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Lugli GA, Argentini C, Tarracchini C, Mancabelli L, Viappiani A, Anzalone R, Angelini L, Alessandri G, Longhi G, Bianchi MG, Taurino G, Bussolati O, Milani C, Turroni F, Ventura M. Characterization of a Bifidobacterium animalis subsp. lactis reference strain based on ecology and transcriptomics. Appl Environ Microbiol 2024:e0108024. [PMID: 39235395 DOI: 10.1128/aem.01080-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 08/18/2024] [Indexed: 09/06/2024] Open
Abstract
Bifidobacteria are recognized as health-promoting bacteria that reside in the human gut, helping in the digestion of fiber, preventing infections, and producing essential compounds like vitamins. To date, Bifidobacterium animalis subsp. lactis, together with Bifidobacterium adolescentis, Bifidobacterium bifidum, Bifidobacterium breve, and Bifidobacterium longum, represents one of the species that are used as probiotic bacteria. Despite the extensive and detailed scientific research conducted on this microbial taxon, the molecular mechanisms by which B. animalis subsp. lactis exerts health benefits to its host are still largely unknown. Thus, we dissected the genetic repertoire and phylogenetic relationship of 162 strains of B. animalis subsp. lactis to select a representative reference strain of this taxon suitable for investigating its interaction with the host. The B. animalis subsp. lactis PRL2013 strain, which was isolated by a mucosal sample of a healthy adult, was chosen as the reference of the monophyletic cluster of human origin and revealed a greater adhesion index than that observed for another B. animalis subsp. lactis strain used in the industry as a probiotic supplement. Transcriptomics analyses of PRL2013 strain, when exposed to human cell monolayers, revealed 291 significantly upregulated genes, among which were found genes predicted to encode extracellular structures that may directly interact with human cells, such as extracellular polymeric substances, wall teichoic acids, and pili. IMPORTANCE To date, many Bifidobacterium animalis subsp. lactis strains have been isolated from human fecal samples. However, their presence in these samples does not necessarily suggest an ability to colonize the human gut. Furthermore, probiotics of non-human origin may not effectively interact with the gut epithelium, resulting in transient bacteria of the gut microbiota. In vitro experiments with human cells revealed that B. animalis subsp. lactis PRL2013, an autochthonous member of the human gut, shows colonization capability, leading to future applications in functional foods.
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Affiliation(s)
- 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 Argentini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Chiara Tarracchini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 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
| | - Giulia Longhi
- 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
- Laboratory of General Pathology, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Giuseppe Taurino
- Microbiome Research Hub, University of Parma, Parma, Italy
- Laboratory of General Pathology, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Ovidio Bussolati
- Microbiome Research Hub, University of Parma, Parma, Italy
- Laboratory of General Pathology, Department of Medicine and Surgery, 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
| | - 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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Longhi G, Lugli GA, Tarracchini C, Fontana F, Bianchi MG, Carli E, Bussolati O, van Sinderen D, Turroni F, Ventura M. From raw milk cheese to the gut: investigating the colonization strategies of Bifidobacterium mongoliense. Appl Environ Microbiol 2024:e0124424. [PMID: 39150265 DOI: 10.1128/aem.01244-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Accepted: 07/18/2024] [Indexed: 08/17/2024] Open
Abstract
The microbial ecology of raw milk cheeses is determined by bacteria originating from milk and milk-producing animals. Recently, it has been shown that members of the Bifidobacterium mongoliense species may become transmitted along the Parmigiano Reggiano cheese production chain and ultimately may colonize the consumer intestine. However, there is a lack of knowledge regarding the molecular mechanisms that mediate the interaction between B. mongoliense and the human gut. Based on 128 raw milk cheeses collected from different Italian regions, we isolated and characterized 10 B. mongoliense strains. Comparative genomics allowed us to unveil the presence of enzymes required for the degradation of sialylated host-glycans in B. mongoliense, corroborating the appreciable growth on de Man-Rogosa-Sharpe (MRS) medium supplemented with 3'-sialyllactose (3'-SL) or 6'-sialyllactose (6'-SL). The B. mongoliense BMONG18 was chosen, due to its superior ability to utilize 3'-SL and mucin as representative strain, to investigate its behavior when co-inoculated with other bifidobacterial species. Conversely, members of other bifidobacterial species did not appear to benefit from the presence of BMONG18, highlighting a competitive scenario for nutrient acquisition. Transcriptomic data of BMONG18 reveal no significant differences in gene expression when cultivated in a gut simulating medium (GSM), regardless of whether cheese was included or not. Furthermore, BMONG18 was shown to exhibit high adhesion capabilities to HT29-MTX human cells, in line with its colonization ability of a human host.IMPORTANCEFermented foods are nourishments produced through controlled microbial growth that play an essential role in worldwide human nutrition. Research interest in fermented foods has increased since the 80s, driven by growing awareness of their potential health benefits beyond mere nutritional content. Bifidobacterium mongoliense, previously identified throughout the production process of Parmigiano Reggiano cheese, was found to be capable of establishing itself in the intestines of its consumers. Our study underscores molecular mechanisms through which this bifidobacterial species, derived from food, interacts with the host and other gut microbiota members.
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Affiliation(s)
- Giulia Longhi
- 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
| | | | - Elisa Carli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Ovidio Bussolati
- Department of Medicine and Surgery, Laboratory of General Pathology, 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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Wang P, Wang S, Wang D, Li Y, Yip RCS, Chen H. Postbiotics-peptidoglycan, lipoteichoic acid, exopolysaccharides, surface layer protein and pili proteins-Structure, activity in wounds and their delivery systems. Int J Biol Macromol 2024; 274:133195. [PMID: 38885869 DOI: 10.1016/j.ijbiomac.2024.133195] [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: 03/20/2024] [Revised: 06/06/2024] [Accepted: 06/13/2024] [Indexed: 06/20/2024]
Abstract
Chronic wound healing is a pressing global public health concern. Abuse and drug resistance of antibiotics are the key problems in the treatment of chronic wounds at present. Postbiotics are a novel promising strategy. Previous studies have reported that postbiotics have a wide range of biological activities including antimicrobial, immunomodulatory, antioxidant and anti-inflammatory abilities. However, several aspects related to these postbiotic activities remain unexplored or poorly known. Therefore, this work aims to outline general aspects and emerging trends in the use of postbiotics for wound healing, such as the production, characterization, biological activities and delivery strategies of postbiotics. In this review, a comprehensive overview of the physiological activities and structures of postbiotic biomolecules that contribute to wound healing is provided, such as peptidoglycan, lipoteichoic acid, bacteriocins, exopolysaccharides, surface layer proteins, pili proteins, and secretory proteins (p40 and p75 proteins). Considering the presence of readily degradable components in postbiotics, potential natural polymer delivery materials and delivery systems are emphasized, followed by the potential applications and commercialization prospects of postbiotics. These findings suggest that the treatment of chronic wounds with postbiotic ingredients will help provide new insights into wound healing and better guidance for the development of postbiotic products.
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Affiliation(s)
- Pu Wang
- Marine College, Shandong University, No. 180 Wen Hua West Road, Gao Strict, Weihai 264209, China.
| | - Shuxin Wang
- Marine College, Shandong University, No. 180 Wen Hua West Road, Gao Strict, Weihai 264209, China.
| | - Donghui Wang
- Marine College, Shandong University, No. 180 Wen Hua West Road, Gao Strict, Weihai 264209, China.
| | - Yuanyuan Li
- Department of Food Science, College of Agriculture and Life Sciences, Cornell University, Stocking Hall, 411 Tower Road, Ithaca, NY 14853, USA.
| | - Ryan Chak Sang Yip
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord St, Toronto, ON M5S 3G5, Canada.
| | - Hao Chen
- Marine College, Shandong University, No. 180 Wen Hua West Road, Gao Strict, Weihai 264209, China.
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Sanchez-Gallardo R, Bottacini F, Friess L, Esteban-Torres M, Somers C, Moore RL, McAuliffe FM, Cotter PD, van Sinderen D. Unveiling metabolic pathways of selected plant-derived glycans by Bifidobacterium pseudocatenulatum. Front Microbiol 2024; 15:1414471. [PMID: 39081887 PMCID: PMC11286577 DOI: 10.3389/fmicb.2024.1414471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 06/25/2024] [Indexed: 08/02/2024] Open
Abstract
Bifidobacteria are commonly encountered members of the human gut microbiota that possess the enzymatic machinery necessary for the metabolism of certain plant-derived, complex carbohydrates. In the current study we describe differential growth profiles elicited by a panel of 21 newly isolated Bifidobacterium pseudocatenulatum strains on various plant-derived glycans. Using a combination of gene-trait matching and comparative genome analysis, we identified two distinct xylanases responsible for the degradation of xylan. Furthermore, three distinct extracellular α-amylases were shown to be involved in starch degradation by certain strains of B. pseudocatenulatum. Biochemical characterization showed that all three α-amylases can cleave the related substrates amylose, amylopectin, maltodextrin, glycogen and starch. The genes encoding these enzymes are variably found in the species B. pseudocatenulatum, therefore constituting a strain-specific adaptation to the gut environment as these glycans constitute common plant-derived carbohydrates present in the human diet. Overall, our study provides insights into the metabolism of these common dietary carbohydrates by a human-derived bifidobacterial species.
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Affiliation(s)
- Rocio Sanchez-Gallardo
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Francesca Bottacini
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Biological Sciences, Munster Technological University, Cork, Ireland
| | - Lisa Friess
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Maria Esteban-Torres
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Clarissa Somers
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Rebecca L. Moore
- UCD Perinatal Research Centre, School of Medicine, National Maternity Hospital, University College Dublin, Dublin, Ireland
| | - Fionnuala M. McAuliffe
- UCD Perinatal Research Centre, School of Medicine, National Maternity Hospital, University College Dublin, Dublin, Ireland
| | - Paul D. Cotter
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc Food Research Centre Moorepark, Cork, Ireland
| | - Douwe van Sinderen
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
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Moreno-Muñoz JA, Ojeda JD, López JJ. A Probiotic Bacterium with Activity against the Most Frequent Bacteria and Viruses Causing Pediatric Diarrhea: Bifidobacterium longum subsp. infantis CECT 7210 ( B. infantis IM1 ®). Microorganisms 2024; 12:1183. [PMID: 38930565 PMCID: PMC11206103 DOI: 10.3390/microorganisms12061183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 05/07/2024] [Accepted: 05/31/2024] [Indexed: 06/28/2024] Open
Abstract
The second leading cause of death in children under five years old is diarrheal disease. Probiotics, specifically bifidobacteria, have been associated with a reduction in the number of diarrhea episodes and their severity in babies. In this paper, we summarize the preclinical and clinical evidence of the efficacy of B. longum subsp. infantis IM1® against various gastrointestinal pathogens using in vitro models, animal models, and clinical studies carried out in our laboratory. The preclinical data demonstrate that IM1® effectively inhibits rotavirus replication (by up to 36.05%) in MA-104 and HT-29 cells and from infection (up to 48.50%) through the production of an 11-amino-acid peptide. IM1® displays the capability to displace pathogens from enterocytes, particularly Cronobacter sakazakii and Salmonella enterica, and to reduce the adhesion to the HT29 cells of C. sakazakii and Shigella sonnei. In animal models, the IM1® strain exhibits in vivo protection against rotavirus and improves the clinical symptomatology of bacterial gastroenteritis. A clinical study involving infants under 3 months of age revealed that IM1® reduced episodes of diarrhea, proving to be safe, well tolerated, and associated with a lower prevalence of constipation. B. infantis IM1® emerges as an effective probiotic, diminishing episodes of diarrhea caused by gastrointestinal pathogens.
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Affiliation(s)
- José Antonio Moreno-Muñoz
- Laboratorios Ordesa S.L., Parc Científic de Barcelona, C/Baldiri Reixac 15-21, 08028 Barcelona, Spain; (J.D.O.); (J.J.L.)
