51
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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: 53] [Impact Index Per Article: 17.7] [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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52
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Taniguchi M, Nambu M, Katakura Y, Yamasaki-Yashiki S. Adhesion mechanisms of Bifidobacterium animalis subsp. lactis JCM 10602 to dietary fiber. BIOSCIENCE OF MICROBIOTA FOOD AND HEALTH 2021; 40:59-64. [PMID: 33520570 PMCID: PMC7817516 DOI: 10.12938/bmfh.2020-003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 09/07/2020] [Indexed: 12/18/2022]
Abstract
Adherence of probiotics to dietary fibers present in the intestinal tract may affect
adhesion to intestinal epithelial cells. The properties of the adhesion of bifidobacteria
to mucin or epithelial cells have been well studied; however, adhesion of bifidobacteria
to dietary fiber has not been investigated. The adhesion ratio of six
Bifidobacterium strains to cellulose and chitin was examined; among the
strains, Bifidobacterium animalis subsp. lactis JCM
10602 showed high adherence to both cellulose and chitin, and two strains showed high
adherence to only chitin. The ratios of adhesion of B. animalis to
cellulose and chitin were positively and negatively correlated with ionic strength,
respectively. These data suggest that hydrophobic and electrostatic interactions are
involved in the adhesion to cellulose and chitin, respectively. The adhesion ratios of the
cells in the late logarithmic phase to cellulose and chitin decreased by approximately 40%
and 70% of the cells in the early logarithmic phase, respectively. Furthermore, the
adhesion ratio to cellulose decreased with increasing bile concentration regardless of the
culture phase of the cells. On the other hand, the adhesion ratio to chitin of cells in
the early logarithmic phase decreased with increasing bile concentration; however, that of
cells in the late logarithmic phase increased slightly, suggesting that adhesins differ
depending on the culture phase. Our results indicated the importance of considering
adhesion to both dietary fibers and the intestinal mucosa when using bifidobacteria as
probiotics.
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Affiliation(s)
- Maria Taniguchi
- Chemistry, Materials and Bioengineering Major, Graduate School of Science and Engineering, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan
| | - Minori Nambu
- Department of Life Science and Biotechnology, Faculty of Chemistry, Materials and Bioengineering, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan
| | - Yoshio Katakura
- Department of Life Science and Biotechnology, Faculty of Chemistry, Materials and Bioengineering, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan
| | - Shino Yamasaki-Yashiki
- Department of Life Science and Biotechnology, Faculty of Chemistry, Materials and Bioengineering, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan
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53
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Rozman V, Accetto T, Duncan SH, Flint HJ, Vodovnik M. Type IV pili are widespread among non-pathogenic Gram-positive gut bacteria with diverse carbohydrate utilization patterns. Environ Microbiol 2021; 23:1527-1540. [PMID: 33331146 DOI: 10.1111/1462-2920.15362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 12/15/2020] [Indexed: 12/23/2022]
Abstract
Type IV pili (T4P) are bacterial surface-exposed appendages that have been extensively studied in Gram-negative pathogenic bacteria. Despite recent sequencing efforts, little is known regarding these structures in non-pathogenic anaerobic Gram-positive species, particularly commensals of the mammalian gut. Early studies revealed that T4P in two ruminal Gram-positive species are associated with growth on cellulose, suggesting possible associations of T4P with substrate utilization patterns. In the present study, genome sequences of 118 taxonomically diverse, mainly Gram-positive, bacterial strains isolated from anaerobic (gastrointestinal) environments, have been analysed. The genes likely to be associated with T4P biogenesis were analysed and grouped according to T4P genetic organization. In parallel, consortia of Carbohydrate Active enZYmes (CAZymes) were also analysed and used to predict carbohydrate utilization abilities of selected strains. The predictive power of this approach was additionally confirmed by experimental assessment of substrate-related growth patterns of selected strains. Our analysis revealed that T4P systems with diverse genetic organization are widespread among Gram-positive anaerobic non-pathogenic bacteria isolated from different environments, belonging to two phylogenetically distantly related phyla: Firmicutes and Actinobacteria.
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Affiliation(s)
- Vita Rozman
- Chair of Microbiology and Microbial Biotechnology, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
| | - Tomaž Accetto
- Chair of Microbiology and Microbial Biotechnology, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
| | - Sylvia H Duncan
- Gut Health Group, Rowett Institute, University of Aberdeen, Aberdeen, UK
| | - Harry J Flint
- Gut Health Group, Rowett Institute, University of Aberdeen, Aberdeen, UK
| | - Maša Vodovnik
- Chair of Microbiology and Microbial Biotechnology, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia
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54
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Exploring the Ecology of Bifidobacteria and Their Genetic Adaptation to the Mammalian Gut. Microorganisms 2020; 9:microorganisms9010008. [PMID: 33375064 PMCID: PMC7822027 DOI: 10.3390/microorganisms9010008] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/16/2020] [Accepted: 12/18/2020] [Indexed: 12/14/2022] Open
Abstract
The mammalian gut is densely inhabited by microorganisms that have coevolved with their host. Amongst these latter microorganisms, bifidobacteria represent a key model to study host–microbe interaction within the mammalian gut. Remarkably, bifidobacteria naturally occur in a range of ecological niches that are either directly or indirectly connected to the animal gastrointestinal tract. They constitute one of the dominant bacterial members of the intestinal microbiota and are among the first colonizers of the mammalian gut. Notably, the presence of bifidobacteria in the gut has been associated with several health-promoting activities. In this review, we aim to provide an overview of current knowledge on the genetic diversity and ecology of bifidobacteria. Furthermore, we will discuss how this important group of gut bacteria is able to colonize and survive in the mammalian gut, so as to facilitate host interactions.
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55
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Xiong Y, Zhai Z, Lei Y, Xiao B, Hao Y. A Novel Major Pilin Subunit Protein FimM Is Involved in Adhesion of Bifidobacterium longum BBMN68 to Intestinal Epithelial Cells. Front Microbiol 2020; 11:590435. [PMID: 33329468 PMCID: PMC7719627 DOI: 10.3389/fmicb.2020.590435] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 10/27/2020] [Indexed: 12/16/2022] Open
Abstract
Adhesion to the gastrointestinal tract is considered to be important for bifidobacteria to colonize the human gut and exert their probiotic effects. Some cell surface proteins of bifidobacteria, known as adhesins, play critical roles in the binding to host cells or the extracellular matrix (ECM). To elucidate the mechanisms associated with the adhesion of Bifidobacterium longum BBMN68, a centenarian originated potential probiotic, PSORTdb was employed to identify putative extracellular localized proteins in the B. longum BBMN68. Of the 560 predicted extracellular proteins, 21 were further identified as putative adhesion proteins using the conserved domain database of NCBI, and four were successfully overexpressed in the heterologous host, Lactococcus lactis NZ9000. Notably, a recombinant strain expressing FimM showed a significantly increased adhesive affinity for both HT-29 and mucus-secreting LS174T goblet cells (2.2- and 5.4-fold higher than that of the control strain, respectively). Amino acid sequence alignment showed that FimM is a major pilin subunit protein containing a Cna-B type domain and a C-terminal LPKTG sequence. However, in silico analysis of the fimM-coding cluster revealed that BBMN68_RS10200, encoding a pilus-specific class C sortase, was a pseudogene, indicating that FimM may function as a surface adhesin that cannot polymerize into a pili-like structure. Immunogold electron microscopy results further confirmed that FimM localized to the surface of L. lactis NZfimM and B. longum BBMN68 but did not assemble into pilus filaments. Moreover, the adhesive affinity of L. lactis NZfimM to fibronectin, fibrinogen, and mucin were 3.8-, 2.1-, and 3.1-fold higher than that of the control. The affinity of FimM for its attachment receptors was further verified through an inhibition assay using anti-FimM antibodies. In addition, homologs of FimM were found in Bifidobacterium bifidum 85B, Bifidobacterium gallinarum CACC 514, and 23 other B. longum strains by sequence similarity analysis using BLASTP. Our results suggested that FimM is a novel surface adhesin that is mainly present in B. longum strains.
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Affiliation(s)
- Yao Xiong
- 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, Co-constructed by Ministry of Education and Beijing Municipality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Zhengyuan Zhai
- 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, Co-constructed by Ministry of Education and Beijing Municipality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Yuanqiu Lei
- Key Laboratory of Functional Dairy, Co-constructed by Ministry of Education and Beijing Municipality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Bingbing Xiao
- Department of Obstetrics and Gynecology, Peking University First Hospital, Beijing, China
| | - Yanling Hao
- 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, Co-constructed by Ministry of Education and Beijing Municipality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
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56
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Munoz J, James K, Bottacini F, Van Sinderen D. Biochemical analysis of cross-feeding behaviour between two common gut commensals when cultivated on plant-derived arabinogalactan. Microb Biotechnol 2020; 13:1733-1747. [PMID: 32385941 PMCID: PMC7533333 DOI: 10.1111/1751-7915.13577] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 03/30/2020] [Accepted: 03/30/2020] [Indexed: 12/12/2022] Open
Abstract
In this paper, we reveal and characterize cross-feeding behaviour between the common gut commensal Bacteroides cellulosilyticus (Baccell) and certain bifidobacterial strains, including Bifidobacterium breve UCC2003, when grown on a medium containing Larch Wood Arabinogalactan (LW-AG). We furthermore show that cross-feeding is dependent on the release of β-1,3-galacto-di/trisaccharides (β-1,3-GOS), and identified that the bga gene cluster of B. breve UCC2003 allows β-1,3-GOS metabolism. The product of bgaB is presumed to be responsible for the import of β-1,3-GOS, while the bgaA gene product, a glycoside hydrolase family 2 member, was shown to hydrolyse both β-1,3-galactobiose and β-1,3-galactotriose into galactose monomers. This study advances our understanding of strain-specific syntrophic interactions between two glycan degraders in the human gut in the presence of AG-type dietary polysaccharides.
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Affiliation(s)
- Jose Munoz
- Microbial Enzymology GroupDepartment of Applied SciencesNorthumbria UniversityNewcastle Upon TyneNE1 8STUK
| | - Kieran James
- School of Microbiology & APC Microbiome IrelandUniversity College CorkIreland University College CorkCorkIreland
| | - Francesca Bottacini
- School of Microbiology & APC Microbiome IrelandUniversity College CorkIreland University College CorkCorkIreland
| | - Douwe Van Sinderen
- School of Microbiology & APC Microbiome IrelandUniversity College CorkIreland University College CorkCorkIreland
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57
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Yadav M, Chauhan NS. Overview of the rules of the microbial engagement in the gut microbiome: a step towards microbiome therapeutics. J Appl Microbiol 2020; 130:1425-1441. [PMID: 33022786 DOI: 10.1111/jam.14883] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/18/2020] [Accepted: 09/26/2020] [Indexed: 12/14/2022]
Abstract
Human gut microbiome is a diversified, resilient, immuno-stabilized, metabolically active and physiologically essential component of the human body. Scientific explorations have been made to seek in-depth information about human gut microbiome establishment, microbiome functioning, microbiome succession, factors influencing microbial community dynamics and the role of gut microbiome in health and diseases. Extensive investigations have proposed the microbiome therapeutics as a futuristic medicine for various physiological and metabolic disorders. A comprehensive outlook of microbial colonization, host-microbe interactions, microbial adaptation, commensal selection and immuno-survivability is still required to catalogue the essential genetic and physiological features for the commensal engagement. Evolution of a structured human gut microbiome relies on the microbial flexibility towards genetic, immunological and physiological adaptation in the human gut. Key features for commensalism could be utilized in developing tailor-made microbiome-based therapy to overcome various physiological and metabolic disorders. This review describes the key genetics and physiological traits required for host-microbe interaction and successful commensalism to institute a human gut microbiome.
