in health and disease.
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Affiliation(s)
- Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Francesca Bottacini
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Eoghan Casey
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Jennifer Mahony
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Susana Delgado Palacio
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, IPLA-CSIC, Villaviciosa, Asturias, Spain
| | - Silvia Arboleya Montes
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, IPLA-CSIC, Villaviciosa, Asturias, Spain
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Juan Miguel Rodriguez
- Department of Nutrition, Food Science and Food Technology, Complutense University of Madrid, Madrid, Spain
| | - Lars Bode
- Department of Pediatrics and Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence, University of California-San Diego, La Jolla, California, USA
| | - Willem de Vos
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Department of Bacteriology & Immunology, RPU Immunobiology, University of Helsinki, Helsinki, Finland
| | - Miguel Gueimonde
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, IPLA-CSIC, Villaviciosa, Asturias, Spain
| | - Abelardo Margolles
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, IPLA-CSIC, Villaviciosa, Asturias, Spain
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
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46
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Quorum-Sensing Systems as Targets for Antivirulence Therapy. Trends Microbiol 2017; 26:313-328. [PMID: 29132819 DOI: 10.1016/j.tim.2017.10.005] [Citation(s) in RCA: 266] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 09/26/2017] [Accepted: 10/20/2017] [Indexed: 02/08/2023]
Abstract
The development of novel therapies to control diseases caused by antibiotic-resistant pathogens is one of the major challenges we are currently facing. Many important plant, animal, and human pathogens regulate virulence by quorum sensing, bacterial cell-to-cell communication with small signal molecules. Consequently, a significant research effort is being undertaken to identify and use quorum-sensing-interfering agents in order to control diseases caused by these pathogens. In this review, an overview of our current knowledge of quorum-sensing systems of Gram-negative model pathogens is presented as well as the link with virulence of these pathogens, and recent advances and challenges in the development of quorum-sensing-interfering therapies are discussed.
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47
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Liu L, Wu R, Zhang J, Shang N, Li P. D-Ribose Interferes with Quorum Sensing to Inhibit Biofilm Formation of Lactobacillus paraplantarum L-ZS9. Front Microbiol 2017; 8:1860. [PMID: 29018429 PMCID: PMC5622935 DOI: 10.3389/fmicb.2017.01860] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 09/12/2017] [Indexed: 01/31/2023] Open
Abstract
Biofilms help bacteria survive under adverse conditions, and the quorum sensing (QS) system plays an important role in regulating their activities. Quorum sensing inhibitors (QSIs) have great potential to inhibit pathogenic biofilm formation and are considered possible replacements for antibiotics; however, further investigation is required to understand the mechanisms of action of QSIs and to avoid inhibitory effects on beneficial bacteria. Lactobacillus paraplantarum L-ZS9, isolated from fermented sausage, is a bacteriocin-producing bacteria that shows potential to be a probiotic starter. Since exogenous autoinducer-2 (AI-2) promoted biofilm formation of the strain, expression of genes involved in AI-2 production was determined in L. paraplantarum L-ZS9, especially the key gene luxS. D-Ribose was used to inhibit biofilm formation because of its AI-2 inhibitory activity. Twenty-seven differentially expressed proteins were identified by comparative proteomic analysis following D-ribose treatment and were functionally classified into six groups. Real-time quantitative PCR showed that AI-2 had a counteractive effect on transcription of the genes tuf, fba, gap, pgm, nfo, rib, and rpoN. Over-expression of the tuf, fba, gap, pgm, and rpoN genes promoted biofilm formation of L. paraplantarum L-ZS9, while over-expression of the nfo and rib genes inhibited biofilm formation. In conclusion, D-ribose inhibited biofilm formation of L. paraplantarum L-ZS9 by regulating multiple genes involved in the glycolytic pathway, extracellular DNA degradation and transcription, and translation. This research provides a new mechanism of QSI regulation of biofilm formation of Lactobacillus and offers a valuable reference for QSI application in the future.
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Affiliation(s)
- Lei Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.,Key Laboratory of Functional Dairy, China Agricultural University, Beijing, China
| | - Ruiyun Wu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Jinlan Zhang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Nan Shang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.,Department of Agricultural, Food and Nutritional Sciences, University of Alberta, Edmonton, AB, Canada
| | - Pinglan Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.,Key Laboratory of Functional Dairy, China Agricultural University, Beijing, China
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48
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Ruiz L, Bottacini F, Boinett CJ, Cain AK, O'Connell-Motherway M, Lawley TD, van Sinderen D. The essential genomic landscape of the commensal Bifidobacterium breve UCC2003. Sci Rep 2017; 7:5648. [PMID: 28717159 PMCID: PMC5514069 DOI: 10.1038/s41598-017-05795-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 06/02/2017] [Indexed: 01/15/2023] Open
Abstract
Bifidobacteria are common gut commensals with purported health-promoting effects. This has encouraged scientific research into bifidobacteria, though recalcitrance to genetic manipulation and scarcity of molecular tools has hampered our knowledge on the precise molecular determinants of their health-promoting attributes and gut adaptation. To overcome this problem and facilitate functional genomic analyses in bifidobacteria, we created a large Tn5 transposon mutant library of the commensal Bifidobacterium breve UCC2003 that was further characterized by means of a Transposon Directed Insertion Sequencing (TraDIS) approach. Statistical analysis of transposon insertion distribution revealed a set of 453 genes that are essential for or markedly contribute to growth of this strain under laboratory conditions. These essential genes encode functions involved in the so-called bifid-shunt, most enzymes related to nucleotide biosynthesis and a range of housekeeping functions. Comparison to the Bifidobacterium and B. breve core genomes highlights a high degree of conservation of essential genes at the species and genus level, while comparison to essential gene datasets from other gut bacteria identified essential genes that appear specific to bifidobacteria. This work establishes a useful molecular tool for scientific discovery of bifidobacteria and identifies targets for further studies aimed at characterizing essential functions not previously examined in bifidobacteria.
