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Argentini C, Lugli GA, Tarracchini C, Fontana F, Mancabelli L, Viappiani A, Anzalone R, Angelini L, Alessandri G, Bianchi MG, Taurino G, Bussolati O, Milani C, van Sinderen D, Turroni F, Ventura M. Ecology- and genome-based identification of the Bifidobacterium adolescentis prototype of the healthy human gut microbiota. Appl Environ Microbiol 2024; 90:e0201423. [PMID: 38294252 PMCID: PMC10880601 DOI: 10.1128/aem.02014-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 11/20/2023] [Indexed: 02/01/2024] Open
Abstract
Bifidobacteria are among the first microbial colonizers of the human gut, being frequently associated with human health-promoting activities. In the current study, an in silico methodology based on an ecological and phylogenomic-driven approach allowed the selection of a Bifidobacterium adolescentis prototype strain, i.e., B. adolescentis PRL2023, which best represents the overall genetic content and functional features of the B. adolescentis taxon. Such features were confirmed by in vitro experiments aimed at evaluating the ability of this strain to survive in the gastrointestinal tract of the host and its ability to interact with human intestinal cells and other microbial gut commensals. In this context, co-cultivation of B. adolescentis PRL2023 and several gut commensals revealed various microbe-microbe interactions and indicated co-metabolism of particular plant-derived glycans, such as xylan.IMPORTANCEThe use of appropriate bacterial strains in experimental research becomes imperative in order to investigate bacterial behavior while mimicking the natural environment. In the current study, through in silico and in vitro methodologies, we were able to identify the most representative strain of the Bifidobacterium adolescentis species. The ability of this strain, B. adolescentis PRL2023, to cope with the environmental challenges imposed by the gastrointestinal tract, together with its ability to switch its carbohydrate metabolism to compete with other gut microorganisms, makes it an ideal choice as a B. adolescentis prototype and a member of the healthy microbiota of adults. This strain possesses a genetic blueprint appropriate for its exploitation as a candidate for next-generation probiotics.
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Affiliation(s)
- Chiara Argentini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Chiara Tarracchini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Federico Fontana
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- GenProbio srl, Parma, Italy
| | - Leonardo Mancabelli
- Microbiome Research Hub, University of Parma, Parma, Italy
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | | | | | | | - Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Massimiliano G. Bianchi
- Microbiome Research Hub, University of Parma, Parma, Italy
- Department of Medicine and Surgery, Laboratory of General Pathology, University of Parma, Parma, Italy
| | - Giuseppe Taurino
- Microbiome Research Hub, University of Parma, Parma, Italy
- Department of Medicine and Surgery, Laboratory of General Pathology, University of Parma, Parma, Italy
| | - Ovidio Bussolati
- Microbiome Research Hub, University of Parma, Parma, Italy
- Department of Medicine and Surgery, Laboratory of General Pathology, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- 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
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
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2
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Zhai Z, Xiong Y, Gu Y, Lei Y, An H, Yi H, Zhao L, Ren F, Hao Y. Up-regulation of sortase-dependent pili in Bifidobacterium longum BBMN68 in response to bile stress enhances its adhesion to HT-29 cells. Int J Biol Macromol 2024; 257:127527. [PMID: 37866558 DOI: 10.1016/j.ijbiomac.2023.127527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/14/2023] [Accepted: 10/16/2023] [Indexed: 10/24/2023]
Abstract
Adhesion to gastrointestinal tract is crucial for bifidobacteria to exert their probiotic effects. Our previous work found that bile salts significantly enhance the adhesion ability of Bifidobacterium longum BBMN68 to HT-29 cells. In this study, trypsin-shaving and LC-MS/MS-based surface proteomics were employed to identify surface proteins involved in bile stress response. Among the 829 differentially expressed proteins, 56 up-regulated proteins with a fold change >1.5 were subjected to further analysis. Notably, the minor pilin subunit FimB was 4.98-fold up-regulated in response to bile stress. In silico analysis and RT-PCR confirmed that gene fimB, fimA and srtC were co-transcribed and contributed to the biosynthesis of sortase-dependent pili Pil1. Moreover, scanning electron microscopy and immunogold electron microscopy assays showed increased abundance and length of Pil1 on BBMN68 under bile stress. As the major pilin subunit FimA serves as adhesion component of Pil1, an inhibition assay using anti-FimA antibodies further confirmed the critical role of Pil1 in mediating the adhesion of BBMN68 to HT-29 cells under bile stress. Our findings suggest that the up-regulation of Pil1 in response to bile stress enhances the adhesion of BBMN68 to intestinal epithelial cells, highlighting a novel mechanism of gut persistence in B. longum strains.
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Affiliation(s)
- Zhengyuan Zhai
- 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 100083, China; Food Laboratory of Zhongyuan, Luohe 462300, Henan, China
| | - Yao Xiong
- 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 100083, China
| | - Yaxin Gu
- 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 100083, 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 100083, China
| | - Haoran An
- Center for Infectious Disease Research, Tsinghua-Peking Joint Center for Life Science, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Huaxi Yi
- Food Laboratory of Zhongyuan, Luohe 462300, Henan, China; College of Food Science and Engineering, Ocean University of China, Qingdao 266100, Shandong, China
| | - Liang Zhao
- 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 100083, China
| | - Fazheng Ren
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100093, China
| | - Yanling Hao
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100093, China; Food Laboratory of Zhongyuan, Luohe 462300, Henan, China.
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3
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Nishiyama K, Yong CC, Moritoki N, Kitazawa H, Odamaki T, Xiao JZ, Mukai T. Sharing of Moonlighting Proteins Mediates the Symbiotic Relationship among Intestinal Commensals. Appl Environ Microbiol 2023; 89:e0219022. [PMID: 36847513 PMCID: PMC10053696 DOI: 10.1128/aem.02190-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 01/26/2023] [Indexed: 03/01/2023] Open
Abstract
The human gastrointestinal tract is inhabited by trillions of symbiotic bacteria that form a complex ecological community and influence human physiology. Symbiotic nutrient sharing and nutrient competition are the most studied relationships in gut commensals, whereas the interactions underlying homeostasis and community maintenance are not fully understood. Here, we provide insights into a new symbiotic relationship wherein the sharing of secreted cytoplasmic proteins, called "moonlighting proteins," between two heterologous bacterial strains (Bifidobacterium longum and Bacteroides thetaiotaomicron) was observed to affect the adhesion of bacteria to mucins. B. longum and B. thetaiotaomicron were cocultured using a membrane-filter system, and in this system the cocultured B. thetaiotaomicron cells showed greater adhesion to mucins compared to that shown by monoculture cells. Proteomic analysis showed the presence of 13 B. longum-derived cytoplasmic proteins on the surface of B. thetaiotaomicron. Moreover, incubation of B. thetaiotaomicron with the recombinant proteins GroEL and elongation factor Tu (EF-Tu)-two well-known mucin-adhesive moonlighting proteins of B. longum-led to an increase in the adhesion of B. thetaiotaomicron to mucins, a result attributed to the localization of these proteins on the B. thetaiotaomicron cell surface. Furthermore, the recombinant EF-Tu and GroEL proteins were observed to bind to the cell surface of several other bacterial species; however, the binding was species dependent. The present findings indicate a symbiotic relationship mediated by the sharing of moonlighting proteins among specific strains of B. longum and B. thetaiotaomicron. IMPORTANCE The adhesion of intestinal bacteria to the mucus layer is an important colonization strategy in the gut environment. Generally, the bacterial adhesion process is a characteristic feature of the individual cell surface-associated adhesion factors secreted by a particular bacterium. In this study, coculture experiments between Bifidobacterium and Bacteroides show that the secreted moonlighting proteins adhere to the cell surface of coexisting bacteria and alter the adhesiveness of the bacteria to mucins. This finding indicates that the moonlighting proteins act as adhesion factors for not only homologous strains but also for coexisting heterologous strains. The presence of a coexisting bacterium in the environment can significantly alter the mucin-adhesive properties of another bacterium. The findings from this study contribute to a better understanding of the colonization properties of gut bacteria through the discovery of a new symbiotic relationship between them.
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Affiliation(s)
- Keita Nishiyama
- Department of Microbiology and Immunology, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
- Next Generation Science Institute, Morinaga Milk Industry Co., Ltd., Zama, Kanagawa, Japan
- Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Aobaku, Sendai, Japan
- Livestock Immunology Unit, International Education and Research Center for Food Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Aobaku, Sendai, Japan
| | - Cheng-Chung Yong
- Next Generation Science Institute, Morinaga Milk Industry Co., Ltd., Zama, Kanagawa, Japan
| | - Nobuko Moritoki
- Electron Microscope Laboratory, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Haruki Kitazawa
- Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Aobaku, Sendai, Japan
- Livestock Immunology Unit, International Education and Research Center for Food Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Aobaku, Sendai, Japan
| | - Toshitaka Odamaki
- Next Generation Science Institute, Morinaga Milk Industry Co., Ltd., Zama, Kanagawa, Japan
| | - Jin-Zhong Xiao
- Next Generation Science Institute, Morinaga Milk Industry Co., Ltd., Zama, Kanagawa, Japan
| | - Takao Mukai
- Department of Animal Science, School of Veterinary Medicine, Kitasato University, Aomori, Japan
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The Pleiotropic Effects of Carbohydrate-Mediated Growth Rate Modifications in Bifidobacterium longum NCC 2705. Microorganisms 2023; 11:microorganisms11030588. [PMID: 36985162 PMCID: PMC10059941 DOI: 10.3390/microorganisms11030588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/17/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
Bifidobacteria are saccharolytic bacteria that are able to metabolize a relatively large range of carbohydrates through their unique central carbon metabolism known as the “bifid-shunt”. Carbohydrates have been shown to modulate the growth rate of bifidobacteria, but unlike for other genera (e.g., E. coli or L. lactis), the impact it may have on the overall physiology of the bacteria has not been studied in detail to date. Using glucose and galactose as model substrates in Bifidobacterium longum NCC 2705, we established that the strain displayed fast and slow growth rates on those carbohydrates, respectively. We show that these differential growth conditions are accompanied by global transcriptional changes and adjustments of central carbon fluxes. In addition, when grown on galactose, NCC 2705 cells were significantly smaller, exhibited an expanded capacity to import and metabolized different sugars and displayed an increased acid-stress resistance, a phenotypic signature associated with generalized fitness. We predict that part of the observed adaptation is regulated by the previously described bifidobacterial global transcriptional regulator AraQ, which we propose to reflect a catabolite-repression-like response in B. longum. With this manuscript, we demonstrate that not only growth rate but also various physiological characteristics of B. longum NCC 2705 are responsive to the carbon source used for growth, which is relevant in the context of its lifestyle in the human infant gut where galactose-containing oligosaccharides are prominent.