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Meng J, Liu S, Wu X. Engineered probiotics as live biotherapeutics for diagnosis and treatment of human diseases. Crit Rev Microbiol 2024; 50:300-314. [PMID: 36946080 DOI: 10.1080/1040841x.2023.2190392] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 01/09/2023] [Indexed: 03/23/2023]
Abstract
The use of probiotics to regulate the intestinal microbiota to prevent and treat a large number of disorders and diseases has been an international research hotspot. Although conventional probiotics have a certain regulatory role in nutrient metabolism, inhibiting pathogens, inducing immune regulation, and maintaining intestinal epithelial barrier function, they are unable to treat certain diseases. In recent years, aided by the continuous development of synthetic biology, engineering probiotics with desired characteristics and functionalities to benefit human health has made significant progress. In this article, we summarise the mechanism of action of conventional probiotics and their limitations and highlight the latest developments in the design and construction of probiotics as living diagnostics and therapeutics for the detection and treatment of a series of diseases, including pathogen infections, cancer, intestinal inflammation, metabolic disorders, vaccine delivery, cognitive health, and fatty liver. Besides we discuss the concerns regarding engineered probiotics and corresponding countermeasures and outline the desired features in the future development of engineered live biotherapeutics.
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Affiliation(s)
- Jiao Meng
- Laboratory of Nutrient Resources and Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Science, Tianjin, China
| | - Shufan Liu
- Laboratory of Nutrient Resources and Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Science, Tianjin, China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology; College of Bioengineering, Tianjin University of Science and Technology, Tianjin, China
| | - Xin Wu
- Laboratory of Nutrient Resources and Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Science, Tianjin, China
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
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7
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Pei B, Peng S, Huang C, Zhou F. Bifidobacterium modulation of tumor immunotherapy and its mechanism. Cancer Immunol Immunother 2024; 73:94. [PMID: 38564002 PMCID: PMC10987355 DOI: 10.1007/s00262-024-03665-x] [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: 11/29/2023] [Accepted: 02/29/2024] [Indexed: 04/04/2024]
Abstract
The advent of tumor immunotherapy in patients has revolutionized the treatment of tumors and significantly improved survival rates for a wide range of tumors. However, the full therapeutic potential of immune checkpoint inhibitors (ICIs) has yet to be realized, as not all patients have a lasting survival benefit from them, and a significant proportion of patients show primary or acquired resistance to immunotherapy. Bifidobacterium is one of the most common probiotics, and its antitumor and immunomodulatory effects have been demonstrated in recent years, but its immunomodulatory effects in tumors, especially on ICIs and in combination, have not been extensively studied in clinical practice, and its effects on the immune system and the mechanisms that modulate immunotherapy are largely unknown. Therefore, this review will focus on the immunomodulatory effects of Bifidobacteria in malignancies and the possible mechanisms of action of Bifidobacteria on immunotherapy in the hope of providing a basis for further research and better application of Bifidobacteria in clinical practice.
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Affiliation(s)
- Bo Pei
- Hubei Key Laboratory of Tumor Biological Behaviors, Department of Radiation Oncology and Medical Oncology, Zhongnan Hospital of Wuhan University, Hubei Cancer Clinical Study Center, Wuhan, China
- Department of Oncology, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi Clinical College of Wuhan University, Enshi, China
| | - Shixuan Peng
- Department of Oncology, Graduate Collaborative Training Base of The First People's Hospital of Xiangtan City, Hengyang Medical School, University of South China, Hengyang, China
| | - Chuying Huang
- Department of Oncology, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi Clinical College of Wuhan University, Enshi, China
- Hubei Selenium and Human Health Institute, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, China
- Hubei Provincial Key Laboratory of Selenium Resources and Bioapplications, Enshi, China
| | - Fuxiang Zhou
- Hubei Key Laboratory of Tumor Biological Behaviors, Department of Radiation Oncology and Medical Oncology, Zhongnan Hospital of Wuhan University, Hubei Cancer Clinical Study Center, Wuhan, China.
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Huang T, Liang X, Bao H, Ma G, Tang X, Luo H, Xiao X. Multi-omics analysis reveals the associations between altered gut microbiota, metabolites, and cytokines during pregnancy. mSystems 2024; 9:e0125223. [PMID: 38323818 PMCID: PMC10949498 DOI: 10.1128/msystems.01252-23] [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: 11/21/2023] [Accepted: 12/28/2023] [Indexed: 02/08/2024] Open
Abstract
For embryo implantation and fetal development, the maternal immune system undergoes dramatic changes. The mechanisms involved in inducing alterations of maternal immunity have not been fully clarified. Gut microbiome and metabolites were thought to influence the host immune response. During normal pregnancy, notable changes occur in the gut microbiota and metabolites. However, the relationship of these alterations to immune function during pregnancy remains unclear. In this study, we examined gut microbiota, fecal metabolites, plasma metabolites, and cytokines in pregnant women and non-pregnant women. Our findings revealed that, in comparison to non-pregnant women, pregnant women exhibit a significant increase in the relative abundance of Actinobacteriota and notable differences in metabolic pathways related to bile acid secretion. Furthermore, there was a marked reduction in pro-inflammatory cytokines levels in pregnant women. Correlation analyses indicated that these alterations in cytokines may be linked to specific gut bacteria and metabolites. Bacteria within the same microbial modules exhibited consistent effects on cytokines, suggesting that gut bacteria may function as functional groups. Mediation analysis further identified that certain bacteria might influence cytokines through metabolites, such as bile acids and arachidonic acid. Our findings propose potential biological connections between bacteria, metabolites, and immunity, which require further validation in future studies.IMPORTANCEA great number of studies have focused on diseases induced by intestinal microecological disorders and immune imbalances. However, the understanding of how intestinal microbiota interacts with immunity during normal pregnancy, which is fundamental to studying pathological pregnancies related to intestinal microbiota disturbances, has not been well elucidated. Our study employed multi-omics analysis to discover that changes in gut microbiota and metabolites during pregnancy can impact immune function. In addition, we identified several metabolites that may mediate the effect of gut microbes on plasma cytokines. Our study offered new insights into our understanding of the connections between the gut microbiome, metabolome, and the immune system during pregnancy.
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Affiliation(s)
- Ting Huang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Xinyuan Liang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jinan University, Guangzhou, China
- Department of Obstetrics, The Second Clinical Medical College, Jinan University (Shenzhen People’s Hospital), Shenzhen, China
| | - Han Bao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Guangyu Ma
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Xiaomei Tang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Huijuan Luo
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Xiaomin Xiao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Jinan University, Guangzhou, China
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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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10
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Argentini C, Lugli GA, Tarracchini C, Fontana F, Mancabelli L, Viappiani A, Anzalone R, Angelini L, Alessandri G, Longhi G, Bianchi MG, Taurino G, Bussolati O, Milani C, van Sinderen D, Turroni F, Ventura M. Genomic and ecological approaches to identify the Bifidobacterium breve prototype of the healthy human gut microbiota. Front Microbiol 2024; 15:1349391. [PMID: 38426063 PMCID: PMC10902438 DOI: 10.3389/fmicb.2024.1349391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/29/2024] [Indexed: 03/02/2024] Open
Abstract
Members of the genus Bifidobacterium are among the first microorganisms colonizing the human gut. Among these species, strains of Bifidobacterium breve are known to be commonly transmitted from mother to her newborn, while this species has also been linked with activities supporting human wellbeing. In the current study, an in silico approach, guided by ecology- and phylogenome-based analyses, was employed to identify a representative strain of B. breve to be exploited as a novel health-promoting candidate. The selected strain, i.e., B. breve PRL2012, was found to well represent the genetic content and functional genomic features of the B. breve taxon. We evaluated the ability of PRL2012 to survive in the gastrointestinal tract and to interact with other human gut commensal microbes. When co-cultivated with various human gut commensals, B. breve PRL2012 revealed an enhancement of its metabolic activity coupled with the activation of cellular defense mechanisms to apparently improve its survivability in a simulated ecosystem resembling the human microbiome.
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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
| | - Giulia Longhi
- 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
- Laboratory of General Pathology, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Giuseppe Taurino
- Microbiome Research Hub, University of Parma, Parma, Italy
- Laboratory of General Pathology, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Ovidio Bussolati
- Microbiome Research Hub, University of Parma, Parma, Italy
- Laboratory of General Pathology, Department of Medicine and Surgery, 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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11
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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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12
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Rizzo SM, Vergna LM, Alessandri G, Lee C, Fontana F, Lugli GA, Carnevali L, Bianchi MG, Barbetti M, Taurino G, Sgoifo A, Bussolati O, Turroni F, van Sinderen D, Ventura M. GH136-encoding gene (perB) is involved in gut colonization and persistence by Bifidobacterium bifidum PRL2010. Microb Biotechnol 2024; 17:e14406. [PMID: 38271233 PMCID: PMC10884991 DOI: 10.1111/1751-7915.14406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/21/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024] Open
Abstract
Bifidobacteria are commensal microorganisms that typically inhabit the mammalian gut, including that of humans. As they may be vertically transmitted, they commonly colonize the human intestine from the very first day following birth and may persist until adulthood and old age, although generally at a reduced relative abundance and prevalence compared to infancy. The ability of bifidobacteria to persist in the human intestinal environment has been attributed to genes involved in adhesion to epithelial cells and the encoding of complex carbohydrate-degrading enzymes. Recently, a putative mucin-degrading glycosyl hydrolase belonging to the GH136 family and encoded by the perB gene has been implicated in gut persistence of certain bifidobacterial strains. In the current study, to better characterize the function of this gene, a comparative genomic analysis was performed, revealing the presence of perB homologues in just eight bifidobacterial species known to colonize the human gut, including Bifidobacterium bifidum and Bifidobacterium longum subsp. longum strains, or in non-human primates. Mucin-mediated growth and adhesion to human intestinal cells, in addition to a rodent model colonization assay, were performed using B. bifidum PRL2010 as a perB prototype and its isogenic perB-insertion mutant. These results demonstrate that perB inactivation reduces the ability of B. bifidum PRL2010 to grow on and adhere to mucin, as well as to persist in the rodent gut niche. These results corroborate the notion that the perB gene is one of the genetic determinants involved in the persistence of B. bifidum PRL2010 in the human gut.
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Affiliation(s)
- Sonia Mirjam Rizzo
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental SustainabilityUniversity of ParmaParmaItaly
| | - Laura Maria Vergna
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental SustainabilityUniversity of ParmaParmaItaly
| | - Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental SustainabilityUniversity of ParmaParmaItaly
| | - Ciaran Lee
- APC Microbiome Institute and School of Microbiology, Bioscience InstituteNational University of IrelandCorkIreland
| | - Federico Fontana
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental SustainabilityUniversity of ParmaParmaItaly
- GenProbio srlParmaItaly
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental SustainabilityUniversity of ParmaParmaItaly
- Interdepartmental Research Centre “Microbiome Research Hub”University of ParmaParmaItaly
| | - Luca Carnevali
- Interdepartmental Research Centre “Microbiome Research Hub”University of ParmaParmaItaly
- Stress Physiology Lab, Department of Chemistry, Life Sciences and Environmental SustainabilityUniversity of ParmaParmaItaly
| | - Massimiliano G. Bianchi
- Interdepartmental Research Centre “Microbiome Research Hub”University of ParmaParmaItaly
- Laboratory of General Pathology, Department of Medicine and SurgeryUniversity of ParmaParmaItaly
| | - Margherita Barbetti
- Stress Physiology Lab, Department of Chemistry, Life Sciences and Environmental SustainabilityUniversity of ParmaParmaItaly
| | - Giuseppe Taurino
- Interdepartmental Research Centre “Microbiome Research Hub”University of ParmaParmaItaly
- Laboratory of General Pathology, Department of Medicine and SurgeryUniversity of ParmaParmaItaly
| | - Andrea Sgoifo
- Interdepartmental Research Centre “Microbiome Research Hub”University of ParmaParmaItaly
- Stress Physiology Lab, Department of Chemistry, Life Sciences and Environmental SustainabilityUniversity of ParmaParmaItaly
| | - Ovidio Bussolati
- Interdepartmental Research Centre “Microbiome Research Hub”University of ParmaParmaItaly
- Laboratory of General Pathology, Department of Medicine and SurgeryUniversity of ParmaParmaItaly
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental SustainabilityUniversity of ParmaParmaItaly
- Interdepartmental Research Centre “Microbiome Research Hub”University of ParmaParmaItaly
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience InstituteNational University of IrelandCorkIreland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental SustainabilityUniversity of ParmaParmaItaly
- Interdepartmental Research Centre “Microbiome Research Hub”University of ParmaParmaItaly
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13
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Walsh C, Owens RA, Bottacini F, Lane JA, van Sinderen D, Hickey RM. HMO-primed bifidobacteria exhibit enhanced ability to adhere to intestinal epithelial cells. Front Microbiol 2023; 14:1232173. [PMID: 38163079 PMCID: PMC10757668 DOI: 10.3389/fmicb.2023.1232173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/06/2023] [Indexed: 01/03/2024] Open
Abstract
The ability of gut commensals to adhere to the intestinal epithelium can play a key role in influencing the composition of the gut microbiota. Bifidobacteria are associated with a multitude of health benefits and are one of the most widely used probiotics for humans. Enhanced bifidobacterial adhesion may increase host-microbe, microbe-nutrient, and/or microbe-microbe interactions, thereby enabling consolidated health benefits to the host. The objective of this study was to determine the ability of human milk oligosaccharides (HMOs) to enhance bifidobacterial intestinal adhesion in vitro. This study assessed the colonisation-promoting effects of HMOs on four commercial infant-associated Bifidobacterium strains (two B. longum subsp. infantis strains, B. breve and B. bifidum). HT29-MTX cells were used as an in vitro intestinal model for bacterial adhesion. Short-term exposure of four commercial infant-associated Bifidobacterium strains to HMOs derived from breastmilk substantially increased the adherence (up to 47%) of these probiotic strains. Interestingly, when strains were incubated with HMOs as a four-strain combination, the number of viable bacteria adhering to intestinal cells increased by >90%. Proteomic analysis of this multi-strain bifidobacterial mixture revealed that the increased adherence resulting from exposure to HMOs was associated with notable increases in the abundance of sortase-dependent pili and glycosyl hydrolases matched to Bifidobacterium bifidum. This study suggests that HMOs may prime infant gut-associated Bifidobacterium for colonisation to intestinal epithelial cells by influencing the expression of various colonization factors.
