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Acharya B, Tofthagen M, Maciej-Hulme ML, Suissa MR, Karlsson NG. Limited support for a direct connection between prebiotics and intestinal permeability - a systematic review. Glycoconj J 2024; 41:323-342. [PMID: 39287885 PMCID: PMC11522178 DOI: 10.1007/s10719-024-10165-8] [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: 02/07/2024] [Revised: 08/20/2024] [Accepted: 08/29/2024] [Indexed: 09/19/2024]
Abstract
The intestinal barrier is a selective interface between the body´s external and the internal environment. Its layer of epithelial cells is joined together by tight junction proteins. In intestinal permeability (IP), the barrier is compromised, leading to increased translocation of luminal contents such as large molecules, toxins and even microorganisms. Numerous diseases including Inflammatory Bowel Disease (IBD), Coeliac disease (CD), autoimmune disorders, and diabetes are believed to be associated with IP. Dietary interventions, such as prebiotics, may improve the intestinal barrier. Prebiotics are non-digestible food compounds, that promote the growth and activity of beneficial bacteria in the gut. This systematic review assesses the connection between prebiotic usage and IP. PubMed and Trip were used to identify relevant studies conducted between 2010-2023. Only six studies were found, which all varied in the characteristics of the population, study design, and types of prebiotics interventions. Only one study showed a statistically significant effect of prebiotics on IP. Alteration of intestinal barrier function was measured by lactulose/mannitol, chromium-labelled Ethylenediaminetetraacetic acid (51Cr-EDTA), lactulose/rhamnose, and sucralose/erythritol excretion as well as zonulin and glucagon-like peptide 2 levels. Three studies also conducted gut microbiota assessment, and one of them showed statistically significant improvement of the gut microbiome. This study also reported a decrease in zonulin level. The main conclusion from this review is that there is a lack of human studies in this important field. Futhermore, large population studies and using standardized protocols, would be required to properly assess the impact of prebiotic intervention and improvement on IP.
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Affiliation(s)
- Binayak Acharya
- Department of Life Sciences and Health, Faculty of Health Sciences, Oslo Metropolitan University, St. Olavs Plass, P.O. Box 4, N-0130, Oslo, Norway
| | - Marthe Tofthagen
- Department of Life Sciences and Health, Faculty of Health Sciences, Oslo Metropolitan University, St. Olavs Plass, P.O. Box 4, N-0130, Oslo, Norway
| | - Marissa L Maciej-Hulme
- Department of Life Sciences and Health, Faculty of Health Sciences, Oslo Metropolitan University, St. Olavs Plass, P.O. Box 4, N-0130, Oslo, Norway
| | - Michal Rachel Suissa
- Department of Life Sciences and Health, Faculty of Health Sciences, Oslo Metropolitan University, St. Olavs Plass, P.O. Box 4, N-0130, Oslo, Norway
| | - Niclas G Karlsson
- Department of Life Sciences and Health, Faculty of Health Sciences, Oslo Metropolitan University, St. Olavs Plass, P.O. Box 4, N-0130, Oslo, Norway.
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2
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Rizzo SM, Alessandri G, Tarracchini C, Bianchi MG, Viappiani A, Mancabelli L, Lugli GA, Milani C, Bussolati O, van Sinderen D, Ventura M, Turroni F. Molecular cross-talk among human intestinal bifidobacteria as explored by a human gut model. Front Microbiol 2024; 15:1435960. [PMID: 39314876 PMCID: PMC11418510 DOI: 10.3389/fmicb.2024.1435960] [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: 05/21/2024] [Accepted: 08/28/2024] [Indexed: 09/25/2024] Open
Abstract
Bifidobacteria are well known as common and abundant colonizers of the human gut and are able to exert multiple beneficial effects on their host, although the cooperative and competitive relationships that may occur among bifidobacterial strains are still poorly investigated. Therefore, to dissect possible molecular interactions among bifidobacterial species that typically colonize the human gut, three previously identified bifidobacterial prototypes, i.e., B. bifidum PRL2010, B. breve PRL2012, and B. longum PRL2022 were cultivated individually as well as in bi- and tri-association in a human gut-simulating medium. Transcriptomic analyses of these co-associations revealed up-regulation of genes predicted to be involved in the production of extracellular structures including pili (i.e., flp pilus assembly TadE protein gene), exopolysaccharides (i.e., GtrA family protein gene) and teichoic acids (i.e., ABC transporter permease), along with carbohydrate, amino acid and vitamin metabolism-related genes (i.e., exo-alpha-sialidase; beta-galactosidase and pyridoxamine kinase), suggesting that co-cultivation of bifidobacteria induces a response, in individual bifidobacterial strains, aimed at enhancing their proliferation and survival, as well as their ability to cooperate with their host to promote their persistence. Furthermore, exposure of the selected prototypes to human cell line monolayers unveiled the ability of the bifidobacterial tri-association to communicate with their host by increasing the expression of genes involved in adherence to/interaction with intestinal human cells. Lastly, bifidobacterial tri-association promoted the transcriptional upregulation of genes responsible for maintaining the integrity and homeostasis of the intestinal epithelial barrier.