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5
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Ganesan R, Wierz JC, Kaltenpoth M, Flórez LV. How It All Begins: Bacterial Factors Mediating the Colonization of Invertebrate Hosts by Beneficial Symbionts. Microbiol Mol Biol Rev 2022; 86:e0012621. [PMID: 36301103 PMCID: PMC9769632 DOI: 10.1128/mmbr.00126-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Beneficial associations with bacteria are widespread across animals, spanning a range of symbiont localizations, transmission routes, and functions. While some of these associations have evolved into obligate relationships with permanent symbiont localization within the host, the majority require colonization of every host generation from the environment or via maternal provisions. Across the broad diversity of host species and tissue types that beneficial bacteria can colonize, there are some highly specialized strategies for establishment yet also some common patterns in the molecular basis of colonization. This review focuses on the mechanisms underlying the early stage of beneficial bacterium-invertebrate associations, from initial contact to the establishment of the symbionts in a specific location of the host's body. We first reflect on general selective pressures that can drive the transition from a free-living to a host-associated lifestyle in bacteria. We then cover bacterial molecular factors for colonization in symbioses from both model and nonmodel invertebrate systems where these have been studied, including terrestrial and aquatic host taxa. Finally, we discuss how interactions between multiple colonizing bacteria and priority effects can influence colonization. Taking the bacterial perspective, we emphasize the importance of developing new experimentally tractable systems to derive general insights into the ecological factors and molecular adaptations underlying the origin and establishment of beneficial symbioses in animals.
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Affiliation(s)
- Ramya Ganesan
- Department of Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Jürgen C. Wierz
- Department of Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Martin Kaltenpoth
- Department of Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Laura V. Flórez
- Department of Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
- Department of Plant and Environmental Sciences, Section for Organismal Biology, University of Copenhagen, Copenhagen, Denmark
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6
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Shang J, Yang S, Tang Z, Chen Y, Duan B, Meng X. Bifidobacterium bifidum H3-R2 and Its Molecular Communication within the Context of Ulcerative Colitis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:11678-11688. [PMID: 36095239 DOI: 10.1021/acs.jafc.2c02909] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Bifidobacteria are important mediators of immune system development within the gastrointestinal system and immunological homeostasis. The present study explored the anti-colitic activity of Bifidobacterium bifidum H3-R2 in a murine dextran sulfate sodium (DSS)-induced model of ulcerative colitis (UC). Moreover, this study offers novel insight regarding the molecular basis for the probiotic properties of B. bifidum H3-R2 by analyzing the underlying mechanisms whereby B. bifidum H3-R2-derived proteins affect the intestinal barrier. B. bifidum H3-R2 administration was sufficient to alleviate clinical manifestations consistent with DSS-induced colitis, restoring aberrant inflammatory cytokine production, enhancing tight junction protein expression, and positively impacting overall intestinal microecological homeostasis in these animals. Moreover, the bifidobacteria-derived GroEL and transaldolase (TAL) proteins were found to regulate tight junction protein expression via the NF-κB, myosin light chain kinase (MLCK), RhoA/Rho-associated protein kinase (ROCK), and mitogen-activated protein kinase (MAPK) signaling pathways, preventing the lipopolysaccharide (LPS)-mediated disruption of the intestinal epithelial cell barrier.
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Affiliation(s)
- Jiacui Shang
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
- Food College, Northeast Agricultural University, Harbin 150030, China
| | - Shuo Yang
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
- Food College, Northeast Agricultural University, Harbin 150030, China
| | - Zongxin Tang
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
- Food College, Northeast Agricultural University, Harbin 150030, China
| | - Yuhan Chen
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
- Food College, Northeast Agricultural University, Harbin 150030, China
| | - Bofan Duan
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
- Food College, Northeast Agricultural University, Harbin 150030, China
| | - Xiangchen Meng
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
- Food College, Northeast Agricultural University, Harbin 150030, China
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7
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Yu Y, Ren X, Cao L, Liang Q, Xiao M, Cheng J, Nan S, Zhu C, Kong Q, Fu X, Mou H. Complete‐Genome
Sequence and
in vitro
Probiotic Characteristics Analysis of
Bifidobacterium pseudolongum
YY
‐26. J Appl Microbiol 2022; 133:2599-2617. [DOI: 10.1111/jam.15730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 07/05/2022] [Accepted: 07/18/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Ying Yu
- College of Food Science and Engineering Ocean University of China Qingdao China
| | - Xinmiao Ren
- College of Food Science and Engineering Ocean University of China Qingdao China
| | - Linyuan Cao
- College of Food Science and Engineering Ocean University of China Qingdao China
| | - Qingping Liang
- College of Food Science and Engineering Ocean University of China Qingdao China
| | - Mengshi Xiao
- College of Food Science and Engineering Ocean University of China Qingdao China
| | - Jiaying Cheng
- College of Food Science and Engineering Ocean University of China Qingdao China
| | - Shihao Nan
- State Key Laboratory of Food Science and Technology, China‐Canada Joint Laboratory of Food Science and Technology (Nanchang), Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University
| | - Changliang Zhu
- College of Food Science and Engineering Ocean University of China Qingdao China
| | - Qing Kong
- College of Food Science and Engineering Ocean University of China Qingdao China
| | - Xiaodan Fu
- State Key Laboratory of Food Science and Technology, China‐Canada Joint Laboratory of Food Science and Technology (Nanchang), Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University
| | - Haijin Mou
- College of Food Science and Engineering Ocean University of China Qingdao China
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Maximum depth sequencing reveals an ON/OFF replication slippage switch and apparent in vivo selection for bifidobacterial pilus expression. Sci Rep 2022; 12:9576. [PMID: 35688912 PMCID: PMC9187656 DOI: 10.1038/s41598-022-13668-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 05/16/2022] [Indexed: 11/09/2022] Open
Abstract
The human gut microbiome, of which the genus Bifidobacterium is a prevalent and abundant member, is thought to sustain and enhance human health. Several surface-exposed structures, including so-called sortase-dependent pili, represent important bifidobacterial gut colonization factors. Here we show that expression of two sortase-dependent pilus clusters of the prototype Bifidobacterium breve UCC2003 depends on replication slippage at an intragenic G-tract, equivalents of which are present in various members of the Bifidobacterium genus. The nature and extent of this slippage is modulated by the host environment. Involvement of such sortase-dependent pilus clusters in microbe-host interactions, including bacterial attachment to the gut epithelial cells, has been shown previously and is corroborated here for one case. Using a Maximum Depth Sequencing strategy aimed at excluding PCR and sequencing errors introduced by DNA polymerase reagents, specific G-tract sequences in B. breve UCC2003 reveal a range of G-tract lengths whose plasticity within the population is functionally utilized. Interestingly, replication slippage is shown to be modulated under in vivo conditions in a murine model. This in vivo modulation causes an enrichment of a G-tract length which appears to allow biosynthesis of these sortase-dependent pili. This work provides the first example of productive replication slippage influenced by in vivo conditions. It highlights the potential for microdiversity generation in “beneficial” gut commensals.
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Duboux S, Van Wijchen M, Kleerebezem M. The Possible Link Between Manufacturing and Probiotic Efficacy; a Molecular Point of View on Bifidobacterium. Front Microbiol 2022; 12:812536. [PMID: 35003044 PMCID: PMC8741271 DOI: 10.3389/fmicb.2021.812536] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 12/06/2021] [Indexed: 11/13/2022] Open
Abstract
Probiotics for food or supplement use have been studied in numerous clinical trials, addressing a broad variety of diseases, and conditions. However, discrepancies were observed in the clinical outcomes stemming from the use of lactobacillaceae and bifidobacteria strains. These differences are often attributed to variations in the clinical trial protocol like trial design, included target population, probiotic dosage, or outcome parameters measured. However, a contribution of the methods used to produce the live bioactive ingredients should not be neglected as a possible additional factor in the observed clinical outcome variations. It is well established that manufacturing conditions play a role in determining the survival and viability of probiotics, but much less is known about their influence on the probiotic molecular composition and functionality. In this review, we briefly summarize the evidence obtained for Lacticaseibacillus rhamnosus GG and Lactiplantibacillus plantarum WCFS1, highlighting that expression and presence of probiotic niche factor (NF) and/or effector molecules (EM) may be altered during production of those two well-characterized lactobacillaceae probiotic strains. Subsequently, we summarize in more depth what is the present state of knowledge about bifidobacterial probiotic NF and EM; how their expression may be modified by manufacturing related environmental factors and how that may affect their biological activity in the host. This review highlights the importance of gathering knowledge on probiotic NF and EM, to validate them as surrogate markers of probiotic functionality. We further propose that monitoring of validated NF and/or EM during production and/or in the final preparation could complement viable count assessments that are currently applied in industry. Overall, we suggest that implementation of molecular level quality controls (i.e., based on validated NF and EM), could provide mode of action based in vitro tests contributing to better control the health-promoting reliability of probiotic products.
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Affiliation(s)
- Stéphane Duboux
- Nestlé Research, Lausanne, Switzerland.,Host-Microbe Interactomics Group, Wageningen University and Research, Wageningen, Netherlands
| | - Myrthe Van Wijchen
- Nestlé Research, Lausanne, Switzerland.,Host-Microbe Interactomics Group, Wageningen University and Research, Wageningen, Netherlands
| | - Michiel Kleerebezem
- Host-Microbe Interactomics Group, Wageningen University and Research, Wageningen, Netherlands
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10
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Turroni F, van Sinderen D, Ventura M. Bifidobacteria: insights into the biology of a key microbial group of early life gut microbiota. MICROBIOME RESEARCH REPORTS 2021; 1:2. [PMID: 38045555 PMCID: PMC10688781 DOI: 10.20517/mrr.2021.02] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/29/2021] [Accepted: 11/15/2021] [Indexed: 12/05/2023]
Abstract
The establishment and development of the human gut microbiota constitutes a dynamic and non-random process, which involves positive and negative interactions between key microbial taxa and their host. Remarkably, these early life microbiota-host communications include key events with long-term health consequences. Bifidobacteria arguably represent the most emblematic microbial taxon of the infant gut microbiota. In this context, the interactions among bifidobacteria, their human host, and other members of the human gut microbiota are far from completely understood, despite the crucial role they play in the development and maintenance of human physiology and immune system. Here, we highlight the ecological as well as genetic and functional features of bifidobacteria residing in the human gut using genomic and ecology-based information.