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Affiliation(s)
- Clodagh Walsh
- Teagasc Food Research Centre, Moorepark, Cork, Ireland
- Health and Happiness Group, H&H Research, Cork, Ireland
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
| | | | - Francesca Bottacini
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
- Biological Sciences and ADAPT Research Centre, Munster Technological University, Cork, Ireland
| | | | - Douwe van Sinderen
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
| | - Rita M. Hickey
- Teagasc Food Research Centre, Moorepark, Cork, Ireland
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
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14
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Gavzy SJ, Kensiski A, Lee ZL, Mongodin EF, Ma B, Bromberg JS. Bifidobacterium mechanisms of immune modulation and tolerance. Gut Microbes 2023; 15:2291164. [PMID: 38055306 PMCID: PMC10730214 DOI: 10.1080/19490976.2023.2291164] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 11/30/2023] [Indexed: 12/07/2023] Open
Abstract
Bifidobacterium is a widely distributed commensal bacterial genus that displays beneficial pro-homeostatic and anti-inflammatory immunomodulatory properties. Depletion or absence of Bifidobacterium in humans and model organisms is associated with autoimmune responses and impaired immune homeostasis. At the cellular level, Bifidobacterium upregulates suppressive regulatory T cells, maintains intestinal barrier function, modulates dendritic cell and macrophage activity, and dampens intestinal Th2 and Th17 programs. While there has been a large volume of literature characterizing the probiotic properties of various Bifidobacterial species, the likely multifactorial mechanisms underlying these effects remain elusive, in particular, its immune tolerogenic effect. However, recent work has shed light on Bifidobacterium surface structural polysaccharide and protein elements, as well as its metabolic products, as commensal mediators of immune homeostasis. This review aims to discuss several mechanisms Bifidobacterium utilizes for immune modulation as well as their indirect impact on the regulation of gut microbiome structure and function, from structural molecules to produced metabolites. These mechanisms are pertinent to an increasingly networked understanding of immune tolerance and homeostasis in health and disease.
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Affiliation(s)
- Samuel J Gavzy
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Surgery, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Allison Kensiski
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Zachariah L Lee
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Emmanuel F Mongodin
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Bing Ma
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jonathan S Bromberg
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Surgery, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
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15
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SHIMADA M, KAWASE Y, SONOYAMA K, OGURA Y, HAYASHI T, YOKOTA A, FUKIYA S. Development of an improved colonization system for human-derived Bifidobacterium longum subsp. longum in conventional mice through the feeding of raffinose or 1-kestose. BIOSCIENCE OF MICROBIOTA, FOOD AND HEALTH 2023; 43:110-119. [PMID: 38562544 PMCID: PMC10981944 DOI: 10.12938/bmfh.2023-055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 11/05/2023] [Indexed: 04/04/2024]
Abstract
How bifidobacteria colonize and survive in the intestine is not fully understood. The administration of bifidobacteria to conventional mice can be used to evaluate their ability to colonize the intestine in the presence of endogenous gut microbiota. However, human-derived bifidobacteria do not readily colonize the intestines of conventional mice, and although colonization by Bifidobacterium breve UCC2003 has been achieved, the viability of such populations requires improvement. Therefore, we aimed to establish a colonization system with human-derived bifidobacteria of high viability in conventional mice using Bifidobacterium longum subsp. longum 105-A. Lactose, raffinose, and 1-kestose were identified as the preferred carbohydrate sources for the growth of this strain in culture. The administration of B. longum 105-A to conventional BALB/c mice fed these carbohydrates showed that diets containing 6% (w/w) raffinose or 1-kestose facilitated colonization with >108 colony-forming units/g feces for 2 weeks. The population of this strain was more stable in the raffinose-fed group than in the 1-kestose-fed group. The ingestion of these prebiotics had a greater impact on the composition of the microbiota than the administration of B. longum 105-A. The ingestion of these prebiotics also increased the fecal concentrations of organic acids, which was indicative of greater intestinal fermentation. Collectively, we established a colonization system for B. longum 105-A with high viability in conventional mice by feeding the mice raffinose or 1-kestose. This system should be useful for elucidation of the mechanisms of colonization and survival of bifidobacteria in the intestines in the presence of the endogenous gut microbiota.
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Affiliation(s)
- Mina SHIMADA
- Laboratory of Microbial Physiology, Research Faculty of
Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo, Hokkaido 060-8589,
Japan
| | - Youhei KAWASE
- Laboratory of Microbial Physiology, Research Faculty of
Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo, Hokkaido 060-8589,
Japan
| | - Kei SONOYAMA
- Laboratory of Food Biochemistry, Research Faculty of
Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo, Hokkaido 060-8589,
Japan
| | - Yoshitoshi OGURA
- Department of Bacteriology, Faculty of Medical Sciences,
Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
- Department of Infectious Medicine, Kurume University School
of Medicine, 67 Asahi-machi, Kurume-shi, Fukuoka 830-0011, Japan
| | - Tetsuya HAYASHI
- Department of Bacteriology, Faculty of Medical Sciences,
Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
| | - Atsushi YOKOTA
- Laboratory of Microbial Physiology, Research Faculty of
Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo, Hokkaido 060-8589,
Japan
| | - Satoru FUKIYA
- Laboratory of Microbial Physiology, Research Faculty of
Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo, Hokkaido 060-8589,
Japan
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16
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Xia Q, Lei Y, Wang J, Wang Q. Probiotic management and inflammatory factors as a novel treatment in cirrhosis: A systematic review and meta-analysis. Open Life Sci 2023; 18:20220741. [PMID: 37872967 PMCID: PMC10590617 DOI: 10.1515/biol-2022-0741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 08/18/2023] [Accepted: 09/04/2023] [Indexed: 10/25/2023] Open
Abstract
The interaction between intestinal microecological dysregulation, altered inflammatory factors, and cirrhosis is unclear. The aim of this systematic review and meta-analysis was to synthesize the results of previous studies to assess the efficacy of probiotics in the treatment of cirrhosis and their effect on inflammatory factors, as well as to explore the relationship between gut microecological dysregulation and liver disease to gain a deeper understanding of this interaction. Up to December 2022, eligible studies were identified by searching the following databases: National Knowledge Infrastructure (CNKI), Wanfang Data, Web of Science, PubMed, Embase, Medline, and the Cochrane Library. Statistical analysis was performed using software RevMan Version 5.4. A total of 33 eligible randomized controlled trials were included in the study, and data on probiotic strains, duration of intervention, measures in the control group, and outcomes were extracted and evaluated. Compared to the control group, the experimental group had significant improvements in overall efficacy. The results of the meta-analysis revealed that probiotic use significantly decreased biochemical parameters for liver function, including aspartate transaminase, alanine aminotransferase, and total bilirubin. Similar result was obtained in interleukin-6, tumor necrosis factor-α, and endotoxin. However, probiotic intervention did not significantly affect interleukin-2 and interleukin-10. The current meta-analysis illustrates that probiotic supplementation reduces inflammatory markers and biochemical parameters for liver function in patients with cirrhosis, suggesting that probiotic management may be a novel treatment for cirrhosis. Furthermore, the interaction of the gut microbiota, associated metabolites, and inflammation factors with cirrhosis may provide a promising therapeutic target for the pharmacological and clinical treatment of cirrhosis.
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Affiliation(s)
- Qinglan Xia
- Institute of Infection, Immunology and Tumor Microenvironment, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Medicine, Wuhan University of Science and Technology, Wuhan430065, China
| | - Yumeng Lei
- Institute of Infection, Immunology and Tumor Microenvironment, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Medicine, Wuhan University of Science and Technology, Wuhan430065, China
| | - Jiadun Wang
- Institute of Infection, Immunology and Tumor Microenvironment, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Medicine, Wuhan University of Science and Technology, Wuhan430065, China
| | - Qiang Wang
- Institute of Infection, Immunology and Tumor Microenvironment, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Medicine, Wuhan University of Science and Technology, Wuhan430065, China
- Asia General Hospital Affiliated to Wuhan University of Science and Technology, Wuhan430056, China
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17
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Gutierrez A, Pucket B, Engevik MA. Bifidobacterium and the intestinal mucus layer. MICROBIOME RESEARCH REPORTS 2023; 2:36. [PMID: 38045921 PMCID: PMC10688832 DOI: 10.20517/mrr.2023.37] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/21/2023] [Accepted: 09/13/2023] [Indexed: 12/05/2023]
Abstract
Bifidobacterium species are integral members of the human gut microbiota and these microbes have significant interactions with the intestinal mucus layer. This review delves into Bifidobacterium-mucus dynamics, shedding light on the multifaceted nature of this relationship. We cover conserved features of Bifidobacterium-mucus interactions, such as mucus adhesion and positive regulation of goblet cell and mucus production, as well as species and strain-specific attributes of mucus degradation. For each interface, we explore the molecular mechanisms underlying these interactions and their potential implications for human health. Notably, we emphasize the ability of Bifidobacterium species to positively influence the mucus layer, shedding light on its potential as a mucin-builder and a therapeutic agent for diseases associated with disrupted mucus barriers. By elucidating the complex interplay between Bifidobacterium and intestinal mucus, we aim to contribute to a deeper understanding of the gut microbiota-host interface and pave the way for novel therapeutic strategies.
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Affiliation(s)
- Alyssa Gutierrez
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Brenton Pucket
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Melinda A. Engevik
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC 29425, USA
- Department of Microbiology & Immunology, Medical University of South Carolina, Charleston, SC 29425, USA
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18
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Mandelbaum N, Zhang L, Carasso S, Ziv T, Lifshiz-Simon S, Davidovich I, Luz I, Berinstein E, Gefen T, Cooks T, Talmon Y, Balskus EP, Geva-Zatorsky N. Extracellular vesicles of the Gram-positive gut symbiont Bifidobacterium longum induce immune-modulatory, anti-inflammatory effects. NPJ Biofilms Microbiomes 2023; 9:30. [PMID: 37270554 DOI: 10.1038/s41522-023-00400-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 05/18/2023] [Indexed: 06/05/2023] Open
Abstract
The gut microbiota is now well known to affect the host's immune system. One way of bacterial communication with host cells is via the secretion of vesicles, small membrane structures containing various cargo. Research on vesicles secreted by Gram-positive gut bacteria, their mechanisms of interaction with the host and their immune-modulatory effects are still relatively scarce. Here we characterized the size, protein content, and immune-modulatory effects of extracellular vesicles (EVs) secreted by a newly sequenced Gram-positive human gut symbiont strain - Bifidobacterium longum AO44. We found that B. longum EVs exert anti-inflammatory effects, inducing IL-10 secretion from both splenocytes and dendritic cells (DC)-CD4+ T cells co-cultures. Furthermore, the EVs protein content showed enrichment in ABC transporters, quorum sensing proteins, and extracellular solute-binding proteins, which were previously shown to have a prominent function in the anti-inflammatory effect of other strains of B. longum. This study underlines the importance of bacterial vesicles in facilitating the gut bacterial immune-modulatory effects on the host and sheds light on bacterial vesicles as future therapeutics.