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Affiliation(s)
- Sonia Mirjam Rizzo
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Giulia Alessandri
- 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
| | - Massimiliano G. Bianchi
- Laboratory of General Pathology, Department of Medicine and Surgery, University of Parma, Parma, Italy
- Microbiome Research Hub, 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
| | - 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
| | - 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
| | - Ovidio Bussolati
- Laboratory of General Pathology, 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
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
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Guimarães VHD, Marinho BM, Motta-Santos D, Mendes GDRL, Santos SHS. Nutritional implications in the mechanistic link between the intestinal microbiome, renin-angiotensin system, and the development of obesity and metabolic syndrome. J Nutr Biochem 2023; 113:109252. [PMID: 36509338 DOI: 10.1016/j.jnutbio.2022.109252] [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: 06/10/2022] [Revised: 11/12/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022]
Abstract
Obesity and metabolic disorders represent a significant global health problem and the gut microbiota plays an important role in modulating systemic homeostasis. Recent evidence shows that microbiota and its signaling pathways may affect the whole metabolism and the Renin-Angiotensin System (RAS), which in turn seems to modify microbiota. The present review aimed to investigate nutritional implications in the mechanistic link between the intestinal microbiome, renin-angiotensin system, and the development of obesity and metabolic syndrome components. A description of metabolic changes was obtained based on relevant scientific literature. The molecular and physiological mechanisms that impact the human microbiome were addressed, including the gut microbiota associated with obesity, diabetes, and hepatic steatosis. The RAS interaction signaling and modulation were analyzed. Strategies including the use of prebiotics, symbiotics, probiotics, and biotechnology may affect the gut microbiota and its impact on human health.
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Affiliation(s)
- Victor Hugo Dantas Guimarães
- Laboratory of Health Science, Postgraduate Program in Health Science, Universidade Estadual de Montes Claros (Unimontes), Montes Claros, Minas Gerais, Brazil
| | - Barbhara Mota Marinho
- Laboratory of Health Science, Postgraduate Program in Health Science, Universidade Estadual de Montes Claros (Unimontes), Montes Claros, Minas Gerais, Brazil
| | - Daisy Motta-Santos
- School of Physical Education, Physiotherapy, and Occupational Therapy - EEFFTO, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Gabriela da Rocha Lemos Mendes
- Food Engineering, Institute of Agricultural Sciences (ICA), Universidade Federal de Minas Gerais (UFMG), Montes Claros, Minas Gerais, Brazil
| | - Sérgio Henrique Sousa Santos
- Laboratory of Health Science, Postgraduate Program in Health Science, Universidade Estadual de Montes Claros (Unimontes), Montes Claros, Minas Gerais, Brazil; Food Engineering, Institute of Agricultural Sciences (ICA), Universidade Federal de Minas Gerais (UFMG), Montes Claros, Minas Gerais, Brazil.