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Affiliation(s)
- M Yadav
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana, India
| | - N S Chauhan
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana, India
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58
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Extracellular Vesicles Produced by Bifidobacterium longum Export Mucin-Binding Proteins. Appl Environ Microbiol 2020; 86:AEM.01464-20. [PMID: 32737132 DOI: 10.1128/aem.01464-20] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 07/29/2020] [Indexed: 01/21/2023] Open
Abstract
Extracellular proteins are important factors in host-microbe interactions; however, the specific factors that enable bifidobacterial adhesion and survival in the gastrointestinal (GI) tract are not fully characterized. Here, we discovered that Bifidobacterium longum NCC2705 cultured in bacterium-free supernatants of human fecal fermentation broth released a myriad of particles into the extracellular environment. The aim of this study was to characterize the physiological properties of these extracellular particles. The particles, approximately 50 to 80 nm in diameter, had high protein and double-stranded DNA contents, suggesting that they were extracellular vesicles (EVs). A proteomic analysis showed that the EVs primarily consisted of cytoplasmic proteins with crucial functions in essential cellular processes. We identified several mucin-binding proteins by performing a biomolecular interaction analysis of phosphoketolase, GroEL, elongation factor Tu (EF-Tu), phosphoglycerate kinase, transaldolase (Tal), and heat shock protein 20 (Hsp20). The recombinant GroEL and Tal proteins showed high binding affinities to mucin. Furthermore, the immobilization of these proteins on microbeads affected the permanence of the microbeads in the murine GI tract. These results suggest that bifidobacterial exposure conditions that mimic the intestine stimulate B. longum EV production. The resulting EVs exported several cytoplasmic proteins that may have promoted B. longum adhesion. This study improved our understanding of the Bifidobacterium colonization strategy in the intestinal microbiome.IMPORTANCE Bifidobacterium is a natural inhabitant of the human gastrointestinal (GI) tract. Morphological observations revealed that extracellular appendages of bifidobacteria in complex microbial communities are important for understanding its adaptations to the GI tract environment. We identified dynamic extracellular vesicle (EV) production by Bifidobacterium longum in bacterium-free fecal fermentation broth that was strongly suggestive of differing bifidobacterial extracellular appendages in the GI tract. In addition, export of the adhesive moonlighting proteins mediated by EVs may promote bifidobacterial colonization. This study provides new insight into the roles of EVs in bifidobacterial colonization processes as these bacteria adapt to the GI environment.
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59
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Longhi G, van Sinderen D, Ventura M, Turroni F. Microbiota and Cancer: The Emerging Beneficial Role of Bifidobacteria in Cancer Immunotherapy. Front Microbiol 2020; 11:575072. [PMID: 33013813 PMCID: PMC7507897 DOI: 10.3389/fmicb.2020.575072] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 08/17/2020] [Indexed: 12/15/2022] Open
Abstract
Many intestinal bacteria are believed to be involved in various inflammatory and immune processes that influence tumor etiology because of their metabolic properties and their ability to alter the microbiota homeostasis. Although many functions of the microbiota are still unclear, there is compelling experimental evidence showing that the intestinal microbiota is able to modulate carcinogenesis and the response to anticancer therapies, both in the intestinal tract and other body sites. Among the wide variety of gut-colonizing microorganisms, various species belonging to the Bifidobacterium genus are believed to elicit beneficial effects on human physiology and on the host-immune system. Recent findings, based on preclinical mouse models and on human clinical trials, have demonstrated the impact of gut commensals including bifidobacteria on the efficacy of tumor-targeting immunotherapy. Although the underlying molecular mechanisms remain obscure, bifidobacteria and other microorganisms have become a promising aid to immunotherapeutic procedures that are currently applied to treat cancer. The present review focuses on strategies to recruit the microbiome in order to enhance anticancer responses and develop therapies aimed at fighting the onset and progression of malignancies.
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Affiliation(s)
- Giulia Longhi
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- Alimentary Pharmabotic Centre (APC) Microbiome Institute and School of Microbiology, Bioscience Institute, 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
| | - 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
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60
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Liu L, Wang H, Yu Y, Zeng B, Rao X, Chen J, Zhou C, Zheng P, Pu J, Yang L, Zhang H, Wei H, Xie P. Microbial regulation of a lincRNA-miRNA-mRNA network in the mouse hippocampus. Epigenomics 2020; 12:1377-1387. [PMID: 32878473 DOI: 10.2217/epi-2019-0307] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Aim: To comprehensively understand microbiota-regulated lincRNA-miRNA-mRNA networks in psychiatric disorders. Materials & methods: Integrated analyses of lincRNAs, mRNAs and miRNAs, obtained by microarray analysis of hippocampus from specific pathogen-free, germ-free and colonized germ-free mice, were performed. Results: Expression of 139 mRNAs, seven miRNAs and one lincRNA was restored following colonization. The restored transcripts were mainly involved in CREB and Ras/MAPK signaling pathways. RNA transcription and post-transcriptional regulation were the primary perturbed functions. Finally, 12 lincRNAs, six miRNAs and 47 mRNAs were included in a lincRNA-miRNA-mRNA network, and lincRNA0926-miR-190a-5p-Celf4 interactions may play a pivotal role in this regulatory network. Conclusion: This study provides clues for understanding the molecular basis of gut microbiota-brain interactions in depressive- and anxiety-like behaviors.
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Affiliation(s)
- Lanxiang Liu
- Department of Neurology, Yongchuan Hospital of Chongqing Medical University, Chongqing 402160, China.,NHC Key Laboratory of Diagnosis & Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.,Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Haiyang Wang
- College of Stomatology and Affiliated Stomatological Hospital of Chongqing Medical University, 401147, China.,NHC Key Laboratory of Diagnosis & Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Ying Yu
- NHC Key Laboratory of Diagnosis & Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Benhua Zeng
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, China
| | - Xuechen Rao
- NHC Key Laboratory of Diagnosis & Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.,College of Biomedical Engineering, Chongqing Medical University, Chongqing 400016, China
| | - Jianjun Chen
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Chanjuan Zhou
- NHC Key Laboratory of Diagnosis & Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Peng Zheng
- NHC Key Laboratory of Diagnosis & Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.,Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Juncai Pu
- NHC Key Laboratory of Diagnosis & Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.,Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Lining Yang
- NHC Key Laboratory of Diagnosis & Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Hanping Zhang
- NHC Key Laboratory of Diagnosis & Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.,Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Hong Wei
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, China
| | - Peng Xie
- Department of Neurology, Yongchuan Hospital of Chongqing Medical University, Chongqing 402160, China.,College of Stomatology and Affiliated Stomatological Hospital of Chongqing Medical University, 401147, China.,NHC Key Laboratory of Diagnosis & Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.,Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
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61
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Antibiotics in early life associate with specific gut microbiota signatures in a prospective longitudinal infant cohort. Pediatr Res 2020; 88:438-443. [PMID: 31954376 DOI: 10.1038/s41390-020-0761-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 12/03/2019] [Accepted: 01/08/2020] [Indexed: 01/23/2023]
Abstract
BACKGROUND The effects of antibiotics on infant gut microbiota are unclear. We hypothesized that the use of common antibiotics results in long-term aberration in gut microbiota. METHODS Antibiotic-naive infants were prospectively recruited when hospitalized because of a respiratory syncytial virus infection. Composition of fecal microbiota was compared between those receiving antibiotics during follow-up (prescribed at clinicians' discretion because of complications such as otitis media) and those with no antibiotic exposure. Fecal sampling started on day 1, then continued at 2-day intervals during the hospital stay, and at 1, 3 and 6 months at home. RESULTS One hundred and sixty-three fecal samples from 40 patients (median age 2.3 months at baseline; 22 exposed to antibiotics) were available for microbiota analyses. A single course of amoxicillin or macrolide resulted in aberration of infant microbiota characterized by variation in the abundance of bifidobacteria, enterobacteria and clostridia, lasting for several months. Recovery from the antibiotics was associated with an increase in clostridia. Occasionally, antibiotic use resulted in microbiota profiles associated with inflammatory conditions. CONCLUSIONS Antibiotic use in infants modifies especially bifidobacterial levels. Further studies are warranted whether administration of bifidobacteria will provide health benefits by normalizing the microbiota in infants receiving antibiotics.
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The Infant-Derived Bifidobacterium bifidum Strain CNCM I-4319 Strengthens Gut Functionality. Microorganisms 2020; 8:microorganisms8091313. [PMID: 32872165 PMCID: PMC7565306 DOI: 10.3390/microorganisms8091313] [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: 07/17/2020] [Revised: 08/21/2020] [Accepted: 08/26/2020] [Indexed: 02/06/2023] Open
Abstract
Bifidobacteria are among the first colonisers of the gastrointestinal tract of breast-fed newborns due to, among other things, their ability to metabolise oligosaccharides naturally occurring in human milk. The presence of bifidobacteria in the infant gut has been shown to promote intestinal health and homeostasis as well as to preserve a functional gut barrier, thus positively influencing host health and well-being. Among human-associated gut commensals, Bifidobacterium bifidum has been described as the only species capable of the extracellular degradation of both mucin-type glycans and HMOs, thereby giving this species a special role as a commensal gut forager of both host and diet-derived glycans. In the present study, we assess the possible beneficial properties and probiotic potential of B. bifidum strain CNCM I-4319. In silico genome analysis and growth experiments confirmed the expected ability of this strain to consume HMOs and mucin. By employing various animal models, we were also able to assess the ability of B. bifidum CNCM I-4319 to preserve gut integrity and functionality from stress-induced and inflammatory damage, thereby enforcing its potential as an effective probiotic strain.
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63
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Comparative genomics and gene-trait matching analysis of Bifidobacterium breve from Chinese children. FOOD BIOSCI 2020. [DOI: 10.1016/j.fbio.2020.100631] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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64
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Kiu R, Treveil A, Harnisch LC, Caim S, Leclaire C, van Sinderen D, Korcsmaros T, Hall LJ. Bifidobacterium breve UCC2003 Induces a Distinct Global Transcriptomic Program in Neonatal Murine Intestinal Epithelial Cells. iScience 2020; 23:101336. [PMID: 32683312 PMCID: PMC7371750 DOI: 10.1016/j.isci.2020.101336] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/05/2020] [Accepted: 06/30/2020] [Indexed: 12/19/2022] Open
Abstract
The underlying health-driving mechanisms of Bifidobacterium during early life are not well understood, particularly how this microbiota member may modulate the intestinal barrier via programming of intestinal epithelial cells (IECs). We investigated the impact of Bifidobacterium breve UCC2003 on the transcriptome of neonatal murine IECs. Small IECs from two-week-old neonatal mice administered B. breve UCC2003 or PBS (control) were subjected to global RNA sequencing, and differentially expressed genes, pathways, and affected cell types were determined. We observed extensive regulation of the IEC transcriptome with ∼4,000 genes significantly up-regulated, including key genes linked with epithelial barrier function. Enrichment of cell differentiation pathways was observed, along with an overrepresentation of stem cell marker genes, indicating an increase in the regenerative potential of the epithelial layer. In conclusion, B. breve UCC2003 plays a central role in driving intestinal epithelium homeostatic development during early life and suggests future avenues for next-stage clinical studies.