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Affiliation(s)
- Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma 43126, Italy
- Microbiome Research Hub, University of Parma, Parma 43126, Italy
| | - Douwe van Sinderen
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork Co. Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma 43126, Italy
- Microbiome Research Hub, University of Parma, Parma 43126, Italy
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11
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Zhao L, Xie Q, Etareri Evivie S, Liu D, Dong J, Ping L, Liu F, Li B, Huo G. Bifidobacterium dentium N8 with potential probiotic characteristics prevents LPS-induced intestinal barrier injury by alleviating the inflammatory response and regulating the tight junction in Caco-2 cell monolayers. Food Funct 2021; 12:7171-7184. [PMID: 34269367 DOI: 10.1039/d1fo01164b] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The intestinal barrier is vital for preventing inflammatory bowel disease (IBD). This study aimed to investigate the potential mechanism behind the protective effects of B. dentium N8 on the intestinal barrier using the lipopolysaccharide (LPS)-induced Caco-2 cells model. Our probiotic validation results showed that B. dentium N8 had a higher adhesion ability and a more substantial inhibition effect on Escherichia coli ATCC 25922 adhesion to HT-29 cells. Regarding the epithelial integrity, B. dentium N8 significantly increased the trans-epithelial electrical resistance (TEER) value and decreased the paracellular permeability of Caco-2 cells stimulated by lipopolysaccharide (LPS). In addition, B. dentium N8 significantly increased ZO-1, occludin, and claudin-1 mRNA expression. B. dentium N8 downregulated the mRNA expression level of TLR4 and pro-inflammatory cytokines (TNF-α, IL-1β, IL-6). Furthermore, B. dentium N8 had a better protective effect on the intestinal barrier than that of E7. Comparative genomics of B. dentium N8 and E7 showed B. dentium N8 had the specific genes encoding for adhesion ability and immune system regulation. The findings provide the theoretical basis for B. dentium N8 possessing a protective effect on the intestinal barrier, which indicate that it could be used as a novel therapy for IBD.
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Affiliation(s)
- Li Zhao
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, China.
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Liu Z, Li L, Fang Z, Lee Y, Zhao J, Zhang H, Chen W, Li H, Lu W. Integration of Transcriptome and Metabolome Reveals the Genes and Metabolites Involved in Bifidobacterium bifidum Biofilm Formation. Int J Mol Sci 2021; 22:ijms22147596. [PMID: 34299216 PMCID: PMC8304991 DOI: 10.3390/ijms22147596] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 07/11/2021] [Accepted: 07/12/2021] [Indexed: 01/14/2023] Open
Abstract
Bifidobacterium bifidum strains, an important component of probiotic foods, can form biofilms on abiotic surfaces, leading to increased self-resistance. However, little is known about the molecular mechanism of B. bifidum biofilm formation. A time series transcriptome sequencing and untargeted metabolomics analysis of both B. bifidum biofilm and planktonic cells was performed to identify key genes and metabolites involved in biofilm formation. Two hundred thirty-five nonredundant differentially expressed genes (DEGs) (including vanY, pstS, degP, groS, infC, groL, yajC, tadB and sigA) and 219 nonredundant differentially expressed metabolites (including L-threonine, L-cystine, L-tyrosine, ascorbic acid, niacinamide, butyric acid and sphinganine) were identified. Thirteen pathways were identified during the integration of both transcriptomics and metabolomics data, including ABC transporters; quorum sensing; two-component system; oxidative phosphorylation; cysteine and methionine metabolism; glutathione metabolism; glycine, serine and threonine metabolism; and valine, leucine and isoleucine biosynthesis. The DEGs that relate to the integration pathways included asd, atpB, degP, folC, ilvE, metC, pheA, pstS, pyrE, serB, ulaE, yajC and zwf. The differentially accumulated metabolites included L-cystine, L-serine, L-threonine, L-tyrosine, methylmalonate, monodehydroascorbate, nicotinamide, orthophosphate, spermine and tocopherol. These results indicate that quorum sensing, two-component system and amino acid metabolism are essential during B. bifidum biofilm formation.
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Affiliation(s)
- Zongmin Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (Z.L.); (L.L.); (Z.F.); (J.Z.); (H.Z.); (W.C.); (H.L.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Lingzhi Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (Z.L.); (L.L.); (Z.F.); (J.Z.); (H.Z.); (W.C.); (H.L.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Zhifeng Fang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (Z.L.); (L.L.); (Z.F.); (J.Z.); (H.Z.); (W.C.); (H.L.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yuankun Lee
- Department of Microbiology & Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore;
- International Joint Research Laboratory for Pharmabiotics & Antibiotic Resistance, Jiangnan University, Wuxi 214122, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (Z.L.); (L.L.); (Z.F.); (J.Z.); (H.Z.); (W.C.); (H.L.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (Z.L.); (L.L.); (Z.F.); (J.Z.); (H.Z.); (W.C.); (H.L.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (Z.L.); (L.L.); (Z.F.); (J.Z.); (H.Z.); (W.C.); (H.L.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Haitao Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (Z.L.); (L.L.); (Z.F.); (J.Z.); (H.Z.); (W.C.); (H.L.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Wenwei Lu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (Z.L.); (L.L.); (Z.F.); (J.Z.); (H.Z.); (W.C.); (H.L.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Research Laboratory for Pharmabiotics & Antibiotic Resistance, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
- Correspondence: ; Tel.: +86-510-85197302
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13
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Kaczmarczyk M, Löber U, Adamek K, Węgrzyn D, Skonieczna-Żydecka K, Malinowski D, Łoniewski I, Markó L, Ulas T, Forslund SK, Łoniewska B. The gut microbiota is associated with the small intestinal paracellular permeability and the development of the immune system in healthy children during the first two years of life. J Transl Med 2021; 19:177. [PMID: 33910577 PMCID: PMC8082808 DOI: 10.1186/s12967-021-02839-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 04/16/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The intestinal barrier plays an important role in the defense against infections, and nutritional, endocrine, and immune functions. The gut microbiota playing an important role in development of the gastrointestinal tract can impact intestinal permeability and immunity during early life, but data concerning this problem are scarce. METHODS We analyzed the microbiota in fecal samples (101 samples in total) collected longitudinally over 24 months from 21 newborns to investigate whether the markers of small intestinal paracellular permeability (zonulin) and immune system development (calprotectin) are linked to the gut microbiota. The results were validated using data from an independent cohort that included the calprotectin and gut microbiota in children during the first year of life. RESULTS Zonulin levels tended to increase for up to 6 months after childbirth and stabilize thereafter remaining at a high level while calprotectin concentration was high after childbirth and began to decline from 6 months of life. The gut microbiota composition and the related metabolic potentials changed during the first 2 years of life and were correlated with zonulin and calprotectin levels. Faecal calprotectin correlated inversely with alpha diversity (Shannon index, r = - 0.30, FDR P (Q) = 0.039). It also correlated with seven taxa; i.a. negatively with Ruminococcaceae (r = - 0.34, Q = 0.046), and Clostridiales (r = - 0.34, Q = 0.048) and positively with Staphylococcus (r = 0.38, Q = 0.023) and Staphylococcaceae (r = 0.35, Q = 0.04), whereas zonulin correlated with 19 taxa; i.a. with Bacillales (r = - 0.52, Q = 0.0004), Clostridiales (r = 0.48, Q = 0.001) and the Ruminococcus (torques group) (r = 0.40, Q = 0.026). When time intervals were considered only changes in abundance of the Ruminococcus (torques group) were associated with changes in calprotectin (β = 2.94, SE = 0.8, Q = 0.015). The dynamics of stool calprotectin was negatively associated with changes in two MetaCyc pathways: pyruvate fermentation to butanoate (β = - 4.54, SE = 1.08, Q = 0.028) and Clostridium acetobutylicum fermentation (β = - 4.48, SE = 1.16, Q = 0.026). CONCLUSIONS The small intestinal paracellular permeability, immune system-related markers and gut microbiota change dynamically during the first 2 years of life. The Ruminococcus (torques group) seems to be especially involved in controlling paracellular permeability. Staphylococcus, Staphylococcaceae, Ruminococcaceae, and Clostridiales, may be potential biomarkers of the immune system. Despite observed correlations their clear causation and health consequences were not proven. Mechanistic studies are required.
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Affiliation(s)
- Mariusz Kaczmarczyk
- Department of Clinical Biochemistry, Pomeranian Medical University in Szczecin, 70-111, Szczecin, Poland
| | - Ulrike Löber
- Experimental and Clinical Research Center, A Cooperation of Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, 14195, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
| | - Karolina Adamek
- Department of Neonatal Diseases, Pomeranian Medical University in Szczecin, 70-111, Szczecin, Poland
| | - Dagmara Węgrzyn
- Department of Neonatal Diseases, Pomeranian Medical University in Szczecin, 70-111, Szczecin, Poland
| | | | - Damian Malinowski
- Department of Pharmacology, Pomeranian Medical University in Szczecin, 70-111, Szczecin, Poland
| | - Igor Łoniewski
- Department of Biochemical Sciences, Pomeranian Medical University in Szczecin, 71-460, Szczecin, Poland.
- Department of Human Nutrition and Metabolomics, Broniewskiego 24, 71-460, Szczecin, Poland.
| | - Lajos Markó
- Experimental and Clinical Research Center, A Cooperation of Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, 14195, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
- Berlin Institute of Health (BIH), 10178, Berlin, Germany
| | - Thomas Ulas
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), 53127, Bonn, Germany
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, 53127, Bonn, Germany
| | - Sofia K Forslund
- Experimental and Clinical Research Center, A Cooperation of Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, 14195, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
- Berlin Institute of Health (BIH), 10178, Berlin, Germany
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), 53127, Bonn, Germany
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117, Heidelberg, Germany
| | - Beata Łoniewska
- Department of Neonatal Diseases, Pomeranian Medical University in Szczecin, 70-111, Szczecin, Poland
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14
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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: 52] [Impact Index Per Article: 17.3] [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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15
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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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16
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Corona-Cervantes K, García-González I, Villalobos-Flores LE, Hernández-Quiroz F, Piña-Escobedo A, Hoyo-Vadillo C, Rangel-Calvillo MN, García-Mena J. Human milk microbiota associated with early colonization of the neonatal gut in Mexican newborns. PeerJ 2020; 8:e9205. [PMID: 32509465 PMCID: PMC7247532 DOI: 10.7717/peerj.9205] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 04/25/2020] [Indexed: 12/20/2022] Open
Abstract
Background Human milk microbiota plays a role in the bacterial colonization of the neonatal gut, which has important consequences in the health and development of the newborn. However, there are few studies about the vertical transfer of bacteria from mother to infant in Latin American populations. Methods We performed a cross-sectional study characterizing the bacterial diversity of 67 human milk-neonatal stool pairs by high-throughput sequencing of V3-16S rDNA libraries, to assess the effect of the human milk microbiota on the bacterial composition of the neonate's gut at early days. Results Human milk showed higher microbial diversity as compared to the neonatal stool. Members of the Staphylococcaceae and Sphingomonadaceae families were more prevalent in human milk, whereas the Pseudomonadaceae family, Clostridium and Bifidobacterium genera were in the neonatal stool. The delivery mode showed association with the neonatal gut microbiota diversity, but not with the human milk microbiota diversity; for instance, neonates born by C-section showed greater richness and diversity in stool microbiota than those born vaginally. We found 25 bacterial taxa shared by both ecosystems and 67.7% of bacteria found in neonate stool were predicted to originate from human milk. This study contributes to the knowledge of human milk and neonatal stool microbiota in healthy Mexican population and supports the idea of vertical mother-neonate transmission through exclusive breastfeeding.