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4
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Yu Y, Ren X, Cao L, Liang Q, Xiao M, Cheng J, Nan S, Zhu C, Kong Q, Fu X, Mou H. Complete‐Genome
Sequence and
in vitro
Probiotic Characteristics Analysis of
Bifidobacterium pseudolongum
YY
‐26. J Appl Microbiol 2022; 133:2599-2617. [DOI: 10.1111/jam.15730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 07/05/2022] [Accepted: 07/18/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Ying Yu
- College of Food Science and Engineering Ocean University of China Qingdao China
| | - Xinmiao Ren
- College of Food Science and Engineering Ocean University of China Qingdao China
| | - Linyuan Cao
- College of Food Science and Engineering Ocean University of China Qingdao China
| | - Qingping Liang
- College of Food Science and Engineering Ocean University of China Qingdao China
| | - Mengshi Xiao
- College of Food Science and Engineering Ocean University of China Qingdao China
| | - Jiaying Cheng
- College of Food Science and Engineering Ocean University of China Qingdao China
| | - Shihao Nan
- State Key Laboratory of Food Science and Technology, China‐Canada Joint Laboratory of Food Science and Technology (Nanchang), Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University
| | - Changliang Zhu
- College of Food Science and Engineering Ocean University of China Qingdao China
| | - Qing Kong
- College of Food Science and Engineering Ocean University of China Qingdao China
| | - Xiaodan Fu
- State Key Laboratory of Food Science and Technology, China‐Canada Joint Laboratory of Food Science and Technology (Nanchang), Key Laboratory of Bioactive Polysaccharides of Jiangxi Province, Nanchang University
| | - Haijin Mou
- College of Food Science and Engineering Ocean University of China Qingdao China
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5
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You L, Bao W, Yao C, Zhao F, Jin H, Huang W, Li B, Kwok LY, Liu W. Changes in chemical composition, structural and functional microbiome during alfalfa ( Medicago sativa) ensilage with Lactobacillus plantarum PS-8. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2022; 9:100-109. [PMID: 35509811 PMCID: PMC9046633 DOI: 10.1016/j.aninu.2021.12.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 12/15/2021] [Accepted: 12/28/2021] [Indexed: 06/14/2023]
Abstract
Improving silage production by adding exogenous microorganisms not only maximizes nutrient preservation, but also extends product shelf life. Herein, changes in the quality and quantity of Lactobacillus plantarum PS-8 (PS-8) -inoculated alfalfa (Medicago sativa) during silage fermentation were monitored at d 0, 7, 14, and 28 (inoculum dose of PS-8 was 1 × 105 colony forming units [cfu]/g fresh weight; 50 kg per bag; 10 bags for each time point) by reconstructing metagenomic-assembled genomes (MAG) and Growth Rate InDex (GRiD). Our results showed that the exogenous starter bacterium, PS-8 inoculation, became the most dominating strain by d 7, and possibly played a highly active role throughout the fermentation process. The pH value of the silage decreased greatly, accompanied by the growth of acid-producing microorganisms namely PS-8, which inhibited the growth of harmful microorganisms like molds (4.18 vs. 1.42 log cfu/g) and coliforms (4.95 vs. 0.66 log most probable number [MPN]/g). The content of neutral detergent fiber (NDF) decreased significantly (41.6% vs. 37.6%; dry matter basis). In addition, the abundance and diversity of genes coding microbial carbohydrate-active enzymes (CAZymes) increased significantly and desirably throughout the fermentation, particularly the genes responsible for degrading starch, arabino-xylan, and cellulose. Overall, our results showed that PS-8 was replicating rapidly and consistently during early- and mid-fermentation phases, promoting the growth of beneficial lactic acid bacteria and inhibiting undesirable microbes, ultimately improving the quality of silage.
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Affiliation(s)
| | | | | | - Feiyan Zhao
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Hao Jin
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Weiqiang Huang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Bohai Li
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Lai-Yu Kwok
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Wenjun Liu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, China
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6
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Applicability of rpoB Gene for PCR-RFLP based Discrimination of Bifidobacterial Species Isolated from Human and Animal Sources. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2022. [DOI: 10.22207/jpam.16.1.48] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bifidobacteria are widely used as probiotics for their application in the development of functional food and prophylactic therapy. This has necessitated the development of a molecular approach for the genera to be widely identified up to species and subspecies level. In the current study, PCR-RFLP of the partial RNA polymerase β-subunit (rpoB) gene fragment was evaluated for differential identification of Bifidobacterium species. The rpoB gene partial sequences of 575 bp were amplified from 93 previously identified isolates collected from various sources of human and animal origin along with 12 standard reference strains. The PCR amplified products were digested with three restriction endonucleases HhaI, HinfI and BanI separately. Dendrograms constructed from the patterns of HhaI, were found to be more discriminatory and successfully differentiated all the twelve species and also at sub-species level in between B. longum subsp. longum and B. longum subsp. infantis. However, B. adolescentis and B. pseudocatenulatum group clusters were not separated and represented by one group. The groups were further discriminated by HinfI restriction digestion. A separate combination thereof may be used for inferring the classification of bifidobacterial species targeted on rpoB PCR-RFLP analysis. To our knowledge, this work is the first report based on use of rpoB PCR-RFLP for discrimination of the isolates of genus Bifidobacterium and also provides insights into specific advantages of this method over hsp60 PCR-RFLP in differentiating B. longum subsp. longum and B. longum subsp. infantis.