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Affiliation(s)
- Raymond Kiu
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Agatha Treveil
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Lukas C Harnisch
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Shabhonam Caim
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Charlotte Leclaire
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Douwe van Sinderen
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork T12YT20, Ireland
| | - Tamas Korcsmaros
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Lindsay J Hall
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; Chair of Intestinal Microbiome, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany; ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany.
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65
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Complete Genome Sequence of Bifidobacterium longum Strain Jih1, Isolated from Human Feces. Microbiol Resour Announc 2020; 9:9/22/e00319-20. [PMID: 32467270 PMCID: PMC7256257 DOI: 10.1128/mra.00319-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report the complete genome sequence of Bifidobacterium longum strain Jih1, isolated from human feces. The assembled genome comprised one circular chromosome of 2.37 Mb. The chromosome harbors 1,941 protein-coding genes. We report the complete genome sequence of Bifidobacterium longum strain Jih1, isolated from human feces. The assembled genome comprised one circular chromosome of 2.37 Mb. The chromosome harbors 1,941 protein-coding genes.
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66
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Houeix B, Synowsky S, Cairns MT, Kane M, Kilcoyne M, Joshi L. Identification of putative adhesins and carbohydrate ligands of Lactobacillus paracasei using a combinatorial in silico and glycomics microarray profiling approach. Integr Biol (Camb) 2020; 11:315-329. [PMID: 31712825 DOI: 10.1093/intbio/zyz026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 08/28/2019] [Accepted: 09/02/2019] [Indexed: 01/07/2023]
Abstract
Commensal bacteria must colonize host mucosal surfaces to exert health-promoting properties, and bind to gastrointestinal tract (GIT) mucins via their cell surface adhesins. Considerable effort has been directed towards discovery of pathogen adhesins and their ligands to develop anti-infective strategies; however, little is known about the lectin-like adhesins and associated carbohydrate ligands in commensals. In this study, an in silico approach was used to detect surface exposed adhesins in the human commensal Lactobacillus paracasei subsp. paracasei, a promising probiotic commonly used in dairy product fermentation that presents anti-microbial activity. Of the 13 adhesin candidates, 3 sortase-dependent pili clusters were identified in this strain and expression of the adhesin candidate genes was confirmed in vitro. Mass spectrometry analysis confirmed the presence of surface adhesin elongation factor Tu and the chaperonin GroEL, but not pili expression. Whole cells were subsequently incubated on microarrays featuring a panel of GIT mucins from nine different mammalian species and two human-derived cell lines and a library of carbohydrate structures. Binding profiles were compared to those of two known pili-producing lactobacilli, L. johnsonii and L. rhamnosus and all Lactobacillus species displayed overlapping but distinct signatures, which may indicate different abilities for regiospecific GIT colonization. In addition, L. paracasei whole cells favoured binding to α-(2 → 3)-linked sialic acid and α-(1 → 2)-linked fucose-containing carbohydrate structures including blood groups A, B and O and Lewis antigens x, y and b. This study furthers our understanding of host-commensal cross-talk by identifying potential adhesins and specific GIT mucin and carbohydrate ligands and provides insight into the selection of colonization sites by commensals in the GIT.
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Affiliation(s)
- Benoit Houeix
- Glycoscience Group, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.,Advanced Glycoscience Research Cluster, National Centre for Biomedical Engineering Science, National University of Ireland Galway, Galway, Ireland
| | - Silvia Synowsky
- Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, KY16 9ST, UK
| | - Michael T Cairns
- Glycoscience Group, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.,Advanced Glycoscience Research Cluster, National Centre for Biomedical Engineering Science, National University of Ireland Galway, Galway, Ireland
| | - Marian Kane
- Glycoscience Group, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.,Advanced Glycoscience Research Cluster, National Centre for Biomedical Engineering Science, National University of Ireland Galway, Galway, Ireland
| | - Michelle Kilcoyne
- Advanced Glycoscience Research Cluster, National Centre for Biomedical Engineering Science, National University of Ireland Galway, Galway, Ireland.,Carbohydrate Signalling Group, Discipline of Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Lokesh Joshi
- Glycoscience Group, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.,Advanced Glycoscience Research Cluster, National Centre for Biomedical Engineering Science, National University of Ireland Galway, Galway, Ireland
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67
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Interactions among Redox Regulators and the CtrA Phosphorelay in Dinoroseobacter shibae and Rhodobacter capsulatus. Microorganisms 2020; 8:microorganisms8040562. [PMID: 32295208 PMCID: PMC7232146 DOI: 10.3390/microorganisms8040562] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/03/2020] [Accepted: 04/10/2020] [Indexed: 02/06/2023] Open
Abstract
Bacteria employ regulatory networks to detect environmental signals and respond appropriately, often by adjusting gene expression. Some regulatory networks influence many genes, and many genes are affected by multiple regulatory networks. Here, we investigate the extent to which regulatory systems controlling aerobic–anaerobic energetics overlap with the CtrA phosphorelay, an important system that controls a variety of behavioral processes, in two metabolically versatile alphaproteobacteria, Dinoroseobacter shibae and Rhodobacter capsulatus. We analyzed ten available transcriptomic datasets from relevant regulator deletion strains and environmental changes. We found that in D. shibae, the CtrA phosphorelay represses three of the four aerobic–anaerobic Crp/Fnr superfamily regulator-encoding genes (fnrL, dnrD, and especially dnrF). At the same time, all four Crp/Fnr regulators repress all three phosphorelay genes. Loss of dnrD or dnrF resulted in activation of the entire examined CtrA regulon, regardless of oxygen tension. In R. capsulatus FnrL, in silico and ChIP-seq data also suggested regulation of the CtrA regulon, but it was only with loss of the redox regulator RegA where an actual transcriptional effect on the CtrA regulon was observed. For the first time, we show that there are complex interactions between redox regulators and the CtrA phosphorelays in these bacteria and we present several models for how these interactions might occur.
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68
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Application of Recombinase-Based In Vivo Expression Technology to Bifidobacterium longum subsp. longum for Identification of Genes Induced in the Gastrointestinal Tract of Mice. Microorganisms 2020; 8:microorganisms8030410. [PMID: 32183191 PMCID: PMC7143038 DOI: 10.3390/microorganisms8030410] [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: 01/11/2020] [Revised: 03/07/2020] [Accepted: 03/10/2020] [Indexed: 12/13/2022] Open
Abstract
Bifidobacteria are one of the major components in human gut microbiota and well-known as beneficial microbes. However, clarification of commensal mechanisms of bifidobacteria in the intestines is still ongoing, especially in the presence of the gut microbiota. Here, we applied recombinase-based in vivo expression technology (R-IVET) using the bacteriophage P1 Cre/loxP system to Bifidobacterium longum subsp. longum 105-A (B. longum 105-A) to identify genes that are specifically expressed in the gastrointestinal tract of conventionally raised mice. Oral administration of the genomic DNA library of B. longum 105-A to conventionally raised mice resulted in the identification of 73 in vivo-induced genes. Four out of seven tested genes were verified in vivo-specific induction at least in the cecum by quantitative reverse transcription PCR. Although there is still room for improvement of the system, our findings can contribute to expanding our understanding of the commensal behavior of B. longum in the gut ecosystem.
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69
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Structure of a Core Promoter in Bifidobacterium longum NCC2705. J Bacteriol 2020; 202:JB.00540-19. [PMID: 31964699 DOI: 10.1128/jb.00540-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 01/14/2020] [Indexed: 01/04/2023] Open
Abstract
Bacterial promoters consist of core sequence motifs termed -35 and -10 boxes. The consensus motifs are TTGACA and TATAAT, respectively, which were identified from leading investigations on Escherichia coli However, the consensus sequences are not likely to fit genetically divergent bacteria. The sigma factor of the genus Bifidobacterium has a characteristic polar domain in the N terminus, suggesting the possibility of specific promoter recognition. We reevaluated the structure of Bifidobacterium longum NCC2705 promoters and compared them to other bacteria. Transcriptional start sites (TSSs) of the B. longum NCC2705 strain were identified using transcriptome sequencing (RNA-Seq) analysis to extract promoter regions. Conserved motifs of a bifidobacterial promoter were determined using regions upstream of TSSs and a hidden Markov model. As a result, consensus motifs of the -35 and -10 boxes were TTGTGC and TACAAT, respectively. To assess each base of both motifs, we constructed 37 plasmids based on pKO403-TPCTcon, including the hup promoter connected with a chloramphenicol acetyltransferase as a reporter gene. This reporter assay showed two optimal motifs of the -35 and -10 boxes, namely, TTGNNN and TANNNT, respectively. We further analyzed spacer lengths between the -35 and -10 boxes via a bioinformatics approach. The spacer lengths predominant in bacteria have been generally reported to be approximately 17 bp. In contrast, the predominant spacer lengths in the genus Bifidobacterium and related species were 11 bp, in addition to 17 bp. A reporter assay to assess the spacer lengths indicated that the 11-bp spacer length produced unusually high activity.IMPORTANCE The structures of sigma factors vary among bacterial strains, indicating that recognition rules may also vary. Therefore, we investigated the promoter structure of Bifidobacterium longum NCC2705 using a bioinformatics approach and wet analyses. The most frequent and optimal motifs were similar to other bacterial consensus motifs. The optimal spacer length between the two boxes was reported to be 17 bp. It is widely applied to a bioinformatics approach for other bacteria. Unexpectedly, conserved spacer lengths were 11 bp as well as 17 bp in the genus Bifidobacterium Moreover, the sigma factor of the genus Bifidobacterium has a characteristic domain in the N terminus which may contribute to the additional functions. Hence, it would be valuable to reevaluate the promoter in other organisms.
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70
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Liu Q, Yu Z, Tian F, Zhao J, Zhang H, Zhai Q, Chen W. Surface components and metabolites of probiotics for regulation of intestinal epithelial barrier. Microb Cell Fact 2020; 19:23. [PMID: 32024520 PMCID: PMC7003451 DOI: 10.1186/s12934-020-1289-4] [Citation(s) in RCA: 199] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 01/20/2020] [Indexed: 12/11/2022] Open
Abstract
The gut microbiota can significantly affect the function of the intestinal barrier. Some intestinal probiotics (such as Lactobacillus, Bifidobacteria, a few Escherichia coli strains, and a new generation of probiotics including Bacteroides thetaiotaomicron and Akkermansia muciniphila) can maintain intestinal epithelial homeostasis and promote health. This review first summarizes probiotics' regulation of the intestinal epithelium via their surface compounds. Surface layer proteins, flagella, pili and capsular polysaccharides constitute microbial-associated molecular patterns and specifically bind to pattern recognition receptors, which can regulate signaling pathways to produce cytokines or inhibit apoptosis, thereby attenuating inflammation and enhancing the function of the gut epithelium. The review also explains the effects of metabolites (such as secreted proteins, organic acids, indole, extracellular vesicles and bacteriocins) of probiotics on host receptors and the mechanisms by which these metabolites regulate gut epithelial barrier function. Previous reviews summarized the role of the surface macromolecules or metabolites of gut microbes (including both probiotics and pathogens) in human health. However, these reviews were mostly focused on the interactions between these substances and the intestinal mucosal immune system. In the current review, we only focused on probiotics and discussed the molecular interaction between these bacteria and the gut epithelial barrier.
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Affiliation(s)
- Qing Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, People's Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Zhiming Yu
- Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, 214023, Jiangsu, People's Republic of China
| | - Fengwei Tian
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, People's Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, People's Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, People's Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, Jiangsu, China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou, 225004, China
- International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, People's Republic of China.
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
- Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi, China.