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Affiliation(s)
- Karina Corona-Cervantes
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, CDMX, Mexico
| | - Igrid García-González
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, CDMX, Mexico
| | - Loan Edel Villalobos-Flores
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, CDMX, Mexico
| | - Fernando Hernández-Quiroz
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, CDMX, Mexico
| | - Alberto Piña-Escobedo
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, CDMX, Mexico
| | - Carlos Hoyo-Vadillo
- Departamento de Farmacología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, CDMX, Mexico
| | - Martín Noé Rangel-Calvillo
- Hospital General "Dr. José María Rodríguez", Instituto de Salud del Estado de México, Ecatepec de Morelos, Estado de Mexico, Mexico
| | - Jaime García-Mena
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, CDMX, Mexico
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17
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Dramé I, Formosa-Dague C, Lafforgue C, Chapot-Chartier MP, Piard JC, Castelain M, Dague E. Analysis of Homotypic Interactions of Lactococcus lactis Pili Using Single-Cell Force Spectroscopy. ACS APPLIED MATERIALS & INTERFACES 2020; 12:21411-21423. [PMID: 32314572 DOI: 10.1021/acsami.0c03069] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Cell surface proteins of Gram-positive bacteria play crucial roles in their adhesion to abiotic and biotic surfaces. Pili are long and flexible proteinaceous filaments known to enhance bacterial initial adhesion. They promote surface colonization and are thus considered as essential factors in biofilm cohesion. Our hypothesis is that pili mediate interactions between cells and may thereby directly affect biofilm formation. In this study, we use single-cell force spectroscopy (SCFS) to quantify the force of the homotypic pili interactions between individual bacterial cells, using different Lactococcus lactis strains producing pili or not as model bacteria. Moreover the force-distance curves were analyzed to determine the physical and nanomechanical properties of L. lactis pili. The results for pili-devoided strains showed a weak adhesion between cells (adhesion forces and work in the range of 100 pN and 7 × 10-18 J, respectively). On the contrary, the piliated strains showed high adhesion levels with adhesion forces and adhesion work over 200 pN and 50 × 10-18 J, respectively. The force-extension curves showed multiple adhesion events, typical of the unfolding of macromolecules. These unfolding force peaks were fitted using the physical worm-like chain model to get fundamental knowledge on the pili nanomechanical properties. In addition, SCFS applied to a L. lactis isolate expressing both pili and mucus-binding protein at its surface and two derivative mutants revealed the capacity of pili to interact with other surface proteins including mucus-binding proteins. This study demonstrates that pili are involved in L. lactis homotypic interactions and thus can influence biofilm structuring.
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Affiliation(s)
- Ibrahima Dramé
- TBI, Université de Toulouse, INSA, INRAE, CNRS, 31000 Toulouse, France
- LAAS-CNRS, Université de Toulouse, CNRS, 31000 Toulouse, France
| | | | | | | | - Jean-Christophe Piard
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Mickaël Castelain
- TBI, Université de Toulouse, INSA, INRAE, CNRS, 31000 Toulouse, France
| | - Etienne Dague
- LAAS-CNRS, Université de Toulouse, CNRS, 31000 Toulouse, France
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18
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Turroni F, Milani C, Duranti S, Lugli GA, Bernasconi S, Margolles A, Di Pierro F, van Sinderen D, Ventura M. The infant gut microbiome as a microbial organ influencing host well-being. Ital J Pediatr 2020; 46:16. [PMID: 32024556 PMCID: PMC7003403 DOI: 10.1186/s13052-020-0781-0] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 01/29/2020] [Indexed: 12/16/2022] Open
Abstract
Initial establishment of the human gut microbiota is generally believed to occur immediately following birth, involving key gut commensals such as bifidobacteria that are acquired from the mother. The subsequent development of this early gut microbiota is driven and modulated by specific dietary compounds present in human milk that support selective colonization. This represents a very intriguing example of host-microbe co-evolution, where both partners are believed to benefit. In recent years, various publications have focused on dissecting microbial infant gut communities and their interaction with their human host, being a determining factor in host physiology and metabolic activities. Such studies have highlighted a reduction of microbial diversity and/or an aberrant microbiota composition, sometimes referred to as dysbiosis, which may manifest itself during the early stage of life, i.e., in infants, or later stages of life. There are growing experimental data that may explain how the early human gut microbiota affects risk factors related to adult health conditions. This concept has fueled the development of various nutritional strategies, many of which are based on probiotics and/or prebiotics, to shape the infant microbiota. In this review, we will present the current state of the art regarding the infant gut microbiota and the role of key commensal microorganisms like bifidobacteria in the establishment of the first microbial communities in the human gut.
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Affiliation(s)
- Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | | | - Abelardo Margolles
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, IPLA - CSIC, Villaviciosa, Asturias, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias-ISPA, Oviedo, Spain
| | | | - Douwe van Sinderen
- School of Microbiology & APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy.
- Microbiome Research Hub, University of Parma, Parma, Italy.
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19
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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: 31] [Impact Index Per Article: 6.2] [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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20
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Turroni F, Duranti S, Milani C, Lugli GA, van Sinderen D, Ventura M. Bifidobacterium bifidum: A Key Member of the Early Human Gut Microbiota. Microorganisms 2019; 7:microorganisms7110544. [PMID: 31717486 PMCID: PMC6920858 DOI: 10.3390/microorganisms7110544] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 10/29/2019] [Accepted: 11/07/2019] [Indexed: 12/30/2022] Open
Abstract
Bifidobacteria typically represent the most abundant bacteria of the human gut microbiota in healthy breast-fed infants. Members of the Bifidobacterium bifidum species constitute one of the dominant taxa amongst these bifidobacterial communities and have been shown to display notable physiological and genetic features encompassing adhesion to epithelia as well as metabolism of host-derived glycans. In the current review, we discuss current knowledge concerning particular biological characteristics of the B. bifidum species that support its specific adaptation to the human gut and their implications in terms of supporting host health.
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Affiliation(s)
- Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (S.D.); (C.M.); (G.A.L.); (M.V.)
- Microbiome Research Hub, University of Parma, 43124 Parma, Italy
- Correspondence:
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (S.D.); (C.M.); (G.A.L.); (M.V.)
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (S.D.); (C.M.); (G.A.L.); (M.V.)
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (S.D.); (C.M.); (G.A.L.); (M.V.)
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, T12 YT20 Cork, Ireland;
- APC Microbiome Institute, University College Cork, T12 YT20 Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (S.D.); (C.M.); (G.A.L.); (M.V.)
- Microbiome Research Hub, University of Parma, 43124 Parma, Italy
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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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22
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Bifidobacterial Transfer from Mother to Child as Examined by an Animal Model. Microorganisms 2019; 7:microorganisms7090293. [PMID: 31461893 PMCID: PMC6780879 DOI: 10.3390/microorganisms7090293] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 08/21/2019] [Accepted: 08/22/2019] [Indexed: 01/12/2023] Open
Abstract
Bifidobacteria commonly constitute the most abundant group of microorganisms in the healthy infant gut. Their intestinal establishment is believed to be maternally driven, and their acquisition has even been postulated to occur during pregnancy. In the current study, we evaluated bifidobacterial mother-to infant transmission events in a rat model by means of quantitative PCR (qPCR), as well as by Internally Transcribed Spacer (ITS) bifidobacterial profiling. The occurrence of strains supplied by mothers during pregnancy to their corresponding newborns was observed and identified by analysis immediately following C-section delivery. These findings provide intriguing support for the existence of an unknown route to facilitate bifidobacterial transfer during the very early stages of life.
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23
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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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24
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Ma T, Suzuki Y, Guan LL. Dissect the mode of action of probiotics in affecting host-microbial interactions and immunity in food producing animals. Vet Immunol Immunopathol 2018; 205:35-48. [PMID: 30459000 DOI: 10.1016/j.vetimm.2018.10.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 09/29/2018] [Accepted: 10/16/2018] [Indexed: 02/07/2023]
Abstract
Prophylactic antimicrobials have been widely used in food animal production with the aim to prevent infectious diseases, enhance feed efficiency, and promote growth. However, the extensive use of antimicrobials in food animal production systems has led to the emergence of antimicrobial resistant pathogens, which are potential threats to human and animal health. Probiotics have been proposed to be a promising alternative of prophylactic antimicrobials, with potential beneficial effects on the host animal by improving the balance of intestinal microbiota and host immunity. Although an increasing body of evidence shows that probiotics could directly or indirectly affect gut microbiota and host immune functions, the lack of the understanding of how probiotics influence host-microbial interaction and immunity is one of the reasons for controversial findings from many animal trials, especially in food production animals. Therefore, in this review we focused on the most recent (last ten years) studies on how gut microbiota and host immune function changes in response to probiotics in food production animals (swine, poultry, and ruminant). In addition, the relationship between microbial changes and host immune function was illustrated, and how such relationship differs among animal species was further compared. Moreover, the future directions concerning the mechanisms of how probiotics modulate host-microbial interactions and host immunity were highlighted, which may assist in the optimal supplementation strategy to maximize the efficacy of probiotics to improve animal gut health and productivity.
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Affiliation(s)
- Tao Ma
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada; Feed Research Institute, Chinese Academy of Agricultural Sciences, Key laboratory of Feed Biotechnology of the Ministry of Agriculture, Beijing, China
| | - Yutaka Suzuki
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada; Laboratory of Animal Function and Nutrition, Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada.