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Affiliation(s)
- Noa Mandelbaum
- Department of Cell Biology and Cancer Science, Rappaport Faculty of Medicine and Research Institute, Rappaport Technion Integrated Cancer Center (RTICC), Technion-Israel Institute of Technology, Haifa, 31096, Israel
| | - Lihan Zhang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Shaqed Carasso
- Department of Cell Biology and Cancer Science, Rappaport Faculty of Medicine and Research Institute, Rappaport Technion Integrated Cancer Center (RTICC), Technion-Israel Institute of Technology, Haifa, 31096, Israel
| | - Tamar Ziv
- Smoler Proteomics Center, Lokey Interdisciplinary Center for Life Sciences & Engineering, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Sapir Lifshiz-Simon
- Department of Chemical Engineering and the Russell Berrie Nanotechnology Institute (RBNI), Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Irina Davidovich
- Department of Chemical Engineering and the Russell Berrie Nanotechnology Institute (RBNI), Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Ishai Luz
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University, Beer-Sheva, 84105, Israel
| | - Elliot Berinstein
- Department of Cell Biology and Cancer Science, Rappaport Faculty of Medicine and Research Institute, Rappaport Technion Integrated Cancer Center (RTICC), Technion-Israel Institute of Technology, Haifa, 31096, Israel
| | - Tal Gefen
- Department of Cell Biology and Cancer Science, Rappaport Faculty of Medicine and Research Institute, Rappaport Technion Integrated Cancer Center (RTICC), Technion-Israel Institute of Technology, Haifa, 31096, Israel
| | - Tomer Cooks
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University, Beer-Sheva, 84105, Israel
| | - Yeshayahu Talmon
- Department of Chemical Engineering and the Russell Berrie Nanotechnology Institute (RBNI), Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Naama Geva-Zatorsky
- Department of Cell Biology and Cancer Science, Rappaport Faculty of Medicine and Research Institute, Rappaport Technion Integrated Cancer Center (RTICC), Technion-Israel Institute of Technology, Haifa, 31096, Israel.
- Humans and the Microbiome, CIFAR, Toronto, Canada.
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19
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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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20
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Zhang G, Sun H, Xu Z, Tan Z, Xiao L, He M, Shang J, Tsapieva AN, Zhang L. Screening of Bifidobacteria with Probiotic Potential from Healthy Infant Feces by Using 2'-Fucosyllactose. Foods 2023; 12:foods12040858. [PMID: 36832933 PMCID: PMC9957139 DOI: 10.3390/foods12040858] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/14/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023] Open
Abstract
Using 2'-fucosyllactose (2'-FL) as the sole carbon source can be an efficient way to screen bifidobacteria with superior probiotic capabilities since 2'-FL is a key element in promoting the growth of intestinal bifidobacteria in newborns. This approach was used in this work to screen eight bifidobacteria strains, including one strain of Bifidobacterium longum subsp. infantis BI_Y46 and seven strains of Bifidobacterium bifidum (BB_Y10, BB_Y30, BB_Y39, BB_S40, BB_H4, BB_H5 and BB_H22). Studies on their probiotic properties showed that BI_Y46 had a unique morphology with pilus-like structure, a high resistance to bile salt stimulation and a potent inhibitory action on Escherichia coli ATCC 25922. Similarly, BB_H5 and BB_H22 produced more extracellular polysaccharides and had a higher protein content than other strains. In contrast, BB_Y22 displayed considerable auto-aggregation activity and a high resistance to bile salt stimulation. Interestingly, BB_Y39 with weak self-aggregation ability and acid resistance had very excellent bile salt tolerance, extracellular polysaccharides (EPS) production and bacteriostatic ability. In conclusion, 2'-FL was used as sole carbon source to identify eight bifidobacteria with excellent probiotic properties.
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Affiliation(s)
- Gongsheng Zhang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Hui Sun
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Zihe Xu
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Ze Tan
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Lihong Xiao
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Mingxue He
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Jiaqi Shang
- Key Laboratory of Bionic Engineering, Ministry of Education, College of Biological and Agricultural Engineering, Jilin University, Changchun 130022, China
| | - Anna N. Tsapieva
- Department of Molecular Microbiology, FSBSI Institute of Experimental Medicine, Acad. Pavlov Street, 12, 197376 St. Petersburg, Russia
| | - Lili Zhang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
- Correspondence: ; Tel.: +86-451-5519-0675
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21
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Alessandri G, Fontana F, Tarracchini C, Rizzo SM, Bianchi MG, Taurino G, Chiu M, Lugli GA, Mancabelli L, Argentini C, Longhi G, Anzalone R, Viappiani A, Milani C, Turroni F, Bussolati O, van Sinderen D, Ventura M. Identification of a prototype human gut Bifidobacterium longum subsp. longum strain based on comparative and functional genomic approaches. Front Microbiol 2023; 14:1130592. [PMID: 36846784 PMCID: PMC9945282 DOI: 10.3389/fmicb.2023.1130592] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 01/17/2023] [Indexed: 02/10/2023] Open
Abstract
Bifidobacteria are extensively exploited for the formulation of probiotic food supplements due to their claimed ability to exert health-beneficial effects upon their host. However, most commercialized probiotics are tested and selected for their safety features rather than for their effective abilities to interact with the host and/or other intestinal microbial players. In this study, we applied an ecological and phylogenomic-driven selection to identify novel B. longum subsp. longum strains with a presumed high fitness in the human gut. Such analyses allowed the identification of a prototype microorganism to investigate the genetic traits encompassed by the autochthonous bifidobacterial human gut communities. B. longum subsp. longum PRL2022 was selected due to its close genomic relationship with the calculated model representative of the adult human-gut associated B. longum subsp. longum taxon. The interactomic features of PRL2022 with the human host as well as with key representative intestinal microbial members were assayed using in vitro models, revealing how this bifidobacterial gut strain is able to establish extensive cross-talk with both the host and other microbial residents of the human intestine.
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Affiliation(s)
- Giulia Alessandri
- 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
| | - Chiara Tarracchini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Sonia Mirjam Rizzo
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Massimiliano G. Bianchi
- Department of Medicine and Surgery, University of Parma, Parma, Italy,Microbiome Research Hub, University of Parma, Parma, Italy
| | - Giuseppe Taurino
- Department of Medicine and Surgery, University of Parma, Parma, Italy,Microbiome Research Hub, University of Parma, Parma, Italy
| | - Martina Chiu
- Department of Medicine and Surgery, 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
- Department of Medicine and Surgery, University of Parma, Parma, Italy,Microbiome Research Hub, University of Parma, Parma, Italy
| | - Chiara Argentini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Giulia Longhi
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy,GenProbio srl, 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
| | - 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
| | - Ovidio Bussolati
- Department of Medicine and Surgery, 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
| | - 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,*Correspondence: Marco Ventura, ✉
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22
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Ma B, Gavzy SJ, Saxena V, Song Y, Piao W, Lwin HW, Lakhan R, Iyyathurai J, Li L, France M, Paluskievicz C, Shirkey MW, Hittle L, Munawwar A, Mongodin EF, Bromberg JS. Strain-specific alterations in gut microbiome and host immune responses elicited by tolerogenic Bifidobacterium pseudolongum. Sci Rep 2023; 13:1023. [PMID: 36658194 PMCID: PMC9852428 DOI: 10.1038/s41598-023-27706-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 01/06/2023] [Indexed: 01/20/2023] Open
Abstract
The beneficial effects attributed to Bifidobacterium are largely attributed to their immunomodulatory capabilities, which are likely to be species- and even strain-specific. However, their strain-specificity in direct and indirect immune modulation remain largely uncharacterized. We have shown that B. pseudolongum UMB-MBP-01, a murine isolate strain, is capable of suppressing inflammation and reducing fibrosis in vivo. To ascertain the mechanism driving this activity and to determine if it is specific to UMB-MBP-01, we compared it to a porcine tropic strain B. pseudolongum ATCC25526 using a combination of cell culture and in vivo experimentation and comparative genomics approaches. Despite many shared features, we demonstrate that these two strains possess distinct genetic repertoires in carbohydrate assimilation, differential activation signatures and cytokine responses signatures in innate immune cells, and differential effects on lymph node morphology with unique local and systemic leukocyte distribution. Importantly, the administration of each B. pseudolongum strain resulted in major divergence in the structure, composition, and function of gut microbiota. This was accompanied by markedly different changes in intestinal transcriptional activities, suggesting strain-specific modulation of the endogenous gut microbiota as a key to immune modulatory host responses. Our study demonstrated a single probiotic strain can influence local, regional, and systemic immunity through both innate and adaptive pathways in a strain-specific manner. It highlights the importance to investigate both the endogenous gut microbiome and the intestinal responses in response to probiotic supplementation, which underpins the mechanisms through which the probiotic strains drive the strain-specific effect to impact health outcomes.
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Affiliation(s)
- Bing Ma
- Institute of Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
| | - Samuel J Gavzy
- Department of Surgery, University of Maryland Medical Center, Baltimore, MD, 21201, USA
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Vikas Saxena
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Yang Song
- Institute of Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Wenji Piao
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Hnin Wai Lwin
- Institute of Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Ram Lakhan
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Jegan Iyyathurai
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Lushen Li
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Michael France
- Institute of Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Christina Paluskievicz
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Marina W Shirkey
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Lauren Hittle
- Institute of Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Arshi Munawwar
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Emmanuel F Mongodin
- Institute of Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Division of Lung Diseases, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Jonathan S Bromberg
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Department of Surgery, University of Maryland Medical Center, Baltimore, MD, 21201, USA.
- Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
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23
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Mazziotta C, Tognon M, Martini F, Torreggiani E, Rotondo JC. Probiotics Mechanism of Action on Immune Cells and Beneficial Effects on Human Health. Cells 2023; 12:cells12010184. [PMID: 36611977 PMCID: PMC9818925 DOI: 10.3390/cells12010184] [Citation(s) in RCA: 100] [Impact Index Per Article: 100.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/12/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023] Open
Abstract
Immune cells and commensal microbes in the human intestine constantly communicate with and react to each other in a stable environment in order to maintain healthy immune activities. Immune system-microbiota cross-talk relies on a complex network of pathways that sustain the balance between immune tolerance and immunogenicity. Probiotic bacteria can interact and stimulate intestinal immune cells and commensal microflora to modulate specific immune functions and immune homeostasis. Growing evidence shows that probiotic bacteria present important health-promoting and immunomodulatory properties. Thus, the use of probiotics might represent a promising approach for improving immune system activities. So far, few studies have been reported on the beneficial immune modulatory effect of probiotics. However, many others, which are mainly focused on their metabolic/nutritional properties, have been published. Therefore, the mechanisms behind the interaction between host immune cells and probiotics have only been partially described. The present review aims to collect and summarize the most recent scientific results and the resulting implications of how probiotic bacteria and immune cells interact to improve immune functions. Hence, a description of the currently known immunomodulatory mechanisms of probiotic bacteria in improving the host immune system is provided.
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Affiliation(s)
- Chiara Mazziotta
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
- Center for Studies on Gender Medicine, Department of Medical Sciences, University of Ferrara, 64/b, Fossato di Mortara Street, 44121 Ferrara, Italy
| | - Mauro Tognon
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Fernanda Martini
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
- Center for Studies on Gender Medicine, Department of Medical Sciences, University of Ferrara, 64/b, Fossato di Mortara Street, 44121 Ferrara, Italy
- Laboratory for Technologies of Advanced Therapies (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - Elena Torreggiani
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
- Correspondence: (E.T.); (J.C.R.); Tel.: +39-053-2455-557 (E.T.); +39-053-245-5536 (J.C.R.)
| | - John Charles Rotondo
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
- Center for Studies on Gender Medicine, Department of Medical Sciences, University of Ferrara, 64/b, Fossato di Mortara Street, 44121 Ferrara, Italy
- Correspondence: (E.T.); (J.C.R.); Tel.: +39-053-2455-557 (E.T.); +39-053-245-5536 (J.C.R.)