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, People's Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Beijing Innovation Centre of Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, 100048, People's Republic of China
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71
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Pyclik M, Srutkova D, Schwarzer M, Górska S. Bifidobacteria cell wall-derived exo-polysaccharides, lipoteichoic acids, peptidoglycans, polar lipids and proteins - their chemical structure and biological attributes. Int J Biol Macromol 2019; 147:333-349. [PMID: 31899242 DOI: 10.1016/j.ijbiomac.2019.12.227] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/13/2019] [Accepted: 12/24/2019] [Indexed: 02/07/2023]
Abstract
A variety of health benefits has been documented to be associated with the consumption of probiotic bacteria, namely bifidobacteria and lactobacilli. Thanks to the scientific advances in recent years we are beginning to understand the molecular mechanisms by which bacteria in general and probiotic bacteria in particular act as host physiology and immune system modulators. More recently, the focus has shifted from live bacteria towards bacteria-derived defined molecules, so called postbiotics. These molecules may represent safer alternative compared to the live bacteria while retaining the desired effects on the host. The excellent source of effector macromolecules is the bacterial envelope. It contains compounds that are pivotal in the adhesion phenomenon, provide direct bacteria-to-host signaling capacity and the associated physiological impact and immunomodulatory properties of bacteria. Here we comprehensively review the structure and biological role of Bifidobacterium surface and cell wall molecules: exopolysaccharides, cell wall polysaccharides, lipoteichoic acids, polar lipids, peptidoglycans and proteins. We discuss their involvement in direct signaling to the host cells and their described immunomodulatory effects.
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Affiliation(s)
- Marcelina Pyclik
- Laboratory of Microbiome Immunobiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114 Wroclaw, Poland
| | - Dagmar Srutkova
- Laboratory of Gnotobiology, Institute of Microbiology of the Czech Academy of Sciences, Novy Hradek, Czech Republic
| | - Martin Schwarzer
- Laboratory of Gnotobiology, Institute of Microbiology of the Czech Academy of Sciences, Novy Hradek, Czech Republic.
| | - Sabina Górska
- Laboratory of Microbiome Immunobiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114 Wroclaw, Poland.
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72
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Senizza A, Callegari ML, Senizza B, Minuti A, Rocchetti G, Morelli L, Patrone V. Effects of Linoleic Acid on Gut-Derived Bifidobacterium breve DSM 20213: A Transcriptomic Approach. Microorganisms 2019; 7:microorganisms7120710. [PMID: 31861103 PMCID: PMC6955684 DOI: 10.3390/microorganisms7120710] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/12/2019] [Accepted: 12/16/2019] [Indexed: 02/08/2023] Open
Abstract
Bacterial production of conjugated linoleic acid (CLA) has recently received great attention because of the potential health benefits of this fatty acid. Linoleic acid (LA) can be converted to CLA by several microorganisms, including bifidobacteria, possibly as a detoxification mechanism to avoid the growth inhibition effect of LA. In the present in vitro study, we investigated the gene expression landscape of the intestinal strain Bifidobacterium breve DSM 20213 when exposed to LA. Transcriptomic analysis using RNA-seq revealed that LA induced a multifactorial stress response in the test strain, including upregulation of genes involved in iron uptake and downregulation of genes involved in sugar and oligopeptide transport. We also observed reduced transcription of genes involved in membrane and pili biosynthesis. The upregulation of iron uptake was not related to any putative ability of LA to chelate Fe2+, but was somewhat linked to stress response. Furthermore, we demonstrated that LA increased reactive oxygen species (ROS) production in bacterial cells, activating an oxidative stress response. This response was proved by thioredoxin reductase transcription, and was primarily evident among bacteria cultured in the absence of cysteine. This is the first report of the potential mechanisms involved in bacterial LA transport and stress response in B. breve.
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Affiliation(s)
- Alice Senizza
- Department for Sustainable Food Process (DiSTAS), Università Cattolica del Sacro Cuore, via Emilia Parmense 84, 29122 Piacenza, Italy; (A.S.); (M.L.C.); (B.S.); (G.R.); (L.M.)
| | - Maria Luisa Callegari
- Department for Sustainable Food Process (DiSTAS), Università Cattolica del Sacro Cuore, via Emilia Parmense 84, 29122 Piacenza, Italy; (A.S.); (M.L.C.); (B.S.); (G.R.); (L.M.)
- Biotechnology Research Centre (CRB), via Milano 24, 26100 Cremona, Italy
| | - Biancamaria Senizza
- Department for Sustainable Food Process (DiSTAS), Università Cattolica del Sacro Cuore, via Emilia Parmense 84, 29122 Piacenza, Italy; (A.S.); (M.L.C.); (B.S.); (G.R.); (L.M.)
| | - Andrea Minuti
- Department of Animal Science, Food and Nutrition (DiANA), Università Cattolica del Sacro Cuore, via Emilia Parmense 84, 29122 Piacenza, Italy;
- Nutrigenomics and Proteomics Research Center (PRONUTRIGEN), Università Cattolica del Sacro Cuore, via Emilia Parmense 84, 29122 Piacenza, Italy
| | - Gabriele Rocchetti
- Department for Sustainable Food Process (DiSTAS), Università Cattolica del Sacro Cuore, via Emilia Parmense 84, 29122 Piacenza, Italy; (A.S.); (M.L.C.); (B.S.); (G.R.); (L.M.)
| | - Lorenzo Morelli
- Department for Sustainable Food Process (DiSTAS), Università Cattolica del Sacro Cuore, via Emilia Parmense 84, 29122 Piacenza, Italy; (A.S.); (M.L.C.); (B.S.); (G.R.); (L.M.)
- Biotechnology Research Centre (CRB), via Milano 24, 26100 Cremona, Italy
| | - Vania Patrone
- Department for Sustainable Food Process (DiSTAS), Università Cattolica del Sacro Cuore, via Emilia Parmense 84, 29122 Piacenza, Italy; (A.S.); (M.L.C.); (B.S.); (G.R.); (L.M.)
- Nutrigenomics and Proteomics Research Center (PRONUTRIGEN), Università Cattolica del Sacro Cuore, via Emilia Parmense 84, 29122 Piacenza, Italy
- Correspondence: ; Tel.: +39-0523-599247
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73
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Lanigan N, Kelly E, Arzamasov AA, Stanton C, Rodionov DA, van Sinderen D. Transcriptional control of central carbon metabolic flux in Bifidobacteria by two functionally similar, yet distinct LacI-type regulators. Sci Rep 2019; 9:17851. [PMID: 31780796 PMCID: PMC6882875 DOI: 10.1038/s41598-019-54229-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 11/06/2019] [Indexed: 12/21/2022] Open
Abstract
Bifidobacteria resident in the gastrointestinal tract (GIT) are subject to constantly changing environmental conditions, which require rapid adjustments in gene expression. Here, we show that two predicted LacI-type transcription factors (TFs), designated AraQ and MalR1, are involved in regulating the central, carbohydrate-associated metabolic pathway (the so-called phosphoketolase pathway or bifid shunt) of the gut commensal Bifidobacterium breve UCC2003. These TFs appear to not only control transcription of genes involved in the bifid shunt and each other, but also seem to commonly and directly affect transcription of other TF-encoding genes, as well as genes related to uptake and metabolism of various carbohydrates. This complex and interactive network of AraQ/MalR1-mediated gene regulation provides previously unknown insights into the governance of carbon metabolism in bifidobacteria.
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Affiliation(s)
- Noreen Lanigan
- School of Microbiology & APC Microbiome Ireland, University College Cork, Ireland University College Cork, Cork, Ireland
| | - Emer Kelly
- School of Microbiology & APC Microbiome Ireland, University College Cork, Ireland University College Cork, Cork, Ireland
| | - Aleksandr A Arzamasov
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States.,A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | | | - Dmitry A Rodionov
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States.,A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Douwe van Sinderen
- School of Microbiology & APC Microbiome Ireland, University College Cork, Ireland University College Cork, Cork, Ireland.
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74
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Wang C, Chen W, Xia A, Zhang R, Huang Y, Yang S, Ni L, Jin F. Carbon Starvation Induces the Expression of PprB-Regulated Genes in Pseudomonas aeruginosa. Appl Environ Microbiol 2019; 85:e01705-19. [PMID: 31492668 PMCID: PMC6821963 DOI: 10.1128/aem.01705-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 09/02/2019] [Indexed: 01/02/2023] Open
Abstract
Pseudomonas aeruginosa can cause severe infections in humans. This bacterium often adopts a biofilm lifestyle that is hard to treat. In several previous studies, the PprA-PprB two-component system (TCS), which controls the expression of type IVb pili, BapA adhesin, and CupE fimbriae, was shown to be involved in biofilm formation (M. Romero, H. Silistre, L. Lovelock, V. J. Wright, K.-G. Chan, et al., Nucleic Acids Res 46:6823-6840, 2018, https://doi.org/10.1093/nar/gky324; S. de Bentzmann, C. Giraud, C. S. Bernard, V. Calderon, F. Ewald F, et al., PLoS Pathog 8:e1003052, 2012, https://doi.org/10.1371/journal.ppat.1003052). However, signals or environmental conditions that can trigger the PprA-PprB TCS are still unknown, and the molecular mechanisms of PprB-mediated biofilm formation are poorly characterized. Here, we report that carbon starvation stress (CSS) can induce the expression of pprB and genes in the PprB regulon. CSS-induced pprB transcription is mediated by the stress response sigma factor RpoS rather than the two-component sensor PprA. We also observed a strong negative regulation of PprB on the transcription of itself. Further experiments showed that PprB overexpression greatly enhanced cell-cell adhesion (CCA) and cell-surface adhesion (CSA) in P. aeruginosa Specifically, under the background of PprB overexpression, both the BapA adhesin and CupE fimbriae displayed positive effects on CCA and CSA, while the type IVb pili showed an unexpected negative effect on CCA and no effect on CSA. In addition, expression of the PprB regulon genes were significantly increased in 3-day colony biofilms, indicating a possible carbon limitation state. The CSS-RpoS-PprB-Bap/Flp/CupE pathway identified in this study provides a new perspective on the process of biofilm formation in carbon-limited environments.IMPORTANCE Typically, the determination of the external signals that can trigger a regulatory system is crucial to understand the regulatory logic and inward function of that system. The PprA-PprB two-component system was reported to be involved in biofilm formation in Pseudomonas aeruginosa, but the signals triggering this system are unknown. In this study, we found that carbon starvation stress (CSS) induces transcription of pprB and genes in the PprB regulon through an RpoS-dependent pathway. Increased PprB expression leads to enhanced cell-cell adhesion (CCA) and cell-surface adhesion (CSA) in P. aeruginosa Both CCA and CSA are largely dependent on the Bap secretion system and are moderately dependent on the CupE fimbriae. Our findings suggest that PprB reinforces the structure of biofilms under carbon-limited conditions, and the Bap secretion system and CupE fimbriae are two potential targets for biofilm treatment.