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25
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Luo J, Li Y, Xie J, Gao L, Liu L, Ou S, Chen L, Peng X. The primary biological network of Bifidobacterium in the gut. FEMS Microbiol Lett 2018; 365:4931718. [DOI: 10.1093/femsle/fny057] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 03/08/2018] [Indexed: 12/17/2022] Open
Affiliation(s)
- Jianming Luo
- Department of Food Science and Engineering, Jinan University, Guangzhou 510630, People's Republic of China
| | - Yuetong Li
- Department of Food Science and Engineering, Jinan University, Guangzhou 510630, People's Republic of China
| | - Jinli Xie
- Department of Food Science and Engineering, Jinan University, Guangzhou 510630, People's Republic of China
| | - Lijuan Gao
- Department of Food Science and Engineering, Jinan University, Guangzhou 510630, People's Republic of China
| | - Liu Liu
- Department of Food Science and Engineering, Jinan University, Guangzhou 510630, People's Republic of China
| | - Shiyi Ou
- Department of Food Science and Engineering, Jinan University, Guangzhou 510630, People's Republic of China
| | - Long Chen
- Department of Food Science and Engineering, Jinan University, Guangzhou 510630, People's Republic of China
| | - Xichun Peng
- Department of Food Science and Engineering, Jinan University, Guangzhou 510630, People's Republic of China
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26
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Mahony J, Lugli GA, van Sinderen D, Ventura M. Impact of gut-associated bifidobacteria and their phages on health: two sides of the same coin? Appl Microbiol Biotechnol 2018; 102:2091-2099. [PMID: 29396587 DOI: 10.1007/s00253-018-8795-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 01/15/2018] [Accepted: 01/15/2018] [Indexed: 02/06/2023]
Abstract
Bifidobacteria are among the first microbial colonisers of the human infant gut post-partum. Their early appearance and dominance in the human infant gut and the reported health-promoting or probiotic status of several bifidobacterial strains has culminated in intensive research efforts that focus on their activities as part of the gut microbiota and the concomitant implications for human health. In this mini-review, we evaluate current knowledge on the genomics of this diverse bacterial genus, and on the genetic and functional adaptations that have underpinned the success of bifidobacteria in colonising the infant gut. The growing interest in functional genomics of bifidobacteria has also created interest in the interactions of bifidobacteria and their (bacterio)phages. While virulent phages of bifidobacteria have yet to be isolated, the incidence of integrated (pro)phages in bifidobacterial genomes are widely reported and this mini-review considers the role of these so-called bifidoprophages in modulating bifidobacterial populations in the human gastrointestinal tract and the implications for existing and future development of probiotic therapies.
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Affiliation(s)
- Jennifer Mahony
- School of Microbiology, National University of Ireland, Cork, Ireland.,APC Microbiome Ireland, National University of Ireland, Cork, Ireland
| | - Gabriele A Lugli
- Laboratory of Probiogenomics, Department of Chemical Sciences, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- School of Microbiology, National University of Ireland, Cork, Ireland. .,APC Microbiome Ireland, National University of Ireland, Cork, Ireland.
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemical Sciences, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy. .,Microbiome Research Hub, University of Parma, Parma, Italy.
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27
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Turroni F, Milani C, Duranti S, Ferrario C, Lugli GA, Mancabelli L, van Sinderen D, Ventura M. Bifidobacteria and the infant gut: an example of co-evolution and natural selection. Cell Mol Life Sci 2018; 75:103-118. [PMID: 28983638 PMCID: PMC11105234 DOI: 10.1007/s00018-017-2672-0] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 09/29/2017] [Indexed: 12/16/2022]
Abstract
Throughout the human life, the gut microbiota interacts with us in a number of different ways, thereby influencing our health status. The acquisition of such an interactive gut microbiota commences at birth. Medical and environmental factors including diet, antibiotic exposure and mode of delivery are major factors that shape the composition of the microbial communities in the infant gut. Among the most abundant members of the infant microbiota are species belonging to the Bifidobacterium genus, which are believed to confer beneficial effects upon their host. Bifidobacteria may be acquired directly from the mother by vertical transmission and their persistence in the infant gut is associated with their saccharolytic activity toward glycans that are abundant in the infant gut. Here, we discuss the establishment of the infant gut microbiota and the contribution of bifidobacteria to this early life microbial consortium.
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Affiliation(s)
- Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Chiara Ferrario
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.
- Microbiome Research Hub, University of Parma, Parma, Italy.
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28
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Omics of bifidobacteria: research and insights into their health-promoting activities. Biochem J 2017; 474:4137-4152. [PMID: 29212851 DOI: 10.1042/bcj20160756] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 10/10/2017] [Accepted: 11/06/2017] [Indexed: 12/17/2022]
Abstract
Members of the genus Bifidobacterium include gut commensals that are particularly abundant among the microbial communities residing in the gut of healthy breast-fed infants, where their presence has been linked to many beneficial host effects. Next-generation DNA sequencing and comparative and functional genome methodologies have been shown to be particularly useful in exploring the diversity of this genus. These combined approaches have allowed the identification of genetic features related to bifidobacterial establishment in the gut, involving host-microbe as well as microbe-microbe interactions. Among these, proteinaceous structures, which protrude from the bacterial surface, i.e. pili or fimbriae, and exopolysaccharidic cell surface layers or capsules represent crucial features that assist in their colonization and persistence in the gut. As bifidobacteria are colonizers of the large intestine, they have to be able to cope with various sources of osmotic, oxidative, bile and acid stress during their transit across the gastric barrier and the small intestine. Bifidobacterial genomes thus encode various survival mechanisms, such as molecular chaperones and efflux pumps, to overcome such challenges. Bifidobacteria represent part of an anaerobic gut community, and feed on nondigestible carbohydrates through a specialized fermentative metabolic pathway, which in turn produces growth substrates for other members of the gut community. Conversely, bifidobacteria may also be dependent on other (bifido)bacteria to access host- and diet-derived glycans, and these complex co-operative interactions, based on resource sharing and cross-feeding strategies, represent powerful driving forces that shape gut microbiota composition.
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29
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Ruiz L, Delgado S, Ruas-Madiedo P, Sánchez B, Margolles A. Bifidobacteria and Their Molecular Communication with the Immune System. Front Microbiol 2017; 8:2345. [PMID: 29255450 PMCID: PMC5722804 DOI: 10.3389/fmicb.2017.02345] [Citation(s) in RCA: 186] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 11/15/2017] [Indexed: 12/16/2022] Open
Abstract
Bifidobacterium represents a genus within the phylum Actinobacteria which is one of the major phyla in the healthy intestinal tract of humans. Bifidobacterium is one of the most abundant genera in adults, but its predominance is even more pronounced in infants, especially during lactation, when they can constitute the majority of the total bacterial population. They are one of the pioneering colonizers of the early gut microbiota, and they are known to play important roles in the metabolism of dietary components, otherwise indigestible in the upper parts of the intestine, and in the maturation of the immune system. Bifidobacteria have been shown to interact with human immune cells and to modulate specific pathways, involving innate and adaptive immune processes. In this mini-review, we provide an overview of the current knowledge on the immunomodulatory properties of bifidobacteria and the mechanisms and molecular players underlying these processes, focusing on the corresponding implications for human health. We deal with in vitro models suitable for studying strain-specific immunomodulatory activities. These include peripheral blood mononuclear cells and T cell-mediated immune responses, both effector and regulatory cell responses, as well as the modulation of the phenotype of dendritic cells, among others. Furthermore, preclinical studies, mainly germ-free, gnotobiotic, and conventional murine models, and human clinical trials, are also discussed. Finally, we highlight evidence supporting the immunomodulatory effects of bifidobacterial molecules (proteins and peptides, exopolysaccharides, metabolites, and DNA), as well as the role of bifidobacterial metabolism in maintaining immune homeostasis through cross-feeding mechanisms.
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Affiliation(s)
- Lorena Ruiz
- Dairy Research Institute, Spanish National Research Council (Instituto de Productos Lácteos de Asturias - CSIC), Villaviciosa, Spain
| | - Susana Delgado
- Dairy Research Institute, Spanish National Research Council (Instituto de Productos Lácteos de Asturias - CSIC), Villaviciosa, Spain
| | - Patricia Ruas-Madiedo
- Dairy Research Institute, Spanish National Research Council (Instituto de Productos Lácteos de Asturias - CSIC), Villaviciosa, Spain
| | - Borja Sánchez
- Dairy Research Institute, Spanish National Research Council (Instituto de Productos Lácteos de Asturias - CSIC), Villaviciosa, Spain
| | - Abelardo Margolles
- Dairy Research Institute, Spanish National Research Council (Instituto de Productos Lácteos de Asturias - CSIC), Villaviciosa, Spain
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30
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Milani C, Duranti S, Bottacini F, Casey E, Turroni F, Mahony J, Belzer C, Delgado Palacio S, Arboleya Montes S, Mancabelli L, Lugli GA, Rodriguez JM, Bode L, de Vos W, Gueimonde M, Margolles A, van Sinderen D, Ventura M. The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota. Microbiol Mol Biol Rev 2017; 81:e00036-17. [PMID: 29118049 PMCID: PMC5706746 DOI: 10.1128/mmbr.00036-17] [Citation(s) in RCA: 970] [Impact Index Per Article: 138.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The human gut microbiota is engaged in multiple interactions affecting host health during the host's entire life span. Microbes colonize the neonatal gut immediately following birth. The establishment and interactive development of this early gut microbiota are believed to be (at least partially) driven and modulated by specific compounds present in human milk. It has been shown that certain genomes of infant gut commensals, in particular those of bifidobacterial species, are genetically adapted to utilize specific glycans of this human secretory fluid, thus representing a very intriguing example of host-microbe coevolution, where both partners are believed to benefit. In recent years, various metagenomic studies have tried to dissect the composition and functionality of the infant gut microbiome and to explore the distribution across the different ecological niches of the infant gut biogeography of the corresponding microbial consortia, including those corresponding to bacteria and viruses, in healthy and ill subjects. Such analyses have linked certain features of the microbiota/microbiome, such as reduced diversity or aberrant composition, to intestinal illnesses in infants or disease states that are manifested at later stages of life, including asthma, inflammatory bowel disease, and metabolic disorders. Thus, a growing number of studies have reported on how the early human gut microbiota composition/development may affect risk factors related to adult health conditions. This concept has fueled the development of strategies to shape the infant microbiota composition based on various functional food products. In this review, we describe the infant microbiota, the mechanisms that drive its establishment and composition, and how microbial consortia may be molded by natural or artificial interventions. Finally, we discuss the relevance of key microbial players of the infant gut microbiota, in particular bifidobacteria, with respect to their role in health and disease.