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24
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Genomic, probiotic, and metabolic potentials of Liquorilactobacillus nagelii AGA58, a novel bacteriocinogenic motile strain isolated from lactic acid-fermented shalgam. J Biosci Bioeng 2023; 135:34-43. [PMID: 36384719 DOI: 10.1016/j.jbiosc.2022.10.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 10/19/2022] [Accepted: 10/19/2022] [Indexed: 11/15/2022]
Abstract
This study aimed to perform genomic, probiotic, and metabolic characterization of a novel Liquorilactobacillus nagelii AGA58 isolated from a lactic acid-fermented shalgam beverage to understand its metabolic potentials and probiotic features. AGA58 is gram-positive, motile, catalase-negative and appears as short rods under the light-microscope. The AGA58 chromosome comprises a single linear chromosome of 2,294,635 bp that is predicted to carry 2135 coding sequences, including 45 tRNA genes, 3 mRNA, and 3 rRNA operons. The genome has a G+C content of 36.9%, including 55 pseudogenes and a single intact prophage. AGA58 is micro-anaerobic due to achieving a shorter doubling time and faster growth rate than micro-aerophilic conditions. It carries flagellar biosynthesis protein-encoding genes predicting motile behavior, which was confirmed with the in vitro motility test. AGA58 is an obligatory homofermentative lactobacillus that can ferment hexose sugars such as galactose, glucose, fructose, sucrose, mannose, N-acetyl glucosamine, maltose, and trehalose to lactate through glycolysis. No acid production from pentoses implies that five-carbon sugars are being utilized for purine and pyrimidine synthesis. Putative pyruvate metabolism revealed formate, malate, oxaloacetate, acetate, acetaldehyde, acetoin, and lactate forms from pyruvate. AGA58 is predicted to encode the LuxS gene and biosynthesis of class IIa and Blp family class-II bacteriocins suggesting this bacterium's antimicrobial potential, linked to antagonism tests that AGA58 can inhibit Escherichia coli ATCC 43895, Salmonellaenterica serovar Typhimurium ATCC 14028, and Klebsiellapneumonia ATCC 13883. Moreover, AGA58 is tolerant to acid and bile concentrations simulating the human gastrointestinal conditions depicting the probiotic potential of the organism as the first report in literature within the same species.
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25
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Lei C, Sun R, Xu G, Tan Y, Feng W, McClain CJ, Deng Z. Enteric VIP-producing neurons maintain gut microbiota homeostasis through regulating epithelium fucosylation. Cell Host Microbe 2022; 30:1417-1434.e8. [PMID: 36150396 PMCID: PMC9588764 DOI: 10.1016/j.chom.2022.09.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 05/18/2022] [Accepted: 08/31/2022] [Indexed: 12/12/2022]
Abstract
Interactions between the enteric nervous system (ENS) and intestinal epithelium are thought to play a vital role in intestinal homeostasis. How the ENS monitors the frontier with commensal and pathogenic microbes while maintaining epithelial function remains unclear. Here, by combining subdiaphragmatic vagotomy with transcriptomics, chemogenetic strategy, and coculture of enteric neuron-intestinal organoid, we show that enteric neurons expressing VIP shape the α1,2-fucosylation of intestinal epithelial cells (IECs). Mechanistically, neuropeptide VIP activates fut2 expression via the Erk1/2-c-Fos pathway through the VIPR1 receptor on IECs. We further demonstrate that perturbation of enteric neurons leads to gut dysbiosis through α1,2-fucosylation in the steady state and results in increased susceptibility to alcohol-associated liver disease (ALD). This was attributed to an imbalance between beneficial Bifidobacterium and opportunistic pathogenic Enterococcus faecalis in ALD. In addition, Bifidobacterium α1,2-fucosidase may promote Bifidobacterium adhesion to the mucosal surface, which restricts Enterococcus faecalis overgrowth and prevents ALD progression.
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Affiliation(s)
- Chao Lei
- Department of Surgery, Division of Immunotherapy, University of Louisville, Louisville, KY, USA; Brown Cancer Center, University of Louisville, Louisville, KY, USA
| | - Rui Sun
- Department of Surgery, Division of Immunotherapy, University of Louisville, Louisville, KY, USA; Brown Cancer Center, University of Louisville, Louisville, KY, USA; Central Laboratory and Department of Oncology, Wuhan Fourth Hospital, Puai Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430033, China
| | - Guangzhong Xu
- Department of Medicine, University of Louisville, Louisville, KY, USA
| | - Yi Tan
- Department of Pediatrics, University of Louisville, Louisville, KY, USA
| | - Wenke Feng
- Department of Medicine, University of Louisville, Louisville, KY, USA; Alcohol Research Center, University of Louisville, Louisville, KY, USA; Hepatobiology & Toxicology Center, University of Louisville, Louisville, KY, USA
| | - Craig J McClain
- Department of Medicine, University of Louisville, Louisville, KY, USA; Alcohol Research Center, University of Louisville, Louisville, KY, USA; Hepatobiology & Toxicology Center, University of Louisville, Louisville, KY, USA; Robley Rex VA Medical Center, Louisville, KY, USA
| | - Zhongbin Deng
- Department of Surgery, Division of Immunotherapy, University of Louisville, Louisville, KY, USA; Brown Cancer Center, University of Louisville, Louisville, KY, USA; Alcohol Research Center, University of Louisville, Louisville, KY, USA; Hepatobiology & Toxicology Center, University of Louisville, Louisville, KY, USA.
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26
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Sadiq FA, Wenwei L, Wei C, Jianxin Z, Zhang H. Transcriptional Changes in Bifidobacterium bifidum Involved in Synergistic Multispecies Biofilms. MICROBIAL ECOLOGY 2022; 84:922-934. [PMID: 34676439 DOI: 10.1007/s00248-021-01904-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/15/2021] [Indexed: 06/13/2023]
Abstract
Bifidobacterium bifidum is part of the core microbiota of healthy infant guts where it may form biofilms on epithelial cells, mucosa, and food particles in the gut lumen. Little is known about transcriptional changes in B. bifidum engaged in synergistic multispecies biofilms with ecologically relevant species of the human gut. Recently, we reported prevalence of synergism in mixed-species biofilms formed by the human gut microbiota. This study represents a comparative gene expression analysis of B. bifidum when grown in a single-species biofilm and in two multispecies biofilm consortia with Bifidobacterium longum subsp. infantis, Bacteroides ovatus, and Parabacteroides distasonis in order to identify genes involved in this adaptive process in mixed biofilms and the influence on its metabolic and functional traits. Changes up to 58% and 43% in its genome were found when it grew in three- and four-species biofilm consortia, respectively. Upregulation of genes of B. bifidum involved in carbohydrate metabolism (particularly the galE gene), quorum sensing (luxS and pfs), and amino acid metabolism (especially branched chain amino acids) in both multispecies biofilms, compared to single-species biofilms, suggest that they may be contributing factors for the observed synergistic biofilm production when B. bifidum coexists with other species in a biofilm.
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Affiliation(s)
- Faizan Ahmed Sadiq
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Lu Wenwei
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Chen Wei
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, China
| | - Zhao Jianxin
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, China.
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27
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Exploring Bacterial Attributes That Underpin Symbiont Life in the Monogastric Gut. Appl Environ Microbiol 2022; 88:e0112822. [PMID: 36036591 PMCID: PMC9499014 DOI: 10.1128/aem.01128-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The large bowel of monogastric animals, such as that of humans, is home to a microbial community (microbiota) composed of a diversity of mostly bacterial species. Interrelationships between the microbiota as an entity and the host are complex and lifelong and are characteristic of a symbiosis. The relationships may be disrupted in association with disease, resulting in dysbiosis. Modifications to the microbiota to correct dysbiosis require knowledge of the fundamental mechanisms by which symbionts inhabit the gut. This review aims to summarize aspects of niche fitness of bacterial species that inhabit the monogastric gut, especially of humans, and to indicate the research path by which progress can be made in exploring bacterial attributes that underpin symbiont life in the gut.
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Shao H, Min F, Huang M, Wang Z, Bai T, Lin M, Li X, Chen H. Novel perspective on the regulation of food allergy by probiotic: The potential of its structural components. Crit Rev Food Sci Nutr 2022; 64:172-186. [PMID: 35912422 DOI: 10.1080/10408398.2022.2105304] [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] [Indexed: 11/03/2022]
Abstract
Food allergy (FA) is a global public health issue with growing prevalence. Increasing evidence supports the strong correlation between intestinal microbiota dysbiosis and food allergies. Probiotic intervention as a microbiota-based therapy could alleviate FA effectively. In addition to improving the intestinal microbiota disturbance and affecting microbial metabolites to regulate immune system, immune responses induced by the recognition of pattern recognition receptors to probiotic components may also be one of the mechanisms of probiotics protecting against FA. In this review, it is highlighted in detail about the regulatory effects on the immune system and anti-allergic potential of probiotic components including the flagellin, pili, peptidoglycan, lipoteichoic acid, exopolysaccharides, surface (S)-layer proteins and DNA. Probiotic components could enhance the function of intestinal epithelial barrier as well as regulate the balance of cytokines and T helper (Th) 1/Th2/regulatory T cell (Treg) responses. These evidences suggest that probiotic components could be used as nutritional or therapeutic agents for maintaining immune homeostasis to prevent FA, which will contribute to providing new insights into the resolution of FA and better guidance for the development of probiotic products.
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Affiliation(s)
- Huming Shao
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, China
- School of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, China
- Jiangxi Province Key Laboratory of Food Allergy, Nanchang University, Nanchang, Jiangxi, China
| | - Fangfang Min
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, China
- School of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, China
- Jiangxi Province Key Laboratory of Food Allergy, Nanchang University, Nanchang, Jiangxi, China
| | - Meijia Huang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, China
- School of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, China
- Jiangxi Province Key Laboratory of Food Allergy, Nanchang University, Nanchang, Jiangxi, China
| | - Zhongliang Wang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, China
- School of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, China
- Jiangxi Province Key Laboratory of Food Allergy, Nanchang University, Nanchang, Jiangxi, China
| | - Tianliang Bai
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, China
- School of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, China
- Jiangxi Province Key Laboratory of Food Allergy, Nanchang University, Nanchang, Jiangxi, China
| | - Min Lin
- Department of Dermatology, Jiangxi Provincial Children's Hospital, Nanchang, Jiangxi, China
| | - Xin Li
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, China
- School of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, China
- Jiangxi Province Key Laboratory of Food Allergy, Nanchang University, Nanchang, Jiangxi, China
| | - Hongbing Chen
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, China
- Jiangxi Province Key Laboratory of Food Allergy, Nanchang University, Nanchang, Jiangxi, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, Jiangxi, China
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29
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Deng R, Ma P, Li B, Wu Y, Yang X. Development of allergic asthma and changes of intestinal microbiota in mice under high humidity and/or carbon black nanoparticles. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 241:113786. [PMID: 35738102 DOI: 10.1016/j.ecoenv.2022.113786] [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] [Received: 04/22/2022] [Revised: 06/02/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
In respiratory diseases, the induction of allergic asthma is one of the hottest issues of international concern. The adjuvant effect of air pollutants including nanoparticles (NPs) has be pointed out to facilitate the occurrence and development of allergic asthma. This work studied the development of allergic asthma upon exposures of carbon black nanoparticles (CB NPs, 30-50 nm) and/or high environmental humidity (90% relative humidity). The mechanisms involved were investigated from perspectives of the activation of oxidative stress and transient receptor potential vanilloid 1 (TRPV1) pathways and the alteration in intestinal microbiota. Both high humidity and CB NPs aggravated the airway hyperreactivity, remodeling, and inflammation in Balb/c mice sensitized by ovalbumin. The co-exposure of these two risk factors exhibited adjuvant effect on the development of asthma likely through activating oxidative stress pathway and TRPV1 pathway and then facilitating type I hypersensitivity. Additionally, exposures of high humidity and/or CB NPs reduced the richness of intestinal microbes, altered microbial community composition, and weakened corresponding biological functions, which may interact with the development of asthma. The findings will add new toxicological knowledge to the health risk assessment and management of co-exposures of NPs and other risk factors in the environment.