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Affiliation(s)
- Congcong Wang
- Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
| | - Wenhui Chen
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
| | - Aiguo Xia
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China
| | - Rongrong Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China
| | - Yajia Huang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China
| | - Shuai Yang
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China
| | - Lei Ni
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China
| | - Fan Jin
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China
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Mora D, Filardi R, Arioli S, Boeren S, Aalvink S, de Vos WM. Development of omics-based protocols for the microbiological characterization of multi-strain formulations marketed as probiotics: the case of VSL#3. Microb Biotechnol 2019; 12:1371-1386. [PMID: 31402586 PMCID: PMC6801179 DOI: 10.1111/1751-7915.13476] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 07/30/2019] [Accepted: 07/31/2019] [Indexed: 12/17/2022] Open
Abstract
The growing commercial interest in multi-strain formulations marketed as probiotics has not been accompanied by an equal increase in the evaluation of quality levels of these biotechnological products. The multi-strain product VSL#3 was used as a model to setup a microbiological characterization that could be extended to other formulations with high complexity. Shotgun metagenomics by deep Illumina sequencing was applied to DNA isolated from the commercial VSL#3 product to confirm strains identity safety and composition. Single-cell analysis was used to evaluate the cell viability, and β-galactosidase and urease activity have been used as marker to monitor the reproducibility of the production process. Similarly, these lots were characterized in detail by a metaproteomics approach for which a robust protein extraction protocol was combined with advanced mass spectrometry. The results identified over 1600 protein groups belonging to all strains present in the VSL#3 formulation. Of interest, only 3.2 % proteins showed significant differences mainly related to small variations in strain abundance. The protocols developed in this study addressed several quality criteria that are relevant for marketed multi-strain products and these represent the first efforts to define the quality of complex probiotic formulations such as VSL#3.
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Affiliation(s)
- Diego Mora
- Department of Food Environmental and Nutritional Sciences (DeFENS)University of MilanMilanItaly
| | - Rossella Filardi
- Department of Food Environmental and Nutritional Sciences (DeFENS)University of MilanMilanItaly
| | - Stefania Arioli
- Department of Food Environmental and Nutritional Sciences (DeFENS)University of MilanMilanItaly
| | - Sjef Boeren
- Laboratory of BiochemistryWageningen UniversityWageningenThe Netherlands
| | - Steven Aalvink
- Laboratory of MicrobiologyWageningen UniversityWageningenThe Netherlands
| | - Willem M. de Vos
- Laboratory of MicrobiologyWageningen UniversityWageningenThe Netherlands
- Human Microbiome Research Program Unit, Faculty of MedicineUniversity of HelsinkiHelsinkiFinland
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Metabolism of the predominant human milk oligosaccharide fucosyllactose by an infant gut commensal. Sci Rep 2019; 9:15427. [PMID: 31659215 PMCID: PMC6817895 DOI: 10.1038/s41598-019-51901-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 10/09/2019] [Indexed: 12/22/2022] Open
Abstract
A number of bifidobacterial species are found at a particularly high prevalence and abundance in faecal samples of healthy breastfed infants, a phenomenon that is believed to be, at least partially, due to the ability of bifidobacteria to metabolize Human Milk Oligosaccharides (HMOs). In the current study, we isolated a novel strain of Bifidobacterium kashiwanohense, named APCKJ1, from the faeces of a four-week old breastfed infant, based on the ability of the strain to utilise the HMO component fucosyllactose. We then determined the full genome sequence of this strain, and employed the generated data to analyze fucosyllactose metabolism in B. kashiwanohense APCKJ1. Transcriptomic and growth analyses, combined with metabolite analysis, in vitro hydrolysis assays and heterologous expression, allowed us to elucidate the pathway for fucosyllactose metabolism in B. kashiwanohense APCKJ1. Homologs of the key genes for this metabolic pathway were identified in particular in infant-derived members of the Bifdobacterium genus, revealing the apparent niche-specific nature of this pathway, and allowing a broad perspective on bifidobacterial fucosyllactose and L-fucose metabolism.
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77
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Pelicic V. Monoderm bacteria: the new frontier for type IV pilus biology. Mol Microbiol 2019; 112:1674-1683. [PMID: 31556183 PMCID: PMC6916266 DOI: 10.1111/mmi.14397] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2019] [Indexed: 12/11/2022]
Abstract
In the diverse world of bacterial pili, type IV pili (Tfp) are unique for two reasons: their multifunctionality and ubiquity. This latter feature offers an extraordinary possibility, that is, to perform comparative studies in evolutionarily distant species in order to improve our fragmentary understanding of Tfp biology. Regrettably, such potential has remained largely untapped, because, for 20 years, Tfp have only been characterised in diderm bacteria. However, recent studies of Tfp in monoderms have started closing the gap, revealing many interesting commonalities and a few significant differences, extending the frontiers of knowledge of Tfp biology. Here, I review the current state of the art of the Tfp field in monoderm bacteria and discuss resulting implications for our general understanding of the assembly and function of these widespread filamentous nanomachines.
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Affiliation(s)
- Vladimir Pelicic
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
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78
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Alessandri G, Ossiprandi MC, MacSharry J, van Sinderen D, Ventura M. Bifidobacterial Dialogue With Its Human Host and Consequent Modulation of the Immune System. Front Immunol 2019; 10:2348. [PMID: 31632412 PMCID: PMC6779802 DOI: 10.3389/fimmu.2019.02348] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 09/17/2019] [Indexed: 12/12/2022] Open
Abstract
Since bifidobacteria are among the pioneering colonizers of the human infant gut, their interaction with their host is believed to start soon following birth. Several members of the Bifidobacterium genus are purported to exert various health-promoting effects at local and systemic levels, e.g., limiting pathogen colonization/invasion, influencing gut homeostasis, and influencing the immune system through changes in innate and/or adaptive immune responses. This has promoted extensive research efforts to shed light on the precise mechanisms by which bifidobacteria are able to stimulate and interact with the host immune system. These studies uncovered a variety of secreted or surface-associated molecules that act as essential mediators for the establishment of a bifidobacteria-host immune system dialogue, and that allow interactions with mucosa-associated immune cells. Additionally, the by-products generated from bifidobacterial carbohydrate metabolism act as vectors that directly and indirectly trigger the host immune response, the latter by stimulating growth of other commensal microorganisms such as propionate- or butyrate-producing bacteria. This review is aimed to provide a comprehensive overview on the wide variety of strategies employed by bifidobacteria to engage with the host immune system.
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Affiliation(s)
- Giulia Alessandri
- Department of Veterinary Medical Science, University of Parma, Parma, Italy
| | - Maria Cristina Ossiprandi
- Department of Veterinary Medical Science, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - John MacSharry
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Microbiome Research Hub, University of Parma, Parma, Italy
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
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79
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Probiotic Lactobacillus and Bifidobacterium strains possess safety characteristics, antiviral activities and host adherence factors revealed by genome mining. EPMA J 2019; 10:337-350. [PMID: 31832110 DOI: 10.1007/s13167-019-00184-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 08/11/2019] [Indexed: 02/07/2023]
Abstract
Background Probiotics belonging to Lactobacillus and Bifidobacterium spp. have been exploited for their health benefits in treatment and prevention of many pathological conditions and promoting human health. Recent advances in understanding probiotics-human interaction through microbiome research in the context of various medical conditions suggest their provisional role in preventive, personalized, and predictive medicine. To streamline their application in disease prevention, development of personalized-based treatments, or their use as biomarkers for predictive diagnosis, in vitro screening for strains with potential probiotic properties should be performed. In this work, we aimed to emphasize the probiotic features of four Lactobacillus and two Bifidobacterium probiotic strains which showed antagonistic properties against microbial pathogens. Methods Firstly, cytotoxicity assessment of cell-free preparations from these strains was performed using a baby hamster kidney (BHK) cells and cell viability was measured by means of sulfo-rhodamine B stain. Secondly, Newcastle disease (ND) and infectious bursal disease (IBD) viruses which pose a great threat in infected poultry were used for assessing antiviral activity of probiotics. Thirdly, the genomes of six probiotic strains were used to identify genes encoding host adherence factors that mediate interaction with human tissues. Results Probiotic preparations exhibited insignificant toxicity as indicated by the high survival rate of BHK cells (surviving fraction varied from 0.82 to 0.99) as compared to the untreated control. Cell-free preparations of probiotics mixed with equal volume of ND and IBD viruses (106 and 104 Tissue Culture Infectious Dose 50, respectively) reduced the titer of ND and IBD viruses on chicken embryo fibroblast cells. Genome mining analysis revealed that the draft genomes of these strains were predicted to encode LPXTG-containing proteins, surface layer proteins, tight adherence pili, sortase-dependent pili, fibronectin, or collagen binding proteins and other factors that adhere to human tissues such as mucus. Such adherence factors enable probiotic bacteria to interact and colonize the host. Conclusion Taken together, safety privileges, antiviral activities, and genomically encoded host interaction factors confirmed probiotic features of the six probiotic strains and their potential in promoting human health.
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80
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Andrade M, Wang N. The Tad Pilus Apparatus of ' Candidatus Liberibacter asiaticus' and Its Regulation by VisNR. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:1175-1187. [PMID: 30925227 DOI: 10.1094/mpmi-02-19-0052-r] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Citrus huanglongbing (HLB) is one of the most destructive diseases affecting citrus plants. 'Candidatus Liberibacter asiaticus', an uncultivated α-proteobacteria, is the most widely spread causal agent of HLB and is transmitted by the Asian citrus psyllid Diaphorina citri. 'Ca. L. asiaticus' attachment to the psyllid midgut is believed to be critical to further infect other organs, including the salivary gland. In this study, the type IVc tight adherence (Tad) pilus locus encoded by 'Ca. L. asiaticus' was characterized. The Tad loci are conserved among members of Rhizobiaceae, including 'Ca. L. asiaticus' and Agrobacterium spp. Ectopic expression of the 'Ca. L. asiaticus' cpaF gene, an ATPase essential for the biogenesis and secretion of the Tad pilus, restored the adherence phenotype in cpaF mutant of A. tumefaciens, indicating CpaF of 'Ca. L. asiaticus' was functional and critical for bacterial adherence mediated by Tad pilus. Quantitative reverse transcription PCR (qRT-PCR) analysis revealed that 'Ca. L. asiaticus' Tad pilus-encoding genes and 'Ca. L. asiaticus' pilin gene flp3 were upregulated in psyllids compared with in planta. A bacterial one-hybrid assay showed that 'Ca. L. asiaticus' VisN and VisR, members of the LuxR transcriptional factor family, were bound to the flp3 promoter. VisNR regulate flp3. Negative regulation of the flp3 promoter by both VisN and VisR was demonstrated using a shuttle strategy, with analysis of the phenotypes and immunoblotting together with quantification of the expression of the flp3 promoter fused to the β-galactosidase reporter gene. Comparative expression analysis confirmed that 'Ca. L. asiaticus' visNR was less expressed in the psyllid than in the plant host. Further, motility and biofilm phenotypes of the visNR mutant of A. tumefaciens were fully complemented by expressing 'Ca. L. asiaticus' visNR together. The physical interaction between VisN and VisR was confirmed by pull-down and stability assays. The interaction of the flp3 promoter with VisR was verified by electrophoretic mobility shift assay. Taken together, the results revealed the contribution of the Tad pilus apparatus in the colonization of the insect vector by 'Ca. L. asiaticus' and shed light on the involvement of VisNR in regulation of the Tad locus.