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Affiliation(s)
- Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Francesca Bottacini
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Eoghan Casey
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Jennifer Mahony
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Susana Delgado Palacio
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, IPLA-CSIC, Villaviciosa, Asturias, Spain
| | - Silvia Arboleya Montes
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, IPLA-CSIC, Villaviciosa, Asturias, Spain
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Juan Miguel Rodriguez
- Department of Nutrition, Food Science and Food Technology, Complutense University of Madrid, Madrid, Spain
| | - Lars Bode
- Department of Pediatrics and Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence, University of California-San Diego, La Jolla, California, USA
| | - Willem de Vos
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Department of Bacteriology & Immunology, RPU Immunobiology, University of Helsinki, Helsinki, Finland
| | - Miguel Gueimonde
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, IPLA-CSIC, Villaviciosa, Asturias, Spain
| | - Abelardo Margolles
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, IPLA-CSIC, Villaviciosa, Asturias, Spain
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
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31
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Abstract
Bifidobacteria are members of the intestinal microbiota of mammals and other animals, and some strains are able to exert health-promoting effects. The genus Bifidobacterium belongs to the Actinobacteria phylum. Firmicutes, Bacteroidetes, and Actinobacteria constitute the most abundant phyla in the human intestinal microbiota, Firmicutes and Bacteroidetes being predominant in adults, and Actinobacteria in breast-fed infants, where bifidobacteria can reach levels higher than 90% of the total bacterial population. They are among the first microbial colonizers of the intestines of newborns, and play key roles in the development of their physiology, including maturation of the immune system and use of dietary components. Indeed, some nutrients, such as human milk oligosaccharides, are important drivers of bifidobacterial development. Some Bifidobacterium strains are considered probiotic microorganisms because of their beneficial effects, and they have been included as bioactive ingredients in functional foods, mainly dairy products, as well as in food supplements and pharma products, alone, or together with, other microbes or microbial substrates. Well-documented scientific evidence of their activities is currently available for bifidobacteria-containing preparations in some intestinal and extraintestinal pathologies. In this review, we focus on the role of bifidobacteria as members of the human intestinal microbiota and their use as probiotics in the prevention and treatment of disease.
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32
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The Sortase-Dependent Fimbriome of the Genus Bifidobacterium: Extracellular Structures with Potential To Modulate Microbe-Host Dialogue. Appl Environ Microbiol 2017; 83:AEM.01295-17. [PMID: 28754709 DOI: 10.1128/aem.01295-17] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 07/25/2017] [Indexed: 12/21/2022] Open
Abstract
Bifidobacteria are important gut commensals of mammals, including humans, of any age. However, the molecular mechanisms by which these microorganisms establish themselves in the mammalian gut and persist in this environment are largely unknown. Here, we analyzed the genetic diversity of the predicted arsenal of sortase-dependent pili of known and sequenced members of the Bifidobacterium genus and constructed a bifidobacterial sortase-dependent fimbriome database. Our analyses revealed considerable genetic variability of the sortase-dependent fimbriome among bifidobacterial (sub)species, which appears to have been due to horizontal gene transfer events and for which we were able to perform evolutionary mapping. Functional assessment by transcriptome analysis and binding assays involving different substrates demonstrates how bifidobacterial pili are pivotal in promoting various abilities for adhesion to glycans and extracellular matrix proteins, thereby supporting the ecological success of bifidobacteria in the mammalian gut.IMPORTANCE Adhesion of bifidobacterial cells to the mucosa of the large intestine is considered a hallmark for the persistence and colonization of these bacteria in the human gut. In this context, we analyzed the genetic diversity of the predicted arsenal of sortase-dependent pili of known and sequenced members of the Bifidobacterium genus, and constructed a bifidobacterial sortase-dependent fimbriome database. Our analyses revealed considerable genetic variability of the sortase-dependent fimbriome among bifidobacterial (sub)species, which appears to have been due to horizontal gene transfer events. In addition, functional assessment by transcriptome analysis and binding assays involving different substrates demonstrates how bifidobacterial pili are crucial in promoting various abilities for adhesion to glycans and extracellular matrix proteins, thereby supporting the ecological success of bifidobacteria in the mammalian gut. This study represents a complete genomic study regarding the presence of fimbriae in the genus Bifidobacterium.
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33
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Browne HP, Neville BA, Forster SC, Lawley TD. Transmission of the gut microbiota: spreading of health. Nat Rev Microbiol 2017; 15:531-543. [PMID: 28603278 PMCID: PMC5837012 DOI: 10.1038/nrmicro.2017.50] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Transmission of commensal intestinal bacteria between humans could promote health by establishing, maintaining and replenishing microbial diversity in the microbiota of an individual. Unlike pathogens, the routes of transmission for commensal bacteria remain unappreciated and poorly understood, despite the likely commonalities between both. Consequently, broad infection control measures that are designed to prevent pathogen transmission and infection, such as oversanitation and the overuse of antibiotics, may inadvertently affect human health by altering normal commensal transmission. In this Review, we discuss the mechanisms and factors that influence host-to-host transmission of the intestinal microbiota and examine how a better understanding of these processes will identify new approaches to nurture and restore transmission routes that are used by beneficial bacteria.
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Affiliation(s)
- Hilary P Browne
- Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - B Anne Neville
- Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Samuel C Forster
- Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
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34
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Taibi A, Singh N, Chen J, Arioli S, Guglielmetti S, Comelli EM. Time- and strain-specific downregulation of intestinal EPAS1
via miR-148a by Bifidobacterium bifidum. Mol Nutr Food Res 2017; 61. [DOI: 10.1002/mnfr.201600596] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 10/07/2016] [Accepted: 11/18/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Amel Taibi
- Department of Nutritional Sciences; University of Toronto; ON Canada
| | - Natasha Singh
- Department of Nutritional Sciences; University of Toronto; ON Canada
| | - Jianmin Chen
- Department of Nutritional Sciences; University of Toronto; ON Canada
| | - Stefania Arioli
- Department of Nutritional Sciences; University of Toronto; ON Canada
- Department of Food; Environmental and Nutritional Sciences (DeFENS); University of Milan; Milan Italy
| | - Simone Guglielmetti
- Department of Food; Environmental and Nutritional Sciences (DeFENS); University of Milan; Milan Italy
| | - Elena M. Comelli
- Department of Nutritional Sciences; University of Toronto; ON Canada
- Centre for Child Nutrition and Health; Faculty of Medicine; University of Toronto; ON Canada
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Vazquez-Gutierrez P, Stevens MJA, Gehrig P, Barkow-Oesterreicher S, Lacroix C, Chassard C. The extracellular proteome of two Bifidobacterium species reveals different adaptation strategies to low iron conditions. BMC Genomics 2017; 18:41. [PMID: 28061804 PMCID: PMC5219805 DOI: 10.1186/s12864-016-3472-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 12/26/2016] [Indexed: 12/30/2022] Open
Abstract
Background Bifidobacteria are among the first anaerobic bacteria colonizing the gut. Bifidobacteria require iron for growth and their iron-sequestration mechanisms are important for their fitness and possibly inhibit enteropathogens. Here we used combined genomic and proteomic analyses to characterize adaptations to low iron conditions of B. kashiwanohense PV20-2 and B. pseudolongum PV8-2, 2 strains isolated from the feces of iron-deficient African infants and selected for their high iron-sequestering ability. Results Analyses of the genome contents revealed evolutionary adaptation to low iron conditions. A ferric and a ferrous iron operon encoding binding proteins and transporters were found in both strains. Remarkably, the ferric iron operon of B. pseudolongum PV8-2 is not found in other B. pseudolongum strains and likely acquired via horizontal gene transfer. The genome B. kashiwanohense PV20-2 harbors a unique region encoding genes putatively involved in siderophore production. Additionally, the secretomes of the two strains grown under low-iron conditions were analyzed using a combined genomic-proteomic approach. A ferric iron transporter was found in the secretome of B. pseudolongum PV8-2, while ferrous binding proteins were detected in the secretome of B. kashiwanohense PV20-2, suggesting different strategies to take up iron in the strains. In addition, proteins such as elongation factors, a glyceraldehyde-3-phosphate dehydrogenase, and the stress proteins GroEL and DnaK were identified in both secretomes. These proteins have been previously associated with adhesion of lactobacilli to epithelial cells. Conclusion Analyses of the genome and secretome of B. kashiwanohense PV20-2 and B. pseudolongum PV8-2 revealed different adaptations to low iron conditions and identified extracellular proteins for iron transport. The identified extracellular proteins might be involved in competition for iron in the gastrointestinal tract. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3472-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pamela Vazquez-Gutierrez
- Laboratory of Food Biotechnology, ETH Zurich, Institute of Food, Nutrition and Health, Schmelzbergstrasse 7, 8092, Zurich, Switzerland
| | - Marc J A Stevens
- Laboratory of Food Biotechnology, ETH Zurich, Institute of Food, Nutrition and Health, Schmelzbergstrasse 7, 8092, Zurich, Switzerland
| | - Peter Gehrig
- Functional Genomics Center Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | | | - Christophe Lacroix
- Laboratory of Food Biotechnology, ETH Zurich, Institute of Food, Nutrition and Health, Schmelzbergstrasse 7, 8092, Zurich, Switzerland.
| | - Christophe Chassard
- Laboratory of Food Biotechnology, ETH Zurich, Institute of Food, Nutrition and Health, Schmelzbergstrasse 7, 8092, Zurich, Switzerland.,Present Address: Institut National de la Recherche Agronomique, UR 545 URF, 15000, Aurillac, France
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Zakharova YV. FACTORS OF ADHESION OF BIFIDOBACTERIA. JOURNAL OF MICROBIOLOGY, EPIDEMIOLOGY AND IMMUNOBIOLOGY 2016. [DOI: 10.36233/0372-9311-2016-5-80-87] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Data on fimbrial and afimbrial adhesion factors of bifidobacteria are presented. Pili-like structures, their composition and conditions of formation in various species of bifidobacteria are described. Several sugar-lytic enzymes serve as afimbrial adhesins in bifidobacteria. Transaldolase and enolase are detected in bifidobacteria on cells’ surface. Transaldolase ensures binding of bifidobacteria with mucin and their auto-aggregation. Surface enolase has an affinity to plasminogen, thus bifidobacteria obtain a surface-bound protein with proteolytic activity. Molecular structures giving bifidobacteria hydrophobic properties are described - surface lipoprotein Bop A and lipoteichoic acids.