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7
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Conte M, Porpora M, Nigro F, Nigro R, Budelli AL, Barone MV, Nanayakkara M. Pro-Pre and Postbiotic in Celiac Disease. APPLIED SCIENCES 2021; 11:8185. [DOI: 10.3390/app11178185] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2025]
Abstract
Celiac Disease (CD) is an autoimmune disease characterized by inflammation of the intestinal mucosa due to an immune response to wheat gliadins. It presents in subjects with genetic susceptibility (HLA-DQ2/DQ8 positivity and non-HLA genes) and under the influence of environmental triggers, such as viral infections and intestinal microbiota dysbiosis. The only treatment currently available in CD is a gluten-free diet for life. Despite this, the intestinal dysbiosis that is recorded in celiac subjects persists, even with adherence to dietary therapy. In this review, we have analyzed the literature over the past several decades, which have focused on the use of pro-, pre- and post-biotics in vitro and in vivo in CD. The study of probiotics and their products in CD could be interesting for observing their various effects on several different pathways, including anti-inflammatory properties.
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Affiliation(s)
- Mariangela Conte
- Department of Translational Medical Science (Section of Pediatrics), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
- European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Monia Porpora
- Department of Translational Medical Science (Section of Pediatrics), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
- European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Federica Nigro
- School of Engineering, Niccoló Cusano University, 00166 Rome, Italy
- I.T.P. Innovation and Technology Provider S.r.l., Via Bisignano a Chiaia 68, 80121 Naples, Italy
| | - Roberto Nigro
- DICMAPI, University of Naples Federico II, 80125 Naples, Italy
| | - Andrea Luigi Budelli
- School of Engineering, Niccoló Cusano University, 00166 Rome, Italy
- DICMAPI, University of Naples Federico II, 80125 Naples, Italy
| | - M. Vittoria Barone
- Department of Translational Medical Science (Section of Pediatrics), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
- European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Merlin Nanayakkara
- Department of Translational Medical Science (Section of Pediatrics), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
- European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
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8
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Shivakumar N, Sivadas A, Devi S, Jahoor F, McLaughlin J, Smith CP, Kurpad AV, Mukhopadhyay A. Gut microbiota profiles of young South Indian children: Child sex-specific relations with growth. PLoS One 2021; 16:e0251803. [PMID: 33989353 PMCID: PMC8121364 DOI: 10.1371/journal.pone.0251803] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 05/04/2021] [Indexed: 12/21/2022] Open
Abstract
Gut microbiota has been implicated as a modifier of childhood growth. Here, 16S rRNA sequencing-based fecal microbiota profiles of 18–24 month old Indian children were evaluated (n = 41), in relation to their anthropometric parameters, intestinal permeability, body composition and total energy expenditure. Pathway analyses were conducted to assess microbial functions related to stunting, underweight and wasting. The fecal microbiota was enriched in Prevotella 9, Bifidobacterium and Escherichia-Shigella. Weight, weight-for-age Z-scores (WAZ) and weight-for-length Z-scores (WLZ), along with age, acted as covariates of microbiota variation specifically in boys (n = 23). Bifidobacterium longum subsp longum abundance was positively associated with WAZ while Bifidobacterium bifidum and Bifidobacterium breve abundances were negatively associated with age. The lipopolysaccharide biosynthesis pathway was upregulated in stunted (n = 16) and wasted (n = 8) children. Findings from this study indicate that child sex may be a critical modifier of the role of gut microbiota on childhood growth.