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Affiliation(s)
- Maxuel Andrade
- Citrus Research and Education Center (CREC), Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL 33850, U.S.A
| | - Nian Wang
- Citrus Research and Education Center (CREC), Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL 33850, U.S.A
- China-USA Citrus Huanglongbing Joint Laboratory (A joint laboratory of the University of Florida Institute of Food and Agricultural Sciences and Gannan Normal University), National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou 341000, China
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81
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Zakharevich NV, Nezametdinova VZ, Averina OV, Chekalina MS, Alekseeva MG, Danilenko VN. Complete Genome Sequence of Bifidobacterium angulatum GT102: Potential Genes and Systems of Communication with Host. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419070160] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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82
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Dias GM, de Sousa Pires A, Grilo VS, Castro MR, de Figueiredo Vilela L, Neves BC. Comparative genomics of Paraburkholderia kururiensis and its potential in bioremediation, biofertilization, and biocontrol of plant pathogens. Microbiologyopen 2019; 8:e00801. [PMID: 30811107 PMCID: PMC6692535 DOI: 10.1002/mbo3.801] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 12/19/2018] [Accepted: 12/29/2018] [Indexed: 12/23/2022] Open
Abstract
Burkholderia harbors versatile Gram-negative species and is β-Proteobacteria. Recently, it was proposed to split the genus in two main branches: one of animal and plant pathogens and another, Paraburkholderia, harboring environmental and plant-beneficial species. Currently, Paraburkholderia comprises more than 70 species with ability to occupy very diverse environmental niches. Herein, we sequenced and analyzed the genome of Paraburkholderia kururiensis type strain KP23T , and compared to P. kururiensis M130, isolated in Brazil, and P. kururiensis susbp. thiooxydans, from Korea. This study focused on the gene content of the three genomes with special emphasis on their potential of plant-association, biocontrol, and bioremediation. The comparative analyses revealed several genes related to plant benefits, including biosynthesis of IAA, ACC deaminase, multiple efflux pumps, dioxygenases, and degradation of aromatic compounds. Importantly, a range of genes for protein secretion systems (type III, IV, V, and VI) were characterized, potentially involved in P. kururiensis well documented ability to establish endophytic association with plants. These findings shed light onto bacteria-plant interaction mechanisms at molecular level, adding novel information that supports their potential application in bioremediation, biofertilization, and biocontrol of plant pathogens. P. kururiensis emerges as a promising model to investigate adaptation mechanisms in different ecological niches.
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Affiliation(s)
- Graciela M. Dias
- Department of BiochemistryChemistry InstituteFederal University of Rio de JaneiroRio de JaneiroBrazil
| | - Araceli de Sousa Pires
- Department of BiochemistryChemistry InstituteFederal University of Rio de JaneiroRio de JaneiroBrazil
| | - Vinicius S. Grilo
- Department of BiochemistryChemistry InstituteFederal University of Rio de JaneiroRio de JaneiroBrazil
| | - Michele R. Castro
- Department of BiochemistryChemistry InstituteFederal University of Rio de JaneiroRio de JaneiroBrazil
- Department of BiologyFederal Institute of Rio de JaneiroRio de JaneiroBrazil
| | | | - Bianca C. Neves
- Department of BiochemistryChemistry InstituteFederal University of Rio de JaneiroRio de JaneiroBrazil
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Bottacini F, Morrissey R, Roberts R, James K, van Breen J, Egan M, Lambert J, van Limpt K, Knol J, Motherway M, van Sinderen D. Comparative genome and methylome analysis reveals restriction/modification system diversity in the gut commensal Bifidobacterium breve. Nucleic Acids Res 2019; 46:1860-1877. [PMID: 29294107 PMCID: PMC5829577 DOI: 10.1093/nar/gkx1289] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 12/18/2017] [Indexed: 11/12/2022] Open
Abstract
Bifidobacterium breve represents one of the most abundant bifidobacterial species in the gastro-intestinal tract of breast-fed infants, where their presence is believed to exert beneficial effects. In the present study whole genome sequencing, employing the PacBio Single Molecule, Real-Time (SMRT) sequencing platform, combined with comparative genome analysis allowed the most extensive genetic investigation of this taxon. Our findings demonstrate that genes encoding Restriction/Modification (R/M) systems constitute a substantial part of the B. breve variable gene content (or variome). Using the methylome data generated by SMRT sequencing, combined with targeted Illumina bisulfite sequencing (BS-seq) and comparative genome analysis, we were able to detect methylation recognition motifs and assign these to identified B. breve R/M systems, where in several cases such assignments were confirmed by restriction analysis. Furthermore, we show that R/M systems typically impose a very significant barrier to genetic accessibility of B. breve strains, and that cloning of a methyltransferase-encoding gene may overcome such a barrier, thus allowing future functional investigations of members of this species.
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Affiliation(s)
- Francesca Bottacini
- APC Microbiome Institute & Department of Microbiology, National University of Ireland, Cork, Ireland
| | - Ruth Morrissey
- APC Microbiome Institute & Department of Microbiology, National University of Ireland, Cork, Ireland
| | | | - Kieran James
- APC Microbiome Institute & Department of Microbiology, National University of Ireland, Cork, Ireland
| | - Justin van Breen
- APC Microbiome Institute & Department of Microbiology, National University of Ireland, Cork, Ireland
| | - Muireann Egan
- APC Microbiome Institute & Department of Microbiology, National University of Ireland, Cork, Ireland
| | | | | | - Jan Knol
- Nutricia Research, Utrecht, the Netherlands
- Laboratory of Microbiology, Wageningen Univerisity, Wageningen
| | - Mary O’Connell Motherway
- APC Microbiome Institute & Department of Microbiology, National University of Ireland, Cork, Ireland
| | - Douwe van Sinderen
- APC Microbiome Institute & Department of Microbiology, National University of Ireland, Cork, Ireland
- To whom correspondence should be addressed. Tel: +353 21 4901365; Fax: +353 21 4903101;
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Monteagudo-Mera A, Rastall RA, Gibson GR, Charalampopoulos D, Chatzifragkou A. Adhesion mechanisms mediated by probiotics and prebiotics and their potential impact on human health. Appl Microbiol Biotechnol 2019; 103:6463-6472. [PMID: 31267231 PMCID: PMC6667406 DOI: 10.1007/s00253-019-09978-7] [Citation(s) in RCA: 299] [Impact Index Per Article: 59.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 06/07/2019] [Accepted: 06/10/2019] [Indexed: 12/14/2022]
Abstract
Adhesion ability to the host is a classical selection criterion for potential probiotic bacteria that could result in a transient colonisation that would help to promote immunomodulatory effects, as well as stimulate gut barrier and metabolic functions. In addition, probiotic bacteria have a potential protective role against enteropathogens through different mechanisms including production of antimicrobial compounds, reduction of pathogenic bacterial adhesion and competition for host cell binding sites. The competitive exclusion by probiotic bacteria has a beneficial effect not only on the gut but also in the urogenital tract and oral cavity. On the other hand, prebiotics may also act as barriers to pathogens and toxins by preventing their adhesion to epithelial receptors. In vitro studies with different intestinal cell lines have been widely used along the last decades to assess the adherence ability of probiotic bacteria and pathogen antagonism. However, extrapolation of these results to in vivo conditions still remains unclear, leading to the need of optimisation of more complex in vitro approaches that include interaction with the resident microbiota to address the current limitations. The aim of this mini review is to provide a comprehensive overview on the potential effect of the adhesive properties of probiotics and prebiotics on the host by focusing on the most recent findings related with adhesion and immunomodulatory and antipathogenic effect on human health.
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Affiliation(s)
- Andrea Monteagudo-Mera
- Biomedical Sciences, School of Biological Sciences, University of Reading, Reading, RG6 6AH, UK.
| | - Robert A Rastall
- Department of Food and Nutritional Sciences, University of Reading, Whiteknights, PO Box 226, Reading, RG6 6AP, UK
| | - Glenn R Gibson
- Department of Food and Nutritional Sciences, University of Reading, Whiteknights, PO Box 226, Reading, RG6 6AP, UK
| | - Dimitris Charalampopoulos
- Department of Food and Nutritional Sciences, University of Reading, Whiteknights, PO Box 226, Reading, RG6 6AP, UK
| | - Afroditi Chatzifragkou
- Department of Food and Nutritional Sciences, University of Reading, Whiteknights, PO Box 226, Reading, RG6 6AP, UK.
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Denise R, Abby SS, Rocha EPC. Diversification of the type IV filament superfamily into machines for adhesion, protein secretion, DNA uptake, and motility. PLoS Biol 2019; 17:e3000390. [PMID: 31323028 PMCID: PMC6668835 DOI: 10.1371/journal.pbio.3000390] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 07/31/2019] [Accepted: 07/03/2019] [Indexed: 12/21/2022] Open
Abstract
Processes of molecular innovation require tinkering and shifting in the function of existing genes. How this occurs in terms of molecular evolution at long evolutionary scales remains poorly understood. Here, we analyse the natural history of a vast group of membrane-associated molecular systems in Bacteria and Archaea-the type IV filament (TFF) superfamily-that diversified in systems involved in flagellar or twitching motility, adhesion, protein secretion, and DNA uptake. The phylogeny of the thousands of detected systems suggests they may have been present in the last universal common ancestor. From there, two lineages-a bacterial and an archaeal-diversified by multiple gene duplications, gene fissions and deletions, and accretion of novel components. Surprisingly, we find that the 'tight adherence' (Tad) systems originated from the interkingdom transfer from Archaea to Bacteria of a system resembling the 'EppA-dependent' (Epd) pilus and were associated with the acquisition of a secretin. The phylogeny and content of ancestral systems suggest that initial bacterial pili were engaged in cell motility and/or DNA uptake. In contrast, specialised protein secretion systems arose several times independently and much later in natural history. The functional diversification of the TFF superfamily was accompanied by genetic rearrangements with implications for genetic regulation and horizontal gene transfer: systems encoded in fewer loci were more frequently exchanged between taxa. This may have contributed to their rapid evolution and spread across Bacteria and Archaea. Hence, the evolutionary history of the superfamily reveals an impressive catalogue of molecular evolution mechanisms that resulted in remarkable functional innovation and specialisation from a relatively small set of components.
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Affiliation(s)
- Rémi Denise
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, Paris, France
- Sorbonne Université, Collège doctoral, Paris, France
| | - Sophie S. Abby
- Université Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, Grenoble, France
| | - Eduardo P. C. Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, Paris, France
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86
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87
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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: 42] [Impact Index Per Article: 8.4] [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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88
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Liew-Littorin C, Brüggemann H, Davidsson S, Nilsdotter-Augustinsson Å, Hellmark B, Söderquist B. Clonal diversity of Cutibacterium acnes (formerly Propionibacterium acnes) in prosthetic joint infections. Anaerobe 2019; 59:54-60. [PMID: 31075312 DOI: 10.1016/j.anaerobe.2019.04.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/11/2019] [Accepted: 04/30/2019] [Indexed: 11/20/2022]
Abstract
Prosthetic joint infections (PJIs) are rare but feared complications following joint replacement surgery. Cutibacterium acnes is a skin commensal that is best known for its role in acne vulgaris but can also cause invasive infections such as PJIs. Some phylotypes might be associated with specific diseases, and recently, a plasmid was detected that might harbour important virulence genes. In this study, we characterized C. acnes isolates from 63 patients with PJIs (n = 140 isolates) and from the skin of 56 healthy individuals (n = 56 isolates), using molecular methods to determine the phylotype and investigate the presence of the plasmid. Single-locus sequence typing and a polymerase chain reaction designed to detect the plasmid were performed on all 196 isolates. No statistically significant differences in sequence types were seen between the two study groups indicating that the C. acnes that causes PJIs originates from the patients own normal skin microbiota. Of the 27 patients with multiple tissue samples, 19 displayed the same sequence types among all their samples. Single-locus sequence typing identified different genotypes among consecutive C. acnes isolates from four patients with recurrent infections. The plasmid was found among 17 isolates distributed in both groups, indicating that it might not be a marker for virulence regarding PJIs. Patients presenting multiple sequence types in tissue samples may represent contamination or a true polyclonal infection due to C. acnes.