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Affiliation(s)
- Rui Deng
- School of Civil Engineering, Chongqing University, Chongqing 400045, China.
| | - Ping Ma
- Xianning Engineering Research Center for Healthy Environment, Xianning Medical College, Hubei University of Science and Technology, Xianning 437100, China
| | - Baizhan Li
- School of Civil Engineering, Chongqing University, Chongqing 400045, China
| | - Yang Wu
- Xianning Engineering Research Center for Healthy Environment, Xianning Medical College, Hubei University of Science and Technology, Xianning 437100, China
| | - Xu Yang
- Xianning Engineering Research Center for Healthy Environment, Xianning Medical College, Hubei University of Science and Technology, Xianning 437100, China; Institute of Eastern-Himalaya Biodiversity Research, Dali university, Dali 671003, China
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30
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Genome-wide siRNA screening reveals several host receptors for the binding of human gut commensal Bifidobacterium bifidum. NPJ Biofilms Microbiomes 2022; 8:50. [PMID: 35768415 PMCID: PMC9243078 DOI: 10.1038/s41522-022-00312-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 05/31/2022] [Indexed: 11/08/2022] Open
Abstract
Bifidobacterium spp. are abundant gut commensals, especially in breast-fed infants. Bifidobacteria are associated with many health-promoting effects including maintenance of epithelial barrier and integrity as well as immunomodulation. However, the protective mechanisms of bifidobacteria on intestinal epithelium at molecular level are poorly understood. In this study, we developed a high-throughput in vitro screening assay to explore binding receptors of intestinal epithelial cells for Bifidobacterium bifidum. Short interfering RNAs (siRNA) were used to silence expression of each gene in the Caco-2 cell line one by one. The screen yielded four cell surface proteins, SERPINB3, LGICZ1, PKD1 and PAQR6, which were identified as potential receptors as the siRNA knock-down of their expression decreased adhesion of B. bifidum to the cell line repeatedly during the three rounds of siRNA screening. Furthermore, blocking of these host cell proteins by specific antibodies decreased the binding of B. bifidum significantly to Caco-2 and HT29 cell lines. All these molecules are located on the surface of epithelial cells and three out of four, SERPINB3, PKD1 and PAQR6, are involved in the regulation of cellular processes related to proliferation, differentiation and apoptosis as well as inflammation and immunity. Our results provide leads to the first steps in the mechanistic cascade of B. bifidum-host interactions leading to regulatory effects in the epithelium and may partly explain how this commensal bacterium is able to promote intestinal homeostasis.
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31
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Wang X, Zhao J, Feng Y, Feng Z, Ye Y, Liu L, Kang G, Cao X. Evolutionary Insights Into Microbiota Transplantation in Inflammatory Bowel Disease. Front Cell Infect Microbiol 2022; 12:916543. [PMID: 35811664 PMCID: PMC9257068 DOI: 10.3389/fcimb.2022.916543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
The intestinal microbiome plays an essential role in human health and disease status. So far, microbiota transplantation is considered a potential therapeutic approach for treating some chronic diseases, including inflammatory bowel disease (IBD). The diversity of gut microbiota is critical for maintaining resilience, and therefore, transplantation with numerous genetically diverse gut microbiota with metabolic flexibility and functional redundancy can effectively improve gut health than a single probiotic strain supplement. Studies have shown that natural fecal microbiota transplantation or washing microbiota transplantation can alleviate colitis and improve intestinal dysbiosis in IBD patients. However, unexpected adverse reactions caused by the complex and unclear composition of the flora limit its wider application. The evolving strain isolation technology and modifiable pre-existing strains are driving the development of microbiota transplantation. This review summarized the updating clinical and preclinical data of IBD treatments from fecal microbiota transplantation to washing microbiota transplantation, and then to artificial consortium transplantation. In addition, the factors considered for strain combination were reviewed. Furthermore, four types of artificial consortium transplant products were collected to analyze their combination and possible compatibility principles. The perspective on individualized microbiota transplantation was also discussed ultimately.
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Affiliation(s)
- Xiaoli Wang
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Institute of Digestive Disease, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Jingwen Zhao
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Institute of Digestive Disease, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Yuanhang Feng
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Zelin Feng
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Institute of Digestive Disease, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Yulin Ye
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Institute of Digestive Disease, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Limin Liu
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Institute of Digestive Disease, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Guangbo Kang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- Institute of Shaoxing, Tianjin University, Zhejiang, China
- *Correspondence: Xiaocang Cao, ; Guangbo Kang,
| | - Xiaocang Cao
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Institute of Digestive Disease, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
- *Correspondence: Xiaocang Cao, ; Guangbo Kang,
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32
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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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33
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Kumar V, Murmu S, Krishnan V. Deciphering the substrate specificity of housekeeping sortase A and pilus-specific sortase C of probiotic bacterium Lactococcus lactis. Biochimie 2022; 200:140-152. [PMID: 35654243 DOI: 10.1016/j.biochi.2022.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/25/2022] [Accepted: 05/26/2022] [Indexed: 11/02/2022]
Abstract
Several strains and species of lactic acid bacteria (LAB) are widely used in fermented foods, including dairy products and also as probiotics, because of their contribution to various health benefits in humans. Sortase enzymes decorate the bacterial cell wall with different surface proteins and pili for facilitating the interactions with host and environment for the colonization and beneficial effects. While the sortases and sortase anchored proteins from pathogens have been the prime focus of the research in the past, sortases from many non-pathogenic bacteria, including LAB strains, have attracted attention for their potential applications in vaccine delivery and other clinical interventions. Here, we report the purification and functional characterization of two sortases (housekeeping SrtA and pilus-specific SrtC) from a probiotic Lactococcus lactis. The purified sortases were found to be active against the putative LPXTG motif-based peptide substrates, albeit with differences. The in-silico analysis provides insights into the residues involved in substrate binding and specificity. Overall, this study sheds new light on the aspects of structure, substrate specificity, and function of sortases from non-pathogenic bacteria, which may have physiological ramifications as well as their applications in sortase-mediated protein bioconjugation.
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Affiliation(s)
- Vijay Kumar
- Laboratory of Structural Microbiology, Regional Centre for Biotechnology, NCR Biotech Science Cluster 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, 121001, Haryana (NCR Delhi), India
| | - Sumit Murmu
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India; Regional Centre for Biotechnology, NCR Biotech Science Cluster 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, 121001, Haryana (NCR Delhi), India
| | - Vengadesan Krishnan
- Laboratory of Structural Microbiology, Regional Centre for Biotechnology, NCR Biotech Science Cluster 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, 121001, Haryana (NCR Delhi), India.
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34
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Intestinal ‘Infant-Type’ Bifidobacteria Mediate Immune System Development in the First 1000 Days of Life. Nutrients 2022; 14:nu14071498. [PMID: 35406110 PMCID: PMC9002861 DOI: 10.3390/nu14071498] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/27/2022] [Accepted: 03/31/2022] [Indexed: 01/05/2023] Open
Abstract
Immune system maturation begins early in life, but few studies have examined how early-life gut microbiota colonization educates the neonatal immune system. Bifidobacteria predominate in the intestines of breastfed infants and metabolize human milk oligosaccharides. This glycolytic activity alters the intestinal microenvironment and consequently stimulates immune system maturation at the neonatal stage. However, few studies have provided mechanistic insights into the contribution of ‘infant-type’ Bifidobacterium species, especially via metabolites such as short-chain fatty acids. In this review, we highlight the first 1000 days of life, which provide a window of opportunity for infant-type bifidobacteria to educate the neonatal immune system. Furthermore, we discuss the instrumental role of infant-type bifidobacteria in the education of the neonatal immune system by inducing immune tolerance and suppressing intestinal inflammation, and the potential underlying mechanism of this immune effect in the first 1000 days of life. We also summarize recent research that suggests the administration of infant-type bifidobacteria helps to modify the intestinal microecology and prevent the progress of immune-mediated disorders.
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Tarracchini C, Viglioli M, Lugli GA, Mancabelli L, Fontana F, Alessandri G, Turroni F, Ventura M, Milani C. The Integrated Probiotic Database: a genomic compendium of bifidobacterial health-promoting strains. MICROBIOME RESEARCH REPORTS 2022; 1:9. [PMID: 38045645 PMCID: PMC10688828 DOI: 10.20517/mrr.2021.13] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/14/2022] [Accepted: 02/07/2022] [Indexed: 12/05/2023]
Abstract
Background: The World Health Organization defines probiotics as "live microorganisms, which when administered in adequate amounts confer a health benefit on the host". In this framework, probiotic strains should be regarded as safe for human and animal consumption, i.e., they should possess the GRAS (generally recognized as safe) status, notified by the local authorities. Consistently, strains of selected Bifidobacterium species are extensively used as probiotic agents to prevent and ameliorate a broad spectrum of human and/or animal gastrointestinal disorders. Even though probiotic properties are often genus- or species-associated, strain-level differences in the genetic features conferring individual probiotic properties to commercialized bifidobacterial strains have not been investigated in detail. Methods: In this study, we built a genomic database named Integrated Probiotic DataBase (IPDB), whose first iteration consists of common bifidobacterial strains used in probiotic products for which public genome sequences were available, such as members of B. longum subsp. longum, B. longum subsp. infantis, B. bifidum, B. breve, and B. animalis subsp. lactis taxa. Furthermore, the IPDB was exploited to perform comparative genome analyses focused on genetic factors conferring structural, functional, and chemical features predicted to be involved in microbe-host and microbe-microbe interactions. Results and conclusion: Our analyses revealed strain-level genetic differences, underlining the importance of inspecting the strain-specific and outcome-specific efficacy of probiotics. In this context, IPDB represents a valuable resource for obtaining genetic information of well-established bifidobacterial probiotic strains.
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Affiliation(s)
- Chiara Tarracchini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, Parma 43124, Italy
| | - Martina Viglioli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, Parma 43124, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, Parma 43124, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, Parma 43124, Italy
| | - Federico Fontana
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, Parma 43124, Italy
- GenProbio Srl, Via delle Scienze, 11/A, Parma 43100, Italy
| | - Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, Parma 43124, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, Parma 43124, Italy
- Microbiome Research Hub, University of Parma, Parco Area delle Scienze 11a, Parma 43124, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, Parma 43124, Italy
- Microbiome Research Hub, University of Parma, Parco Area delle Scienze 11a, Parma 43124, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, Parma 43124, Italy
- Microbiome Research Hub, University of Parma, Parco Area delle Scienze 11a, Parma 43124, Italy
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36
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Heiss BE, Ehrlich AM, Maldonado-Gomez MX, Taft DH, Larke JA, Goodson ML, Slupsky CM, Tancredi DJ, Raybould HE, Mills DA. Bifidobacterium catabolism of human milk oligosaccharides overrides endogenous competitive exclusion driving colonization and protection. Gut Microbes 2022; 13:1986666. [PMID: 34705611 PMCID: PMC8555557 DOI: 10.1080/19490976.2021.1986666] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Understanding how exogenous microbes stably colonize the animal gut is essential to reveal mechanisms of action and tailor effective probiotic treatments. Bifidobacterium species are naturally enriched in the gastrointestinal tract of breast-fed infants. Human milk oligosaccharides (HMOs) are associated with this enrichment. However, direct mechanistic proof of the importance of HMOs in this colonization is lacking given milk contains additional factors that impact the gut microbiota. This study examined mice supplemented with the HMO 2'fucosyllactose (2'FL) together with a 2'FL-consuming strain, Bifidobacterium pseudocatenulatum MP80. 2'FL supplementation creates a niche for high levels of B.p. MP80 persistence, similar to Bifidobacterium levels seen in breast-fed infants. This synergism impacted gut microbiota composition, activated anti-inflammatory pathways and protected against chemically-induced colitis. These results demonstrate that bacterial-milk glycan interactions alone drive enrichment of beneficial Bifidobacterium and provide a model for tunable colonization thus facilitating insight into mechanisms of health promotion by bifidobacteriain neonates.