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Duranti S, Gaiani F, Mancabelli L, Milani C, Grandi A, Bolchi A, Santoni A, Lugli GA, Ferrario C, Mangifesta M, Viappiani A, Bertoni S, Vivo V, Serafini F, Barbaro MR, Fugazza A, Barbara G, Gioiosa L, Palanza P, Cantoni AM, de'Angelis GL, Barocelli E, de'Angelis N, van Sinderen D, Ventura M, Turroni F. Elucidating the gut microbiome of ulcerative colitis: bifidobacteria as novel microbial biomarkers. FEMS Microbiol Ecol 2016; 92:fiw191. [PMID: 27604252 DOI: 10.1093/femsec/fiw191] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2016] [Indexed: 12/21/2022] Open
Abstract
Ulcerative colitis (UC) is associated with a substantial alteration of specific gut commensals, some of which may be involved in microbiota-mediated protection. In this study, microbiota cataloging of UC patients by 16S rRNA microbial profiling revealed a marked reduction of bifidobacteria, in particular the Bifidobacterium bifidum species, thus suggesting that this taxon plays a biological role in the aetiology of UC. We investigated this further through an in vivo trial by testing the effects of oral treatment with B. bifidum PRL2010 in a wild-type murine colitis model. TNBS-treated mice receiving 10(9) cells of B. bifidum PRL2010 showed a marked reduction of all colitis-associated histological indices as well as maintenance of mucosal integrity as it was shown by the increase in the expression of many tight junction-encoding genes. The protective role of B. bifidum PRL2010, as well as its sortase-dependent pili, appears to be established through the induction of an innate immune response of the host. These results highlight the importance of B. bifidum as a microbial biomarker for UC, revealing its role in protection against experimentally induced colitis.
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Affiliation(s)
- Sabrina Duranti
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11A, 43124 Parma, Italy
| | - Federica Gaiani
- Gastroenterology Unit, University Hospital of Parma, Via Gramsci 14, 43126 Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11A, 43124 Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11A, 43124 Parma, Italy
| | - Andrea Grandi
- Department of Pharmacy, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Angelo Bolchi
- Laboratory of Molecular Biology, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| | - Andrea Santoni
- Laboratory of Molecular Biology, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11A, 43124 Parma, Italy
| | - Chiara Ferrario
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11A, 43124 Parma, Italy
| | | | - Alice Viappiani
- GenProbio srl, Parco Area delle Scienze 11A, 43124 Parma, Italy
| | - Simona Bertoni
- Department of Pharmacy, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Valentina Vivo
- Department of Pharmacy, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Fausta Serafini
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11A, 43124 Parma, Italy
| | - Maria Raffaella Barbaro
- Department of Medical and Surgical Sciences and Center for Applied Biomedical Research (CRBA), University of Bologna, Via Massarenti 9, Bologna 40138, Italy
| | - Alessandro Fugazza
- Gastroenterology Unit, University Hospital of Parma, Via Gramsci 14, 43126 Parma, Italy
| | - Giovanni Barbara
- Department of Medical and Surgical Sciences and Center for Applied Biomedical Research (CRBA), University of Bologna, Via Massarenti 9, Bologna 40138, Italy
| | - Laura Gioiosa
- Department of Neurosciences, University of Parma, 43124 Parma, Italy
| | - Paola Palanza
- Department of Neurosciences, University of Parma, 43124 Parma, Italy
| | - Anna Maria Cantoni
- Department of Veterinary Science, University of Parma, Via del Taglio 10, 43126 Parma, Italy
| | - Gian Luigi de'Angelis
- Gastroenterology Unit, University Hospital of Parma, Via Gramsci 14, 43126 Parma, Italy
| | - Elisabetta Barocelli
- Department of Pharmacy, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Nicola de'Angelis
- Unit of Digestive, Hepato-Pancreato-Biliary Surgery and Liver Transplantation, Henri Mondor Hospital, 51 Avenue du Maréchal de Lattre de Tassigny, Créteil 94010, France
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11A, 43124 Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11A, 43124 Parma, Italy
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Ruiz L, Hidalgo C, Blanco-Míguez A, Lourenço A, Sánchez B, Margolles A. Tackling probiotic and gut microbiota functionality through proteomics. J Proteomics 2016; 147:28-39. [DOI: 10.1016/j.jprot.2016.03.023] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 02/19/2016] [Accepted: 03/10/2016] [Indexed: 12/24/2022]
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Westermann C, Gleinser M, Corr SC, Riedel CU. A Critical Evaluation of Bifidobacterial Adhesion to the Host Tissue. Front Microbiol 2016; 7:1220. [PMID: 27547201 PMCID: PMC4974247 DOI: 10.3389/fmicb.2016.01220] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 07/22/2016] [Indexed: 01/15/2023] Open
Abstract
Bifidobacteria are common inhabitants of the human gastrointestinal tract that, despite a long history of research, have not shown any pathogenic potential whatsoever. By contrast, some bifidobacteria are associated with a number of health-related benefits for the host. The reported beneficial effects of bifidobacteria include competitive exclusion of pathogens, alleviation of symptoms of irritable bowel syndrome and inflammatory bowel disease, and modulation of intestinal and systemic immune responses. Based on these effects, bifidobacteria are widely used as probiotics by pharmaceutical and dairy industries. In order to exert a beneficial effect bifidobacteria have to, at least transiently, colonize the host in a sufficient population size. Besides other criteria such as resistance to manufacturing processes and intestinal transit, potential probiotic bacteria are tested for adhesion to the host structures including intestinal epithelial cells, mucus, and extracellular matrix components. In the present review article, we summarize the current knowledge on bifidobacterial structures that mediate adhesion to host tissue and compare these to similar structures of pathogenic bacteria. This reveals that most of the adhesive structures and mechanisms involved in adhesion of bifidobacteria to host tissue are similar or even identical to those employed by pathogens to cause disease. It is thus reasonable to assume that these structures and mechanisms are equally important for commensal or probiotic bacteria and play a similar role in the beneficial effects exerted by bifidobacteria.
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Affiliation(s)
| | - Marita Gleinser
- Institute of Microbiology and Biotechnology, University of Ulm Ulm, Germany
| | - Sinéad C Corr
- Department of Microbiology, Moyne Institute of Preventative Medicine, School of Genetics and Microbiology, Trinity College Dublin Dublin, Ireland
| | - Christian U Riedel
- Institute of Microbiology and Biotechnology, University of Ulm Ulm, Germany
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40
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Genomic analysis of three Bifidobacterium species isolated from the calf gastrointestinal tract. Sci Rep 2016; 6:30768. [PMID: 27468806 PMCID: PMC4965825 DOI: 10.1038/srep30768] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 07/07/2016] [Indexed: 12/27/2022] Open
Abstract
Ruminant animals contribute significantly to the global value of agriculture and rely on a complex microbial community for efficient digestion. However, little is known of how this microbial-host relationship develops and is maintained. To begin to address this, we have determined the ability of three Bifidobacterium species isolated from the faeces of newborn calves to grow on carbohydrates typical of a newborn ruminant diet. Genome sequences have been determined for these bacteria with analysis of the genomes providing insights into the host association and identification of several genes that may mediate interactions with the ruminant gastrointestinal tract. The present study provides a starting point from which we can define the role of potential beneficial microbes in the nutrition of young ruminants and begin to influence the interactions between the microbiota and the host. The differences observed in genomic content hint at niche partitioning among the bifidobacterial species analysed and the different strategies they employ to successfully adapt to this habitat.
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41
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Evaluation of genetic diversity among strains of the human gut commensal Bifidobacterium adolescentis. Sci Rep 2016; 6:23971. [PMID: 27035119 PMCID: PMC4817515 DOI: 10.1038/srep23971] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 03/17/2016] [Indexed: 12/31/2022] Open
Abstract
Bifidobacteria are members of the human gut microbiota, being numerically dominant in the colon of infants, while also being prevalent in the large intestine of adults. In this study, we determined and analyzed the pan-genome of Bifidobacterium adolescentis, which is one of many bacteria found in the human adult gut microbiota. In silico analysis of the genome sequences of eighteen B. adolescentis strains isolated from various environments, such as human milk, human feces and bovine rumen, revealed a high level of genetic variability, resulting in an open pan-genome. Compared to other bifidobacterial taxa such as Bifidobacterium bifidum and Bifidobacterium breve, the more extensive B. adolescentis pan-genome supports the hypothesis that the genetic arsenal of this taxon expanded so as to become more adaptable to the variable and changing ecological niche of the gut. These increased genetic capabilities are particularly evident for genes required for dietary glycan-breakdown.
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42
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Tytgat HLP, van Teijlingen NH, Sullan RMA, Douillard FP, Rasinkangas P, Messing M, Reunanen J, Satokari R, Vanderleyden J, Dufrêne YF, Geijtenbeek TBH, de Vos WM, Lebeer S. Probiotic Gut Microbiota Isolate Interacts with Dendritic Cells via Glycosylated Heterotrimeric Pili. PLoS One 2016; 11:e0151824. [PMID: 26985831 PMCID: PMC4795749 DOI: 10.1371/journal.pone.0151824] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 03/06/2016] [Indexed: 02/06/2023] Open
Abstract
Mapping of the microbial molecules underlying microbiota-host interactions is key to understand how microbiota preserve mucosal homeostasis. A pivotal family of such bacterial molecules are pili. Pili are proteinaceous cell wall appendages with a well-documented role in adhesion, whilst their role in immune interaction with the host is less established. Gram-positive pili are often posttranslationally modified by sortase-specific cleavage reactions and the formation of intramolecular peptide bonds. Here we report glycosylation as a new level of posttranslational modification of sortase-dependent pili of a beneficial microbiota species and its role in immune modulation. We focused on the SpaCBA pili of the model probiotic and beneficial human gut microbiota isolate Lactobacillus rhamnosus GG. A unique combination of molecular techniques, nanoscale mechanical and immunological approaches led to the identification of mannose and fucose residues on the SpaCBA pili. These glycans on the pili are recognized by human dendritic cells via the C-type lectin receptor DC-SIGN, a key carbohydrate-dependent immune tailoring pattern recognition receptor. This specific lectin-sugar interaction is moreover of functional importance and modulated the cytokine response of dendritic cells. This provides insight into the direct role bacterial glycoproteins can play in the immunomodulation of the host. Modification of the complex heterotrimeric pili of a model probiotic and microbiota isolate with mannose and fucose is of importance for the functional interaction with the host immune lectin receptor DC-SIGN on human dendritic cells. Our findings shed light on the yet underappreciated role of glycoconjugates in bacteria-host interactions.