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Affiliation(s)
- C Liew-Littorin
- Department of Laboratory Medicine, Clinical Microbiology, Örebro University Hospital, Sweden.
| | - H Brüggemann
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - S Davidsson
- Department of Urology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Å Nilsdotter-Augustinsson
- Department of Infectious Diseases and Department of Clinical and Experimental Medicine, Linköping University, Norrköping, Sweden
| | - B Hellmark
- Department of Laboratory Medicine, Clinical Microbiology, Örebro University Hospital, Sweden
| | - B Söderquist
- Department of Laboratory Medicine, Clinical Microbiology, Örebro University Hospital, Sweden; School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Sweden
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89
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Béthencourt L, Boubakri H, Taib N, Normand P, Armengaud J, Fournier P, Brochier-Armanet C, Herrera-Belaroussi A. Comparative genomics and proteogenomics highlight key molecular players involved in Frankia sporulation. Res Microbiol 2019; 170:202-213. [PMID: 31018159 DOI: 10.1016/j.resmic.2019.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 04/15/2019] [Accepted: 04/16/2019] [Indexed: 10/27/2022]
Abstract
Sporulation is a microbial adaptive strategy to resist inhospitable conditions for vegetative growth and to disperse to colonise more favourable environments. This microbial trait is widespread in Actinobacteria. Among them, Frankia strains are able to differentiate sporangia in pure culture, while others can sporulate even when in symbiosis with sporulation occurring within host cells. The molecular determinants controlling Frankia sporulation have not been yet described. In order to highlight, for the first time, the molecular players potentially involved in Frankia sporulation, we conducted (i) a comparison of protein contents between Frankia spores and hyphae and (ii) a comparative genomic analysis of Frankia proteomes with sporulating and non-sporulating Actinobacteria. Among the main results, glycogen-metabolism related proteins, as well as oxidative stress response and protease-like proteins were overdetected in hyphae, recalling lytic processes that allow Streptomyces cells to erect sporogenic hyphae. Several genes encoding transcriptional regulators, including GntR-like, appeared up-regulated in spores, as well as tyrosinase, suggesting their potential role in mature spore metabolism. Finally, our results highlighted new proteins potentially involved in Frankia sporulation, including a pyrophosphate-energized proton pump and YaaT, described as involved in the phosphorelay allowing sporulation in Bacillus subtilis, leading us to discuss the role of a phosphorelay in Frankia sporulation.
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Affiliation(s)
- Lorine Béthencourt
- Écologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMR 1418, Villeurbanne, 69622 Cedex, France
| | - Hasna Boubakri
- Écologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMR 1418, Villeurbanne, 69622 Cedex, France
| | - Najwa Taib
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, F-69622, Villeurbanne, France
| | - Philippe Normand
- Écologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMR 1418, Villeurbanne, 69622 Cedex, France
| | - Jean Armengaud
- Laboratoire Innovations Technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, Bagnols sur Cèze, F-30207, France
| | - Pascale Fournier
- Écologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMR 1418, Villeurbanne, 69622 Cedex, France
| | - Céline Brochier-Armanet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, F-69622, Villeurbanne, France
| | - Aude Herrera-Belaroussi
- Écologie Microbienne, Centre National de la Recherche Scientifique UMR 5557, Université de Lyon, Université Claude Bernard Lyon I, INRA, UMR 1418, Villeurbanne, 69622 Cedex, France.
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90
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Megta AK, Mishra AK, Palva A, von Ossowski I, Krishnan V. Crystal structure of basal pilin SpaE reveals the molecular basis of its incorporation in the lactobacillar SpaFED pilus. J Struct Biol 2019; 207:74-84. [PMID: 31026587 DOI: 10.1016/j.jsb.2019.04.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 04/15/2019] [Accepted: 04/23/2019] [Indexed: 11/16/2022]
Abstract
For some Gram-positive genera and species, the long-extended and adhesive sortase-dependent pilus plays an essential role during host colonization, biofilm formation, and immune modulation. Lactobacillus rhamnosus GG is a gut-adapted commensal strain that harbors the operonic genes for the SpaCBA and SpaFED pili, both being comprised of three different protein subunits termed the backbone, tip, and basal pilins. Crystal structures of the backbone pilins (SpaA and SpaD) have recently been solved, and here we describe the high-resolution (1.5 Å) structural determination of the SpaE basal pilin. SpaE consists of two immunoglobulin-like CnaB domains, with each displaying a spontaneously formed internal isopeptide bond, though apparently slow forming in the N-terminal domain. Remarkably, SpaE contains an atypically lengthy unstructured C-terminal tail, along with an YPKN pilin motif peptide, which is normally reserved for backbone subunits. Based on our analysis of the crystal structure data, we provide a molecular model for the basal positioning of the SpaE pilin within the SpaFED pilus.
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Affiliation(s)
- Abhin Kumar Megta
- Laboratory of Structural Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana 121 001, India; School of Biotechnology, KIIT University, Odisha 751024, India
| | - Arjun K Mishra
- Laboratory of Structural Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana 121 001, India
| | - Airi Palva
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | | | - Vengadesan Krishnan
- Laboratory of Structural Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana 121 001, India.
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91
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Koppenhöfer S, Wang H, Scharfe M, Kaever V, Wagner-Döbler I, Tomasch J. Integrated Transcriptional Regulatory Network of Quorum Sensing, Replication Control, and SOS Response in Dinoroseobacter shibae. Front Microbiol 2019; 10:803. [PMID: 31031742 PMCID: PMC6473078 DOI: 10.3389/fmicb.2019.00803] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 03/28/2019] [Indexed: 12/13/2022] Open
Abstract
Quorum sensing (QS) coordinates population wide gene expression of bacterial species. Highly adaptive traits like gene transfer agents (GTA), morphological heterogeneity, type 4 secretion systems (T4SS), and flagella are QS controlled in Dinoroseobacter shibae, a Roseobacter model organism. Its QS regulatory network is integrated with the CtrA phosphorelay that controls cell division in alphaproteobacteria. To elucidate the network topology, we analyzed the transcriptional response of the QS-negative D. shibae strain ΔluxI1 toward externally added autoinducer (AI) over a time period of 3 h. The signaling cascade is initiated by the CtrA phosphorelay, followed by the QS genes and other target genes, including the second messenger c-di-GMP, competence, flagella and pili. Identification of transcription factor binding sites in promoters of QS induced genes revealed the integration of QS, CtrA phosphorelay and the SOS stress response mediated by LexA. The concentration of regulatory genes located close to the origin or terminus of replication suggests that gene regulation and replication are tightly coupled. Indeed, addition of AI first stimulates and then represses replication. The restart of replication comes along with increased c-di-GMP levels. We propose a model in which QS induces replication followed by differentiation into GTA producing and non-producing cells. CtrA-activity is controlled by the c-di-GMP level, allowing some of the daughter cells to replicate again. The size of the GTA producing subpopulation is tightly controlled by QS via the AI Synthase LuxI2. Finally, induction of the SOS response allows for integration of GTA DNA into the host chromosome.
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Affiliation(s)
- Sonja Koppenhöfer
- Group Microbial Communication, Technical University of Braunschweig, Braunschweig, Germany.,Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Hui Wang
- Group Microbial Communication, Technical University of Braunschweig, Braunschweig, Germany
| | - Maren Scharfe
- Group Genomic Analytics, Helmholtz Centre for Infection Research, Helmholtz Association of German Research Centers, Braunschweig, Germany
| | - Volkhard Kaever
- Research Core Unit Metabolomics, Institute of Pharmacology, Hannover Medical School, Hanover, Germany
| | - Irene Wagner-Döbler
- Group Microbial Communication, Technical University of Braunschweig, Braunschweig, Germany
| | - Jürgen Tomasch
- Group Microbial Communication, Technical University of Braunschweig, Braunschweig, Germany
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92
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Alessandri G, Milani C, Duranti S, Mancabelli L, Ranjanoro T, Modica S, Carnevali L, Statello R, Bottacini F, Turroni F, Ossiprandi MC, Sgoifo A, van Sinderen D, Ventura M. Ability of bifidobacteria to metabolize chitin-glucan and its impact on the gut microbiota. Sci Rep 2019; 9:5755. [PMID: 30962486 PMCID: PMC6453949 DOI: 10.1038/s41598-019-42257-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 03/22/2019] [Indexed: 01/26/2023] Open
Abstract
Chitin-glucan (CG) represents a natural carbohydrate source for certain microbial inhabitants of the human gut and may act as a prebiotic for a number of bacterial taxa. However, the bifidogenic activity of this substrate is still unknown. In the current study, we evaluated the ability of chitin-glucan to influence growth of 100 bifidobacterial strains belonging to those species commonly identified within the bifidobacterial communities residing in the infant and adult human gut. Such analyses were coupled with transcriptome experiments directed to explore the transcriptional effects of CG on Bifidobacterium breve 2L, which was shown to elicit the highest growth performance on this natural polysaccharide. In addition, an in vivo trial involving a rat model revealed how the colonization efficiency of this bifidobacterial strain was enhanced when the animals were fed with a diet containing CG. Altogether our analyses indicate that CG is a valuable novel prebiotic compound that may be added to the human diet in order to re-establish/reinforce bifidobacteria colonization in the mammalian gut.
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Affiliation(s)
- Giulia Alessandri
- Department of Veterinary Medical Science, 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
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | | | | | - Luca Carnevali
- Stress Physiology Laboratory, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Rosario Statello
- Stress Physiology Laboratory, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Francesca Bottacini
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Andrea Sgoifo
- Stress Physiology Laboratory, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Department of Veterinary Medical Science, University of Parma, Parma, Italy.
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93
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Dissecting the Evolutionary Development of the Species Bifidobacterium animalis through Comparative Genomics Analyses. Appl Environ Microbiol 2019; 85:AEM.02806-18. [PMID: 30709821 DOI: 10.1128/aem.02806-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 01/28/2019] [Indexed: 12/20/2022] Open
Abstract
Bifidobacteria are members of the gut microbiota of animals, including mammals, birds, and social insects. In this study, we analyzed and determined the pangenome of Bifidobacterium animalis species, encompassing B. animalis subsp. animalis and the B. animalis subsp. lactis taxon, which is one of the most intensely exploited probiotic bifidobacterial species. In order to reveal differences within the B. animalis species, detailed comparative genomics and phylogenomics analyses were performed, indicating that these two subspecies recently arose through divergent evolutionary events. A subspecies-specific core genome was identified for both B. animalis subspecies, revealing the existence of subspecies-defining genes involved in carbohydrate metabolism. Notably, these in silico analyses coupled with carbohydrate profiling assays suggest genetic adaptations toward a distinct glycan milieu for each member of the B. animalis subspecies, resulting in a divergent evolutionary development of the two subspecies.IMPORTANCE The majority of characterized B. animalis strains have been isolated from human fecal samples. In order to explore genome variability within this species, we isolated 15 novel strains from the gastrointestinal tracts of different animals, including mammals and birds. The present study allowed us to reconstruct the pangenome of this taxon, including the genome contents of 56 B. animalis strains. Through careful assessment of subspecies-specific core genes of the B. animalis subsp. animalis/lactis taxon, we identified genes encoding enzymes involved in carbohydrate transport and metabolism, while unveiling specific gene acquisition and loss events that caused the evolutionary emergence of these two subspecies.