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Affiliation(s)
- Lorena Ruiz
- School of Microbiology and APC Microbiome Institute, National University of Ireland, Cork, Western Road, Ireland.,Department of Nutrition, Bromatology and Food Technology, Complutense University, Avda Puerta de Hierro s/n, 28040, Madrid, Spain
| | - Francesca Bottacini
- School of Microbiology and APC Microbiome Institute, National University of Ireland, Cork, Western Road, Ireland
| | | | - Amy K Cain
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Mary O'Connell-Motherway
- School of Microbiology and APC Microbiome Institute, National University of Ireland, Cork, Western Road, Ireland
| | | | - Douwe van Sinderen
- School of Microbiology and APC Microbiome Institute, National University of Ireland, Cork, Western Road, Ireland.
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49
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Park H, Lee K, Yeo S, Shin H, Holzapfel WH. Autoinducer-2 Quorum Sensing Influences Viability of Escherichia coli O157:H7 under Osmotic and In Vitro Gastrointestinal Stress Conditions. Front Microbiol 2017; 8:1077. [PMID: 28659895 PMCID: PMC5468425 DOI: 10.3389/fmicb.2017.01077] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 05/29/2017] [Indexed: 12/22/2022] Open
Abstract
Bacteria use autoinducer molecules to communicate both at intra-species and inter-species levels by quorum sensing. One such cell density-dependent signaling system is the luxS-mediated universal quorum sensing using autoinducer-2 (AI-2). Virulence of several pathogens is determined by an AI-2 system and is related to colonization and infection of the host. From this concept, numerous papers have suggested that AI-2 inhibition is an important strategy toward designing of new antimicrobial agents. However, recent studies indicate that the AI-2 system is also involved in adaptation and survival under environmental stress conditions. Therefore, we hypothesized that interaction between quorum sensing and environmental conditions may be critical in influencing predicted results in a control and when combating of target pathogens. We investigated the growth of enterohemorrhagic Escherichia coli O157:H7 (EHEC) and its luxS-deficient (non AI-2 producing) mutant strain under various stress conditions, and found significant differences in the growth rate under osmotic stress. Moreover, we could also show the impact of the AI-2 molecule on viability in the gastrointestinal tract model representing a complex environmental condition. Differences in vital responses of the strains suggest that AI-2 quorum sensing has a significant influence on the viability of EHEC under environmental stress conditions.
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Affiliation(s)
- Hyunjoon Park
- Department of Advanced Green Energy and Environment, Handong Global UniversityPohang, South Korea
| | - Kyuyeon Lee
- Department of Advanced Green Energy and Environment, Handong Global UniversityPohang, South Korea
| | - Soyoung Yeo
- Research Institute of Eco-friendly Livestock Science, Institute of Green-Bio Science and Technology, Seoul National UniversityPyeongchang, South Korea
| | - Heuynkil Shin
- School of Life Science, Handong Global UniversityPohang, South Korea
| | - Wilhelm H Holzapfel
- Department of Advanced Green Energy and Environment, Handong Global UniversityPohang, South Korea
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50
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Lanigan N, Bottacini F, Casey PG, O'Connell Motherway M, van Sinderen D. Genome-Wide Search for Genes Required for Bifidobacterial Growth under Iron-Limitation. Front Microbiol 2017; 8:964. [PMID: 28620359 PMCID: PMC5449479 DOI: 10.3389/fmicb.2017.00964] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 05/15/2017] [Indexed: 11/13/2022] Open
Abstract
Bacteria evolved over millennia in the presence of the vital micronutrient iron. Iron is involved in numerous processes within the cell and is essential for nearly all living organisms. The importance of iron to the survival of bacteria is obvious from the large variety of mechanisms by which iron may be acquired from the environment. Random mutagenesis and global gene expression profiling led to the identification of a number of genes, which are essential for Bifidobacterium breve UCC2003 survival under iron-restrictive conditions. These genes encode, among others, Fe-S cluster-associated proteins, a possible ferric iron reductase, a number of cell wall-associated proteins, and various DNA replication and repair proteins. In addition, our study identified several presumed iron uptake systems which were shown to be essential for B. breve UCC2003 growth under conditions of either ferric and/or ferrous iron chelation. Of these, two gene clusters encoding putative iron-uptake systems, bfeUO and sifABCDE, were further characterised, indicating that sifABCDE is involved in ferrous iron transport, while the bfeUO-encoded transport system imports both ferrous and ferric iron. Transcription studies showed that bfeUO and sifABCDE constitute two separate transcriptional units that are induced upon dipyridyl-mediated iron limitation. In the anaerobic gastrointestinal environment ferrous iron is presumed to be of most relevance, though a mutation in the sifABCDE cluster does not affect B. breve UCC2003's ability to colonise the gut of a murine model.
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Affiliation(s)
- Noreen Lanigan
- APC Microbiome Institute and School of Microbiology, University College CorkCork, Ireland
| | - Francesca Bottacini
- APC Microbiome Institute and School of Microbiology, University College CorkCork, Ireland
| | - Pat G Casey
- APC Microbiome Institute and School of Microbiology, University College CorkCork, Ireland
| | | | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, University College CorkCork, Ireland
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