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Affiliation(s)
- Britta E. Heiss
- Department of Food Science and Technology, University of California-Davis, Davis, CA, USA,Foods for Health Institute, University of California-Davis, Davis, CA, USA
| | - Amy M. Ehrlich
- Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA
| | - Maria X. Maldonado-Gomez
- Department of Food Science and Technology, University of California-Davis, Davis, CA, USA,Foods for Health Institute, University of California-Davis, Davis, CA, USA
| | - Diana H. Taft
- Department of Food Science and Technology, University of California-Davis, Davis, CA, USA,Foods for Health Institute, University of California-Davis, Davis, CA, USA
| | - Jules A. Larke
- Department of Nutrition, University of California-Davis, Davis, CA, USA
| | - Michael L. Goodson
- Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA
| | - Carolyn M. Slupsky
- Department of Food Science and Technology, University of California-Davis, Davis, CA, USA,Foods for Health Institute, University of California-Davis, Davis, CA, USA,Department of Nutrition, University of California-Davis, Davis, CA, USA
| | - Daniel J. Tancredi
- Center for Healthcare Policy and Research, Department of Pediatrics, University of California-Davis, Sacramento, CA, USA
| | - Helen E. Raybould
- Foods for Health Institute, University of California-Davis, Davis, CA, USA,Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA,CONTACT Helen E. Raybould Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA
| | - David A. Mills
- Department of Food Science and Technology, University of California-Davis, Davis, CA, USA,Foods for Health Institute, University of California-Davis, Davis, CA, USA,David A. Mills Department of Food Science and Technology, University of California-Davis, Davis, CA, USA
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37
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Probiotic Molecules That Inhibit Inflammatory Diseases. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12031147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Consumption of probiotics for health purposes has increased vastly in the past few decades, and yet the scientific evidence to support health benefits from probiotics is only beginning to emerge. As more probiotics are studied, we are beginning to understand the mechanisms of action by which they benefit human health, as well as to identify the bacterial molecules responsible for these benefits. A new era of therapeutics is on the horizon in which purified molecules from probiotics will be used to prevent and treat diseases. In this review, we summarize the active molecules from probiotic bacteria that have been shown to affect innate and adaptive immunity and have health benefits in experimental settings. We focus particularly on the cellular and molecular mechanisms of the probiotic Bacillus subtilis and its active molecule, exopolysaccharide (ESPBs).
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38
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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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Bukharin OV, Andryushchenko SV, Perunova NB, Ivanova EV. Environmental Determination of Indigenous Bifidobacteria of the Human Intestine. HERALD OF THE RUSSIAN ACADEMY OF SCIENCES 2022; 92:629-635. [PMID: 36340323 PMCID: PMC9628474 DOI: 10.1134/s1019331622050033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/25/2022] [Accepted: 05/12/2022] [Indexed: 11/09/2022]
Abstract
The environmental determination of indigenous (constantly present) bifidobacteria of the human large intestine is considered in this review. Environmental determination (from the Latin determinere, "I determine") is understood as a set of natural phenomena of a habitat (biotope) that determine the role of indigenous microorganisms in the microbiocenosis. Using the symbiotic approach, an attempt is made to identify the environmental conditions for the habitat of bifidobacteria and their physiological effects in the microsymbiocenosis. The features of indigenous bifidobacteria in terms of their nature have been established: evolutionary-genetic (phylogenetic remoteness, genome conservation, metabolic specialization), biochemical (lysozyme resistance, constitutive acetate production), and physiological (microbial "friend-foe" identification, immunoregulation), which are important in adaptation (persistence) and the provision of mutualistic effects and stability of the bifidoflora in the population.
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Affiliation(s)
- O. V. Bukharin
- Institute for Cellular and Intracellular Symbiosis (ICIS), Ural Branch, Russian Academy of Sciences, Orenburg, Russia
| | - S. V. Andryushchenko
- Institute for Cellular and Intracellular Symbiosis (ICIS), Ural Branch, Russian Academy of Sciences, Orenburg, Russia
| | - N. B. Perunova
- Institute for Cellular and Intracellular Symbiosis (ICIS), Ural Branch, Russian Academy of Sciences, Orenburg, Russia
| | - E. V. Ivanova
- Institute for Cellular and Intracellular Symbiosis (ICIS), Ural Branch, Russian Academy of Sciences, Orenburg, Russia
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40
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Gorreja F, Walker WA. The potential role of adherence factors in probiotic function in the gastrointestinal tract of adults and pediatrics: a narrative review of experimental and human studies. Gut Microbes 2022; 14:2149214. [PMID: 36469568 PMCID: PMC9728474 DOI: 10.1080/19490976.2022.2149214] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022] Open
Abstract
Numerous studies point to the important role of probiotic bacteria in gastrointestinal health. Probiotics act through mechanisms affecting enteric pathogens, epithelial barrier function, immune signaling, and conditioning of indigenous microbiota. Once administered, probiotics reach the gastrointestinal tract and interact with the host through bacterial surface molecules, here called adhesion factors, which are either strain- or specie-specific. Probiotic adhesion, through structural adhesion factors, is a mechanism that facilitates persistence within the gastrointestinal tract and triggers the initial host responses. Thus, an understanding of specific probiotic adhesion mechanisms could predict how specific probiotic strains elicit benefits and the potential of adherence factors as a proxy to predict probiotic function. This review summarizes the present understanding of probiotic adherence in the gastrointestinal tract. It highlights the bacterial adhesion structure types, their molecular communication with the host and the consequent impact on intestinal diseases in both adult and pediatric populations. Finally, we discuss knockout/isolation studies as direct evidence for adhesion factors conferring anti-inflammatory and pathogen inhibition properties to a probiotic.What is known: Probiotics can be used to treat clinical conditions.Probiotics improve dysbiosis and symptoms.Clinical trials may not confirm in vitro and animal studies.What is new: Adhesion structures may be important for probiotic function.Need to systematically determine physical characteristics of probiotics before selecting for clinical trials.Probiotics may be genetically engineered to add to clinical efficacy.
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Affiliation(s)
- Frida Gorreja
- Department of Microbiology and Immunology, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Nutrition-Gut-Brain Interactions Research Centre, School of Medical Sciences, Örebro University, Örebro, Sweden
| | - W. Allan Walker
- Mucosal Immunology and Biology Research Center, Massachusetts General Hospital for Children, Harvard Medical School, Boston, Massachusetts, USA
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41
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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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Radojević D, Tomić S, Mihajlović D, Tolinački M, Pavlović B, Vučević D, Bojić S, Golić N, Čolić M, Đokić J. Fecal microbiota composition associates with the capacity of human peripheral blood monocytes to differentiate into immunogenic dendritic cells in vitro. Gut Microbes 2021; 13:1-20. [PMID: 33970783 PMCID: PMC8115579 DOI: 10.1080/19490976.2021.1921927] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Although promising for active immunization in cancer patients, dendritic cells (DCs) vaccines generated in vitro display high inter-individual variability in their immunogenicity, which mostly limits their therapeutic efficacy. Gut microbiota composition is a key emerging factor affecting individuals' immune responses, but it is unknown how it affects the variability of donors' precursor cells to differentiate into immunogenic DCs in vitro. By analyzing gut microbiota composition in 14 healthy donors, along with the phenotype and cytokines production by monocyte-derived DCs, we found significant correlations between immunogenic properties of DC and microbiota composition. Namely, donors who had higher α-diversity of gut microbiota and higher abundance of short-chain fatty acid (SCFAs) and SCFA-producing bacteria in feces, displayed lower expression of CD1a on immature (im)DC and higher expression of ILT-3, costimulatory molecules (CD86, CD40) proinflammatory cytokines (TNF-α, IL-6, IL-8) and IL-12p70/IL-10 ratio, all of which correlated with their lower maturation potential and immunogenicity upon stimulation with LPS/IFNγ, a well-known Th1 polarizing cocktail. In contrast, imDCs generated from donors with lower α-diversity and higher abundance of Bifidobacterium and Collinsella in feces displayed higher CD1a expression and higher potential to up-regulate CD86 and CD40, increase TNF-α, IL-6, IL-8 production, and IL-12p70/IL-10 ratio upon stimulation. These results emphasize the important role of gut microbiota on the capacity of donor precursor cells to differentiate into immunogenic DCs suitable for cancer therapy, which could be harnessed for improving the actual and future DC-based cancer therapies.
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Affiliation(s)
- Dušan Radojević
- Laboratory for Molecular Microbiology (LMM), Institute of Molecular Genetics and Genetic Engineering (IMGGI), University of Belgrade, Belgrade, Serbia
| | - Sergej Tomić
- Department for Immunology and Immunoparasitology, Institute for the Application of Nuclear Energy, University of Belgrade, Belgrade, Serbia
| | - Dušan Mihajlović
- Faculty of Medicine Foca, University of East Sarajevo, Republic of Srpska, Bosnia and Herzegovina,Medical Faculty of the Military Medical Academy, University of Defence, Belgrade, Serbia
| | - Maja Tolinački
- Laboratory for Molecular Microbiology (LMM), Institute of Molecular Genetics and Genetic Engineering (IMGGI), University of Belgrade, Belgrade, Serbia
| | | | - Dragana Vučević
- Department for Immunology and Immunoparasitology, Institute for the Application of Nuclear Energy, University of Belgrade, Belgrade, Serbia
| | | | - Nataša Golić
- Laboratory for Molecular Microbiology (LMM), Institute of Molecular Genetics and Genetic Engineering (IMGGI), University of Belgrade, Belgrade, Serbia
| | - Miodrag Čolić
- Faculty of Medicine Foca, University of East Sarajevo, Republic of Srpska, Bosnia and Herzegovina,Serbian Academy of Sciences and Arts, Belgrade, Serbia
| | - Jelena Đokić
- Laboratory for Molecular Microbiology (LMM), Institute of Molecular Genetics and Genetic Engineering (IMGGI), University of Belgrade, Belgrade, Serbia,CONTACT Jelena Đokić Laboratory for Molecular Microbiology (LMM), Institute of Molecular Genetics and Genetic Engineering (IMGGE), University of Belgrade, Vojvode Stepe 444a, Belgrade11042, Serbia
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Ishikawa E, Yamada T, Yamaji K, Serata M, Fujii D, Umesaki Y, Tsuji H, Nomoto K, Ito M, Okada N, Nagaoka M, Gomi A. Critical roles of a housekeeping sortase of probiotic Bifidobacterium bifidum in bacterium-host cell crosstalk. iScience 2021; 24:103363. [PMID: 34825137 PMCID: PMC8603203 DOI: 10.1016/j.isci.2021.103363] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 04/09/2021] [Accepted: 10/25/2021] [Indexed: 10/30/2022] Open
Abstract
Bifidobacterium bifidum YIT 10347 (BF-1) is adhesive in vitro. Here we studied the molecular aspects of the BF-1 adhesion process. We identified and characterized non-adhesive mutants and found that a class E housekeeping sortase was critical for the adhesion to mucin. These mutants were significantly less adhesive to GCIY cells than was the wild type (WT), which protected GCIY cells against acid treatment more than did a non-adhesive mutant. The non-adhesive mutants aberrantly accumulated precursors of putative sortase-dependent proteins (SDPs). Recombinant SDPs bound to mucin. Disruption of the housekeeping sortase influenced expression of SDPs and pilus components. Mutants defective in a pilin or in an SDP showed the same adhesion properties as WT. Therefore, multiple SDPs and pili seem to work cooperatively to achieve adhesion, and the housekeeping sortase is responsible for cell wall anchoring of its substrates to ensure their proper biological function.
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Affiliation(s)
- Eiji Ishikawa
- Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
| | - Tetsuya Yamada
- Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
| | - Kazuaki Yamaji
- Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
| | - Masaki Serata
- Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
| | - Daichi Fujii
- Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
| | - Yoshinori Umesaki
- Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
| | - Hirokazu Tsuji
- Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
| | - Koji Nomoto
- Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan.,Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Masahiro Ito
- Department of Microbiology, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Nobuhiko Okada
- Department of Microbiology, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Masato Nagaoka
- Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
| | - Atsushi Gomi
- Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
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44
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Nishiyama K, Yokoi T, Sugiyama M, Osawa R, Mukai T, Okada N. Roles of the Cell Surface Architecture of Bacteroides and Bifidobacterium in the Gut Colonization. Front Microbiol 2021; 12:754819. [PMID: 34721360 PMCID: PMC8551831 DOI: 10.3389/fmicb.2021.754819] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 09/24/2021] [Indexed: 12/12/2022] Open
Abstract
There are numerous bacteria reside within the mammalian gastrointestinal tract. Among the intestinal bacteria, Akkermansia, Bacteroides, Bifidobacterium, and Ruminococcus closely interact with the intestinal mucus layer and are, therefore, known as mucosal bacteria. Mucosal bacteria use host or dietary glycans for colonization via adhesion, allowing access to the carbon source that the host’s nutrients provide. Cell wall or membrane proteins, polysaccharides, and extracellular vesicles facilitate these mucosal bacteria-host interactions. Recent studies revealed that the physiological properties of Bacteroides and Bifidobacterium significantly change in the presence of co-existing symbiotic bacteria or markedly differ with the spatial distribution in the mucosal niche. These recently discovered strategic colonization processes are important for understanding the survival of bacteria in the gut. In this review, first, we introduce the experimental models used to study host-bacteria interactions, and then, we highlight the latest discoveries on the colonization properties of mucosal bacteria, focusing on the roles of the cell surface architecture regarding Bacteroides and Bifidobacterium.