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94
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Milani C, Duranti S, Napoli S, Alessandri G, Mancabelli L, Anzalone R, Longhi G, Viappiani A, Mangifesta M, Lugli GA, Bernasconi S, Ossiprandi MC, van Sinderen D, Ventura M, Turroni F. Colonization of the human gut by bovine bacteria present in Parmesan cheese. Nat Commun 2019; 10:1286. [PMID: 30894548 PMCID: PMC6426854 DOI: 10.1038/s41467-019-09303-w] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 02/28/2019] [Indexed: 12/21/2022] Open
Abstract
The abilities of certain microorganisms to be transferred across the food production chain, persist in the final product and, potentially, colonize the human gut are poorly understood. Here, we provide strain-level evidence supporting that dairy cattle-associated bacteria can be transferred to the human gut via consumption of Parmesan cheese. We characterize the microbial communities in samples taken from five different locations across the Parmesan cheese production chain, confirming that the final product contains microorganisms derived from cattle gut, milk, and the nearby environment. In addition, we carry out a human pilot study showing that Bifidobacterium mongoliense strains from cheese can transiently colonize the human gut, a process that can be enhanced by cow milk consumption. Some microorganisms may be transferred across the food production chain and, potentially, colonize the human gut. Here, Milani et al. provide strain-level evidence supporting that dairy cattle-associated bacteria can be transferred to the human gut via consumption of Parmesan cheese.
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Affiliation(s)
- Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, 43124, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, 43124, Italy
| | | | - Giulia Alessandri
- Department of Veterinary Science, University of Parma, Parma, 43126, Italy
| | | | | | | | | | - Marta Mangifesta
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, 43124, Italy.,GenProbio srl, Parma, 43124, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, 43124, Italy
| | | | | | - Douwe van Sinderen
- Department of Veterinary Science, University of Parma, Parma, 43126, Italy.,APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, 43124, Italy. .,Microbiome Research Hub, University of Parma, Parma, 43124, Italy.
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, 43124, Italy. .,Microbiome Research Hub, University of Parma, Parma, 43124, Italy.
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95
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Douillard FP, de Vos WM. Biotechnology of health-promoting bacteria. Biotechnol Adv 2019; 37:107369. [PMID: 30876799 DOI: 10.1016/j.biotechadv.2019.03.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 02/15/2019] [Accepted: 03/11/2019] [Indexed: 12/20/2022]
Abstract
Over the last decade, there has been an increasing scientific and public interest in bacteria that may positively contribute to human gut health and well-being. This interest is reflected by the ever-increasing number of developed functional food products containing health-promoting bacteria and reaching the market place as well as by the growing revenue and profits of notably bacterial supplements worldwide. Traditionally, the origin of probiotic-marketed bacteria was limited to a rather small number of bacterial species that mostly belong to lactic acid bacteria and bifidobacteria. Intensifying research efforts on the human gut microbiome offered novel insights into the role of human gut microbiota in health and disease, while also providing a deep and increasingly comprehensive understanding of the bacterial communities present in this complex ecosystem and their interactions with the gut-liver-brain axis. This resulted in rational and systematic approaches to select novel health-promoting bacteria or to engineer existing bacteria with enhanced probiotic properties. In parallel, the field of gut microbiomics developed into a fertile framework for the identification, isolation and characterization of a phylogenetically diverse array of health-promoting bacterial species, also called next-generation therapeutic bacteria. The present review will address these developments with specific attention for the selection and improvement of a selected number of health-promoting bacterial species and strains that are extensively studied or hold promise for future food or pharma product development.
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Affiliation(s)
- François P Douillard
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Willem M de Vos
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
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96
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97
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Bovine colostrum-driven modulation of intestinal epithelial cells for increased commensal colonisation. Appl Microbiol Biotechnol 2019; 103:2745-2758. [PMID: 30685814 DOI: 10.1007/s00253-019-09642-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 01/04/2019] [Accepted: 01/10/2019] [Indexed: 01/04/2023]
Abstract
Nutritional intake may influence the intestinal epithelial glycome and in turn the available attachment sites for bacteria. In this study, we tested the hypothesis that bovine colostrum may influence the intestinal cell surface and in turn the attachment of commensal organisms. Human HT-29 intestinal cells were exposed to a bovine colostrum fraction (BCF) rich in free oligosaccharides. The adherence of several commensal bacteria, comprising mainly bifidobacteria, to the intestinal cells was significantly enhanced (up to 52-fold) for all strains tested which spanned species that are found across the human lifespan. Importantly, the changes to the HT-29 cell surface did not support enhanced adhesion of the enteric pathogens tested. The gene expression profile of the HT-29 cells following treatment with the BCF was evaluated by microarray analysis. Many so called "glyco-genes" (glycosyltransferases and genes involved in the complex biosynthetic pathways of glycans) were found to be differentially regulated suggesting modulation of the enzymatic addition of sugars to glycoconjugate proteins. The microarray data was further validated by means of real-time PCR. The current findings provide an insight into how commensal microorganisms colonise the human gut and highlight the potential of colostrum and milk components as functional ingredients that can potentially increase commensal numbers in individuals with lower counts of health-promoting bacteria.
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98
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Li T, Zhang Q, Wang R, Zhang S, Pei J, Li Y, Li L, Zhou R. The roles of flp1 and tadD in Actinobacillus pleuropneumoniae pilus biosynthesis and pathogenicity. Microb Pathog 2019; 126:310-317. [DOI: 10.1016/j.micpath.2018.11.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 11/02/2018] [Accepted: 11/05/2018] [Indexed: 01/07/2023]
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99
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Stefani S, Ngatidjan S, Paotiana M, Sitompul KA, Abdullah M, Sulistianingsih DP, Shankar AH, Agustina R. Dietary quality of predominantly traditional diets is associated with blood glucose profiles, but not with total fecal Bifidobacterium in Indonesian women. PLoS One 2018; 13:e0208815. [PMID: 30576336 PMCID: PMC6303024 DOI: 10.1371/journal.pone.0208815] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 11/25/2018] [Indexed: 12/15/2022] Open
Abstract
Background A high quality modern diet is associated with reduced risk of metabolic disease and diabetes. However, it remains unclear whether the quality of predominantly traditional ethnic diets is associated with such conditions. Moreover, the relationship between dietary quality and microbiota, a potential mediator of metabolic disease, has not been studied. Objective We investigated the relationship of dietary quality of traditional ethnic diets in Indonesia with fasting blood glucose (FBG), HbA1c, and the number of fecal Bifidobacterium. Design A cross-sectional study was conducted in selected districts with predominantly animal- or plant-based traditional diets of West Sumatera and West Java provinces, respectively. A total of 240 apparently healthy women aged 19–50 years were randomly selected from 360 women screened by a cluster sampling design. Dietary quality was assessed by 2-day repeated 24-hour food recall, and scored using the Healthy Eating Index (HEI) 2010. FBG was quantified with the enzymatic colorimetric method, and HbA1c by using hexokinase and high-performance liquid chromatography, and total fecal Bifidobacterium by real-time quantitative polymerase chain reaction. Results The HEI scores of 99% of women were <51, indicating a low-quality diet. In adjusted multivariate regression, HEI was inversely associated with FBG (ß = -0.403; 95% CI = -0.789 to -0.016; p = 0.041) and HbA1c (ß = -0.018; 95% CI = -0.036 to 0.000; p = 0.048) but was not significantly associated with total levels of Bifidobacterium (ß = -0.007, p = 0.275). Bifidobacterium count was not significantly associated with either FBG or HbA1c levels. Conclusion Low dietary quality is clearly associated with risk of increased markers of blood glucose. However, any mediating role of Bifidobacterium between dietary quality and glucose outcomes was not apparent. Innovative interventions for healthy eating should be implemented to increase dietary quality of populations transitioning from predominantly traditional to modern diets, to reduce the risk of diabetes, especially in women.
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Affiliation(s)
- Shiela Stefani
- Department of Nutrition, Faculty of Medicine, Universitas Indonesia—Dr. Cipto Mangunkusumo General Hospital, Jakarta, Indonesia
| | - Sanny Ngatidjan
- Department of Nutrition, Faculty of Medicine, Universitas Indonesia—Dr. Cipto Mangunkusumo General Hospital, Jakarta, Indonesia
| | - Monica Paotiana
- Department of Nutrition, Faculty of Medicine, Universitas Indonesia—Dr. Cipto Mangunkusumo General Hospital, Jakarta, Indonesia
| | - Kurnia A. Sitompul
- Department of Nutrition, Faculty of Medicine, Universitas Indonesia—Dr. Cipto Mangunkusumo General Hospital, Jakarta, Indonesia
| | - Murdani Abdullah
- Department of Internal Medicine, Faculty of Medicine Universitas Indonesia—Dr. Cipto Mangunkusumo General Hospital, Jakarta, Indonesia
- Human Nutrition Research Center, Indonesian Medical Education and Research Institute, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Dyah P. Sulistianingsih
- Department of Internal Medicine, Faculty of Medicine Universitas Indonesia—Dr. Cipto Mangunkusumo General Hospital, Jakarta, Indonesia
| | - Anuraj H. Shankar
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, United States of America
| | - Rina Agustina
- Department of Nutrition, Faculty of Medicine, Universitas Indonesia—Dr. Cipto Mangunkusumo General Hospital, Jakarta, Indonesia
- Human Nutrition Research Center, Indonesian Medical Education and Research Institute, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
- Southeast Asian Ministers of Education Organization Regional Centre for Food and Nutrition (SEAMEO RECFON)/ Pusat Kajian Gizi Regional (PKGR), Universitas Indonesia, Jakarta, Indonesia
- * E-mail: ,
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100
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O'Connell Motherway M, Houston A, O’Callaghan G, Reunanen J, O’Brien F, O’Driscoll T, Casey PG, de Vos WM, van Sinderen D, Shanahan F. A Bifidobacterial pilus-associated protein promotes colonic epithelial proliferation. Mol Microbiol 2018; 111:287-301. [DOI: 10.1111/mmi.14155] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2018] [Indexed: 01/15/2023]
Affiliation(s)
- Mary O'Connell Motherway
- APC Microbiome Ireland, National University of Ireland; Western Road Cork Ireland
- School of Microbiology; National University of Ireland; Western Road Cork Ireland
| | - Aileen Houston
- APC Microbiome Ireland, National University of Ireland; Western Road Cork Ireland
- Department of Medicine; National University of Ireland, Cork University Hospital; Cork Ireland
| | - Grace O’Callaghan
- APC Microbiome Ireland, National University of Ireland; Western Road Cork Ireland
- Department of Medicine; National University of Ireland, Cork University Hospital; Cork Ireland
| | - Justus Reunanen
- Research Programme Unit Immunobiology, Department of Bacteriology and Immunology; Helsinki University; Helsinki Finland
- Cancer and Translational Medicine Research Unit and Biocenter Oulu; University of Oulu; Oulu Finland
| | - Frances O’Brien
- APC Microbiome Ireland, National University of Ireland; Western Road Cork Ireland
| | - Tara O’Driscoll
- APC Microbiome Ireland, National University of Ireland; Western Road Cork Ireland
| | - Patrick G. Casey
- APC Microbiome Ireland, National University of Ireland; Western Road Cork Ireland
| | - Willem M. de Vos
- Research Programme Unit Immunobiology, Department of Bacteriology and Immunology; Helsinki University; Helsinki Finland
- Laboratory of Microbiology; Wageningen University; The Netherlands
| | - Douwe van Sinderen
- APC Microbiome Ireland, National University of Ireland; Western Road Cork Ireland
- School of Microbiology; National University of Ireland; Western Road Cork Ireland
| | - Fergus Shanahan
- APC Microbiome Ireland, National University of Ireland; Western Road Cork Ireland
- Department of Medicine; National University of Ireland, Cork University Hospital; Cork Ireland
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