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Affiliation(s)
- Nirupama Shivakumar
- Division of Nutrition, St. John’s Research Institute, St. John’s National Academy of Health Sciences, Bangalore, India
| | - Ambily Sivadas
- Division of Nutrition, St. John’s Research Institute, St. John’s National Academy of Health Sciences, Bangalore, India
| | - Sarita Devi
- Division of Nutrition, St. John’s Research Institute, St. John’s National Academy of Health Sciences, Bangalore, India
| | - Farook Jahoor
- Department of Pediatrics, USDA/Agricultural Research Service Children’s Nutrition Research Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - John McLaughlin
- Faculty of Biology, Division of Diabetes, Endocrinology and Gastroenterology, School of Medical Sciences, Medicine & Health, Manchester Academic Health Sciences Centre, University of Manchester, Clinical Sciences Building, Salford Royal Hospital, Salford, United Kingdom
| | - Craig P. Smith
- Faculty of Biology, Division of Diabetes, Endocrinology and Gastroenterology, School of Medical Sciences, Medicine & Health, Manchester Academic Health Sciences Centre, University of Manchester, Clinical Sciences Building, Salford Royal Hospital, Salford, United Kingdom
| | - Anura V. Kurpad
- Division of Nutrition, St. John’s Research Institute, St. John’s National Academy of Health Sciences, Bangalore, India
- Department of Physiology, St. John’s Medical College, St. John’s National Academy of Health Sciences, Bangalore, India
| | - Arpita Mukhopadhyay
- Division of Nutrition, St. John’s Research Institute, St. John’s National Academy of Health Sciences, Bangalore, India
- * E-mail:
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9
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Effects of Vitamin B2 Supplementation in Broilers Microbiota and Metabolome. Microorganisms 2020; 8:microorganisms8081134. [PMID: 32727134 PMCID: PMC7464963 DOI: 10.3390/microorganisms8081134] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/24/2020] [Accepted: 07/24/2020] [Indexed: 01/04/2023] Open
Abstract
The study of the microbiome in broiler chickens holds great promise for the development of strategies for health maintenance and performance improvement. Nutritional strategies aimed at modulating the microbiota-host relationship can improve chickens' immunological status and metabolic fitness. Here, we present the results of a pilot trial aimed at analyzing the effects of a nutritional strategy involving vitamin B2 supplementation on the ileum, caeca and litter microbiota of Ross 308 broilers, as well as on the metabolic profile of the caecal content. Three groups of chickens were administered control diets and diets supplemented with two different dosages of vitamin B2. Ileum, caeca, and litter samples were obtained from subgroups of birds at three time points along the productive cycle. Sequencing of the 16S rRNA V3-V4 region and NMR metabolomics were used to explore microbiota composition and the concentration of metabolites of interest, including short-chain fatty acids. Vitamin B2 supplementation significantly modulated caeca microbiota, with the highest dosage being more effective in increasing the abundance of health-promoting bacterial groups, including Bifidobacterium, resulting in boosted production of butyrate, a well-known health-promoting metabolite, in the caeca environment.
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10
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Mancino W, Lugli GA, van Sinderen D, Ventura M, Turroni F. Mobilome and Resistome Reconstruction from Genomes Belonging to Members of the Bifidobacterium Genus. Microorganisms 2019; 7:microorganisms7120638. [PMID: 31810287 PMCID: PMC6956390 DOI: 10.3390/microorganisms7120638] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/27/2019] [Accepted: 11/29/2019] [Indexed: 02/06/2023] Open
Abstract
Specific members of the genus Bifidobacterium are among the first colonizers of the human/animal gut, where they act as important intestinal commensals associated with host health. As part of the gut microbiota, bifidobacteria may be exposed to antibiotics, used in particular for intrapartum prophylaxis, especially to prevent Streptococcus infections, or in the very early stages of life after the birth. In the current study, we reconstructed the in silico resistome of the Bifidobacterium genus, analyzing a database composed of 625 bifidobacterial genomes, including partial assembled strains with less than 100 genomic sequences. Furthermore, we screened bifidobacterial genomes for mobile genetic elements, such as transposases and prophage-like elements, in order to investigate the correlation between the bifido-mobilome and the bifido-resistome, also identifying genetic insertion hotspots that appear to be prone to horizontal gene transfer (HGT) events. These insertion hotspots were shown to be widely distributed among analyzed bifidobacterial genomes, and suggest the acquisition of antibiotic resistance genes through HGT events. These data were further corroborated by growth experiments directed to evaluate bacitracin A resistance in Bifidobacterium spp., a property that was predicted by in silico analyses to be part of the HGT-acquired resistome.
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Affiliation(s)
- Walter Mancino
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (W.M.); (G.A.L.); (M.V.)