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Affiliation(s)
- Hanne L. P. Tytgat
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
- Department of Bioscience Engineering, Environmental Ecology & Applied Microbiology, University of Antwerp, Antwerp, Belgium
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Nienke H. van Teijlingen
- Academic Medical Center, Department of Experimental Immunology, University of Amsterdam, Amsterdam, The Netherlands
| | - Ruby May A. Sullan
- Institute of Life Sciences, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | | | - Pia Rasinkangas
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Marcel Messing
- Immunobiology Research Program and Department of Bacteriology and Immunology, University of Helsinki, Helsinki, Finland
| | - Justus Reunanen
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Reetta Satokari
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Jos Vanderleyden
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Yves F. Dufrêne
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Teunis B. H. Geijtenbeek
- Academic Medical Center, Department of Experimental Immunology, University of Amsterdam, Amsterdam, The Netherlands
| | - Willem M. de Vos
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Immunobiology Research Program and Department of Bacteriology and Immunology, University of Helsinki, Helsinki, Finland
| | - Sarah Lebeer
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
- Department of Bioscience Engineering, Environmental Ecology & Applied Microbiology, University of Antwerp, Antwerp, Belgium
- * E-mail:
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Wei X, Wang S, Zhao X, Wang X, Li H, Lin W, Lu J, Zhurina D, Li B, Riedel CU, Sun Y, Yuan J. Proteomic Profiling of Bifidobacterium bifidum S17 Cultivated Under In Vitro Conditions. Front Microbiol 2016; 7:97. [PMID: 26903976 PMCID: PMC4751264 DOI: 10.3389/fmicb.2016.00097] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 01/18/2016] [Indexed: 01/04/2023] Open
Abstract
Bifidobacteria are frequently used in probiotic food and dairy products. Bifidobacterium bifidum S17 is a promising probiotic candidate strain that displays strong adhesion to intestinal epithelial cells and elicits potent anti-inflammatory capacity both in vitro and in murine models of colitis. The recently sequenced genome of B. bifidum S17 has a size of about 2.2 Mb and encodes 1,782 predicted protein-coding genes. In the present study, a comprehensive proteomic profiling was carried out to identify and characterize proteins expressed by B. bifidum S17. A total of 1148 proteins entries were identified by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS), representing 64.4% of the predicted proteome. 719 proteins could be assigned to functional categories according to cluster of orthologous groups of proteins (COGs). The COG distribution of the detected proteins highly correlates with that of the complete predicted proteome suggesting a good coverage and representation of the genomic content of B. bifidum S17 by the proteome. COGs that were highly present in the proteome of B. bifidum S17 were Translation, Amino Acid Transport and Metabolism, and Carbohydrate Transport and Metabolism. Complete sets of enzymes for both the bifidus shunt and the Embden-Meyerh of pathway were identified. Further bioinformatic analysis yielded 28 proteins with a predicted extracellular localization including 14 proteins with an LPxTG-motif for cell wall anchoring and two proteins (elongation factor Tu and enolase) with a potential moonlighting function in adhesion. Amongst the predicted extracellular proteins were five of six pilin proteins encoded in the B. bifidum S17 genome as well as several other proteins with a potential role in interaction with host structures. The presented results are the first compilation of a proteomic reference profile for a B. bifidum strain and will facilitate analysis of the molecular mechanisms of physiology, host-interactions and beneficial effects of a potential probiotic strain.
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Affiliation(s)
- Xiao Wei
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Simiao Wang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Xiangna Zhao
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Xuesong Wang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Huan Li
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Weishi Lin
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Jing Lu
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Daria Zhurina
- Institute of Microbiology and Biotechnology, University of Ulm Ulm, Germany
| | - Boxing Li
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Christian U Riedel
- Institute of Microbiology and Biotechnology, University of Ulm Ulm, Germany
| | - Yansong Sun
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Jing Yuan
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
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Suzuki K, Nishiyama K, Miyajima H, Osawa R, Yamamoto Y, Mukai T. Adhesion properties of a putative polymorphic fimbrial subunit protein from Bifidobacterium longum subsp. longum. BIOSCIENCE OF MICROBIOTA FOOD AND HEALTH 2015; 35:19-27. [PMID: 26858927 PMCID: PMC4735030 DOI: 10.12938/bmfh.2015-015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 08/27/2015] [Indexed: 02/07/2023]
Abstract
In our previous study, we found that the open reading frame bl0675 in the genome of
Bifidobacterium longum subsp. longum isolated from human feces encoded a
novel putative fimbrial protein, was highly polymorphic, and had five variants (A, B, C, D, and E types). The
aim of this study was to evaluate the affinity of these variants to porcine colonic mucins (PCMs).
Protein-binding properties were examined using the recombinant BL0675 protein containing a C-terminal 6 × His
tag (His-BL0675). Surface plasmon resonance analysis demonstrated that the His-BL0675 A type had strong
affinity to PCMs (KD = 9.82 × 10−8 M), whereas the B, C, D, and E types
exhibited little or no binding. In a competitive enzyme-linked immunosorbent assay, His-BL0675 A type binding
was reduced by addition of mucin oligosaccharides, suggesting that the binding occurs via carbohydrate chains
of PCMs. The localization of BL0675 to the B. longum subsp. longum cell
surface was confirmed by western blot analysis using A type polyclonal antibodies. Bacterial adhesion of
B. longum subsp. longum to PCMs was also blocked by A type-specific
antibodies; however, its adhesion properties were strain specific. Our results suggest that the BL0675
variants significantly contribute to the adhesion of B. longum subsp. longum
strains. The expression and the adhesive properties of this protein are affected by genetic polymorphisms and
are specific for B. longum subsp. longum strains. However, further studies
are required on the properties of binding of these putative fimbrial proteins to the human gastrointestinal
tract.
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Affiliation(s)
- Kenta Suzuki
- Department of Animal Science, School of Veterinary Medicine, Kitasato University, Towada, Aomori, Japan
| | - Keita Nishiyama
- Department of Animal Science, School of Veterinary Medicine, Kitasato University, Towada, Aomori, Japan; Department of Microbiology, School of Pharmacy, Kitasato University, Minato-ku, Tokyo, Japan
| | - Hiroki Miyajima
- Department of Animal Science, School of Veterinary Medicine, Kitasato University, Towada, Aomori, Japan
| | - Ro Osawa
- Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Yuji Yamamoto
- Department of Animal Science, School of Veterinary Medicine, Kitasato University, Towada, Aomori, Japan
| | - Takao Mukai
- Department of Animal Science, School of Veterinary Medicine, Kitasato University, Towada, Aomori, Japan
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45
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Turroni F, Özcan E, Milani C, Mancabelli L, Viappiani A, van Sinderen D, Sela DA, Ventura M. Glycan cross-feeding activities between bifidobacteria under in vitro conditions. Front Microbiol 2015; 6:1030. [PMID: 26441950 PMCID: PMC4585166 DOI: 10.3389/fmicb.2015.01030] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 09/10/2015] [Indexed: 01/20/2023] Open
Abstract
Bifidobacteria colonize the gut of various mammals, including humans, where they may metabolize complex, diet-, and host-derived carbohydrates. The glycan-associated metabolic features encoded by bifidobacteria are believed to be strongly influenced by cross-feeding activities due to the co-existence of strains with different glycan-degrading properties. In this study, we observed an enhanced growth yield of Bifidobacterium bifidum PRL2010 when co-cultivated with Bifidobacterium breve 12L, Bifidobacterium adolescentis 22L, or Bifidobacterium thermophilum JCM1207. This enhanced growth phenomenon was confirmed by whole genome transcriptome analyses, which revealed co-cultivation-associated transcriptional induction of PRL2010 genes involved in carbohydrate metabolism, such as those encoding for carbohydrate transporters and associated energy production, and genes required for translation, ribosomal structure, and biogenesis, thus supporting the idea that co-cultivation of certain bifidobacterial strains with B. bifidum PRL2010 causes enhanced metabolic activity, and consequently increased lactate and/or acetate production. Overall, these data suggest that PRL2010 cells benefit from the presence of other bifidobacterial strains.
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Affiliation(s)
- Francesca Turroni
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma Italy
| | - Ezgi Özcan
- Department of Food Science, University of Massachusetts Amherst, Amherst, MA USA
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma Italy
| | | | - Douwe van Sinderen
- Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Cork Ireland
| | - David A Sela
- Department of Food Science, University of Massachusetts Amherst, Amherst, MA USA ; Center for Microbiome Research, University of Massachusetts Medical School, Worcester, MA USA
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma Italy
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Colagiorgi A, Turroni F, Mancabelli L, Serafini F, Secchi A, van Sinderen D, Ventura M. Insights into teichoic acid biosynthesis byBifidobacterium bifidumPRL2010. FEMS Microbiol Lett 2015; 362:fnv141. [DOI: 10.1093/femsle/fnv141] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2015] [Indexed: 12/23/2022] Open
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Duranti S, Milani C, Lugli GA, Turroni F, Mancabelli L, Sanchez B, Ferrario C, Viappiani A, Mangifesta M, Mancino W, Gueimonde M, Margolles A, van Sinderen D, Ventura M. Insights from genomes of representatives of the human gut commensal Bifidobacterium bifidum. Environ Microbiol 2015; 17:2515-31. [PMID: 25523018 DOI: 10.1111/1462-2920.12743] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 11/25/2014] [Accepted: 12/03/2014] [Indexed: 11/27/2022]
Abstract
Bifidobacteria are bacterial gut commensals of mammals, birds and social insects that are perceived to influence the metabolism/physiology of their host. In this context, members of the Bifidobacterium bifidum species are believed to significantly contribute to the overall microbiota of the human gut at infant stage. However, the molecular reasons for their adaptation to this environment are poorly understood. In this study, we analysed the pan-genome of B. bifidum species by decoding genomes of 15 B. bifidum strains, which highlighted the existence of a conserved gene uniquely present in this bifidobacterial taxon, underscoring a nutrient acquisition strategy that targets host-derived glycans, such as those present in mucin. Growth experiments and corresponding transcriptomic analyses confirmed the in silico data and supported these intriguing and unique host glycan-specific saccharolytic features. The ubiquity of the genetic features of B. bifidum for the breakdown of host glycans was confirmed by interrogating metagenomic datasets, thereby supporting the notion that metabolic access to host-derived glycans is a potent evolutionary force that has shaped B. bifidum genomes and consequently the ecology of the infant intestinal microbiota.
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Affiliation(s)
- Sabrina Duranti
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Francesca Turroni
- Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Borja Sanchez
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, Consejo Superior de Investigaciones Científicas, CSIC, Villaviciosa, Asturias, Spain
| | - Chiara Ferrario
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Alice Viappiani
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Marta Mangifesta
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Walter Mancino
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Miguel Gueimonde
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, Consejo Superior de Investigaciones Científicas, CSIC, Villaviciosa, Asturias, Spain
| | - Abelardo Margolles
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, Consejo Superior de Investigaciones Científicas, CSIC, Villaviciosa, Asturias, Spain
| | - Douwe van Sinderen
- Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
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