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Affiliation(s)
- Keita Nishiyama
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Tatsunari Yokoi
- Department of Microbiology, School of Pharmacy, Kitasato University, Tokyo, Japan
| | - Makoto Sugiyama
- Laboratory of Veterinary Anatomy, School of Veterinary Medicine, Kitasato University, Towada, Japan
| | - Ro Osawa
- Research Center for Food Safety and Security, Kobe University, Kobe, Japan
| | - Takao Mukai
- Department of Animal Science, School of Veterinary Medicine, Kitasato University, Towada, Japan
| | - Nobuhiko Okada
- Department of Microbiology, School of Pharmacy, Kitasato University, Tokyo, Japan
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45
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Lopez-Pier MA, Koppinger MP, Harris PR, Cannon DK, Skaria RS, Hurwitz BL, Watts G, Aras S, Slepian MJ, Konhilas JP. An adaptable and non-invasive method for tracking Bifidobacterium animalis subspecies lactis 420 in the mouse gut. J Microbiol Methods 2021; 189:106302. [PMID: 34391819 PMCID: PMC8473990 DOI: 10.1016/j.mimet.2021.106302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 08/07/2021] [Accepted: 08/09/2021] [Indexed: 11/26/2022]
Abstract
Probiotic strains from the Bifidobacterium or Lactobacillus genera improve health outcomes in models of metabolic and cardiovascular disease. Yet, underlying mechanisms governing these improved health outcomes are rooted in the interaction of gut microbiota, intestinal interface, and probiotic strain. Central to defining the underlying mechanisms governing these improved health outcomes is the development of adaptable and non-invasive tools to study probiotic localization and colonization within the host gut microbiome. The objective of this study was to test labeling and tracking efficacy of Bifidobacterium animalis subspecies lactis 420 (B420) using a common clinical imaging agent, indocyanine green (ICG). ICG was an effective in situ labeling agent visualized in either intact mouse or excised gastrointestinal (GI) tract at different time intervals. Quantitative PCR was used to validate ICG visualization of B420, which also demonstrated that B420 transit time matched normal murine GI motility (~8 hours). Contrary to previous thoughts, B420 did not colonize any region of the GI tract whether following a single bolus or daily administration for up to 10 days. We conclude that ICG may provide a useful tool to visualize and track probiotic species such as B420 without implementing complex molecular and genetic tools. Proof-of-concept studies indicate that B420 did not colonize and establish residency align the murine GI tract.
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Affiliation(s)
- Marissa A Lopez-Pier
- Sarver Molecular Cardiovascular Research Program, University of Arizona, Tucson, AZ, USA; Department of Biomedical Engineering, University of Arizona, Tucson, AZ, USA
| | - Matthew P Koppinger
- Sarver Molecular Cardiovascular Research Program, University of Arizona, Tucson, AZ, USA; Department of Nutritional Sciences, University of Arizona, Tucson, AZ, USA
| | - Preston R Harris
- Sarver Molecular Cardiovascular Research Program, University of Arizona, Tucson, AZ, USA; Department of Nutritional Sciences, University of Arizona, Tucson, AZ, USA
| | - Danielle K Cannon
- Department of Physiology, University of Arizona, Tucson, AZ, USA; Sarver Molecular Cardiovascular Research Program, University of Arizona, Tucson, AZ, USA
| | - Rinku S Skaria
- Department of Physiology, University of Arizona, Tucson, AZ, USA; Sarver Molecular Cardiovascular Research Program, University of Arizona, Tucson, AZ, USA
| | | | - George Watts
- Bio5 Institute, University of Arizona, Tucson, AZ, USA
| | | | - Marvin J Slepian
- Sarver Molecular Cardiovascular Research Program, University of Arizona, Tucson, AZ, USA; Department of Biomedical Engineering, University of Arizona, Tucson, AZ, USA; Bio5 Institute, University of Arizona, Tucson, AZ, USA; Department of Medicine, University of Arizona, Tucson, AZ, USA
| | - John P Konhilas
- Department of Physiology, University of Arizona, Tucson, AZ, USA; Sarver Molecular Cardiovascular Research Program, University of Arizona, Tucson, AZ, USA; Department of Biomedical Engineering, University of Arizona, Tucson, AZ, USA; Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA; Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA; Department of Nutritional Sciences, University of Arizona, Tucson, AZ, USA.
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Prajapati A, Palva A, von Ossowski I, Krishnan V. LrpCBA pilus proteins of gut-dwelling Ligilactobacillus ruminis: crystallization and X-ray diffraction analysis. Acta Crystallogr F Struct Biol Commun 2021; 77:238-245. [PMID: 34341189 PMCID: PMC8329715 DOI: 10.1107/s2053230x21007263] [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: 06/15/2021] [Accepted: 07/13/2021] [Indexed: 11/10/2022] Open
Abstract
Adhesion to host surfaces for bacterial survival and colonization involves a variety of molecular mechanisms. Ligilactobacillus ruminis, a strict anaerobe and gut autochthonous (indigenous) commensal, relies on sortase-dependent pili (LrpCBA) for adherence to the intestinal inner walls, thereby withstanding luminal content flow. Here, the LrpCBA pilus is a promiscuous binder to gut collagen, fibronectin and epithelial cells. Structurally, the LrpCBA pilus displays a representative hetero-oligomeric arrangement and consists of three types of pilin subunit, each with its own location and function, i.e. tip LrpC for adhesion, basal LrpB for anchoring and backbone LrpA for length. To provide further structural insights into the assembly, anchoring and functional mechanisms of sortase-dependent pili, each of the L. ruminis pilus proteins was produced recombinantly for crystallization and X-ray diffraction analysis. Crystals of LrpC, LrpB, LrpA and truncated LrpA generated by limited proteolysis were obtained and diffracted to resolutions of 3.0, 1.5, 2.2 and 1.4 Å, respectively. Anomalous data were also collected from crystals of selenomethionine-substituted LrpC and an iodide derivative of truncated LrpA. Successful strategies for protein production, crystallization and derivatization are reported.
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Affiliation(s)
- Amar Prajapati
- Laboratory of Structural Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad 121 001, India
| | - Airi Palva
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | | | - Vengadesan Krishnan
- Laboratory of Structural Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad 121 001, India
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47
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Exploiting pilus-mediated bacteria-host interactions for health benefits. Mol Aspects Med 2021; 81:100998. [PMID: 34294411 DOI: 10.1016/j.mam.2021.100998] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/30/2021] [Accepted: 07/16/2021] [Indexed: 02/06/2023]
Abstract
Surface pili (or fimbriae) are an important but conspicuous adaptation of several genera and species of Gram-negative and Gram-positive bacteria. These long and non-flagellar multi-subunit adhesins mediate the initial contact that a bacterium has with a host or environment, and thus have come to be regarded as a key colonization factor for virulence activity in pathogens or niche adaptation in commensals. Pili in pathogenic bacteria are well recognized for their roles in the adhesion to host cells, colonization of tissues, and establishment of infection. As an 'anti-adhesive' ploy, targeting pilus-mediated attachment for disruption has become a potentially effective alternative to using antibiotics. In this review, we give a description of the several structurally distinct bacterial pilus types thus far characterized, and as well offer details about the intricacy of their individual structure, assembly, and function. With a molecular understanding of pilus biogenesis and pilus-mediated host interactions also provided, we go on to describe some of the emerging new approaches and compounds that have been recently developed to prevent the adhesion, colonization, and infection of piliated bacterial pathogens.
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48
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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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Dineen RL, Penno C, Kelleher P, Bourin MJB, O'Connell‐Motherway M, van Sinderen D. Molecular analysis of the replication functions of the bifidobacterial conjugative megaplasmid pMP7017. Microb Biotechnol 2021; 14:1494-1511. [PMID: 33939264 PMCID: PMC8313286 DOI: 10.1111/1751-7915.13810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 03/22/2021] [Indexed: 11/29/2022] Open
Abstract
pMP7017 is a conjugative megaplasmid isolated from the gut commensal Bifidobacterium breve JCM7017 and was shown to encode two putative replicases, designated here as RepA and RepB. In the current work, RepB was identified as the pMP7017 replicative initiator, as the repB gene, and its surrounding region was shown to be sufficient to allow autonomous replication in two bifidobacterial species, B. breve and Bifidobacterium longum subsp. longum. RepB was shown to bind to repeat sequence downstream of its coding sequence and this region was determined to be essential for efficient replication. Based on our results, we hypothesize that pMP7017 is an iteron-regulated plasmid (IRP) under strict auto-regulatory control. Recombinantly produced and purified RepB was determined to exist as a dimer in solution, differing from replicases of other IRPs, which exist as a mix of dimers and monomers. Furthermore, a stable low-copy Bifidobacterium-E. coli shuttle vector, pRD1.3, was created which can be employed for cloning and expression of large genes, as was demonstrated by the cloning and heterologous expression of the 5.1 kb apuB gene encoding the extracellular amylopullulanase from B. breve UCC2003 into B. longum subsp. longum NCIMB8809.
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Affiliation(s)
- Rebecca L. Dineen
- APC Microbiome IrelandUniversity College CorkWestern RoadCorkIreland
- School of MicrobiologyUniversity College CorkWestern RoadCorkIreland
| | - Christophe Penno
- CNRS UMR 6553 EcoBioUniversite de Rennes 1Campus de Beaulieu, Bat. 14ARennes cedex35042France
| | - Philip Kelleher
- APC Microbiome IrelandUniversity College CorkWestern RoadCorkIreland
- School of MicrobiologyUniversity College CorkWestern RoadCorkIreland
| | - Maxence J. B. Bourin
- APC Microbiome IrelandUniversity College CorkWestern RoadCorkIreland
- School of MicrobiologyUniversity College CorkWestern RoadCorkIreland
| | | | - Douwe van Sinderen
- APC Microbiome IrelandUniversity College CorkWestern RoadCorkIreland
- School of MicrobiologyUniversity College CorkWestern RoadCorkIreland
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Xiao Y, Zhao J, Zhang H, Zhai Q, Chen W. Mining genome traits that determine the different gut colonization potential of Lactobacillus and Bifidobacterium species. Microb Genom 2021; 7:000581. [PMID: 34100697 PMCID: PMC8461469 DOI: 10.1099/mgen.0.000581] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 04/12/2021] [Indexed: 12/11/2022] Open
Abstract
Although the beneficial effects of probiotics are likely to be associated with their ability to colonize the gut, little is known about the characteristics of good colonizers. In a systematic analysis of the comparative genomics, we tried to elucidate the genomic contents that account for the distinct host adaptability patterns of Lactobacillus and Bifidobacterium species. The Bifidobacterium species, with species-level phylogenetic structures affected by recombination among strains, broad mucin-foraging activity, and dietary-fibre-degrading ability, represented niche conservatism and tended to be host-adapted. The Lactobacillus species stretched across three lifestyles, namely free-living, nomadic and host-adapted, as characterized by the variations of bacterial occurrence time, guanine-cytosine (GC) content and genome size, evolution event frequency, and the presence of human-adapted bacterial genes. The numbers and activity of host-adapted factors, such as bile salt hydrolase and intestinal tissue-anchored elements, were distinctly distributed among the three lifestyles. The strains of the three lifestyles could be separated with such a collection of colonization-related genomic content (genes, genome size and GC content). Thus, our work provided valuable information for rational selection and gut engraftment prediction of probiotics. Here, we have found many interesting predictive results for bacterial gut fitness, which will be validated in vitro and in vivo.
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Affiliation(s)
- Yue Xiao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- Yangzhou Institute of Food Biotechnology, Jiangnan University, Yangzhou, Jiangsu 225004, PR China
- Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi 214122, PR China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, PR China
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