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (W.M.); (G.A.L.); (M.V.)
| | - Douwe van Sinderen
- School of Microbiology, APC Microbiome Institute, University College Cork, Cork T12 K8AF, Ireland;
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (W.M.); (G.A.L.); (M.V.)
- Microbiome Research Hub, University of Parma, 43124 Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (W.M.); (G.A.L.); (M.V.)
- Microbiome Research Hub, University of Parma, 43124 Parma, Italy
- Correspondence: ; Tel.: +39-521-905666; Fax: +39-521-905604
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11
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Division of labor in honey bee gut microbiota for plant polysaccharide digestion. Proc Natl Acad Sci U S A 2019; 116:25909-25916. [PMID: 31776248 DOI: 10.1073/pnas.1916224116] [Citation(s) in RCA: 184] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Bees acquire carbohydrates from nectar and lipids; and amino acids from pollen, which also contains polysaccharides including cellulose, hemicellulose, and pectin. These potential energy sources could be degraded and fermented through microbial enzymatic activity, resulting in short chain fatty acids available to hosts. However, the contributions of individual microbiota members to polysaccharide digestion have remained unclear. Through analysis of bacterial isolate genomes and a metagenome of the honey bee gut microbiota, we identify that Bifidobacterium and Gilliamella are the principal degraders of hemicellulose and pectin. Both Bifidobacterium and Gilliamella show extensive strain-level diversity in gene repertoires linked to polysaccharide digestion. Strains from honey bees possess more such genes than strains from bumble bees. In Bifidobacterium, genes encoding carbohydrate-active enzymes are colocated within loci devoted to polysaccharide utilization, as in Bacteroides from the human gut. Carbohydrate-active enzyme-encoding gene expressions are up-regulated in response to particular hemicelluloses both in vitro and in vivo. Metabolomic analyses document that bees experimentally colonized by different strains generate distinctive gut metabolomic profiles, with enrichment for specific monosaccharides, corresponding to predictions from genomic data. The other 3 core gut species clusters (Snodgrassella and 2 Lactobacillus clusters) possess few or no genes for polysaccharide digestion. Together, these findings indicate that strain composition within individual hosts determines the metabolic capabilities and potentially affects host nutrition. Furthermore, the niche specialization revealed by our study may promote overall community stability in the gut microbiomes of bees.
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12
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Singh RP. Glycan utilisation system in Bacteroides and Bifidobacteria and their roles in gut stability and health. Appl Microbiol Biotechnol 2019; 103:7287-7315. [PMID: 31332487 DOI: 10.1007/s00253-019-10012-z] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 07/02/2019] [Accepted: 07/03/2019] [Indexed: 02/07/2023]
Abstract
Gut residential hundred trillion microbial cells are indispensable for maintaining gut homeostasis and impact on host physiology, development and immune systems. Many of them have displayed excellence in utilising dietary- and host-derived complex glycans and are producing useful postbiotics including short-chain fatty acids to primarily fuel different organs of the host. Therefore, employing individual microbiota is nowadays becoming a propitious target in biomedical for improving gut dysbiosis conditions of the host. Among other gut microbial communities, Bacteroides and Bifidobacteria are coevolved to utilise diverse ranges of diet- and host-derived glycans through harmonising distinct glycan utilisation systems. These gut symbionts frequently share digested oligosaccharides, carbohydrate-active enzymes and fermentable intermediate molecules for sustaining gut microbial symbiosis and improving fitness of own or other communities. Genomics approaches have provided unprecedented insights into these functions, but their precise mechanisms of action have poorly known. Sympathetic glycan-utilising strategy of each gut commensal will provide overview of mechanistic dynamic nature of the gut environment and will then assist in applying aptly personalised nutritional therapy. Thus, the review critically summarises cutting edge understanding of major plant- and host-derived glycan-utilising systems of Bacteroides and Bifidobacteria. Their evolutionary adaptation to gut environment and roles of postbiotics in human health are also highlighted.
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Affiliation(s)
- Ravindra Pal Singh
- Food and Nutritional Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), SAS, Nagar, Punjab, 140306, India.
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13
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Glycan Utilization and Cross-Feeding Activities by Bifidobacteria. Trends Microbiol 2018; 26:339-350. [DOI: 10.1016/j.tim.2017.10.001] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 10/02/2017] [Accepted: 10/12/2017] [Indexed: 01/16/2023]
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14
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Dicks L, Geldenhuys J, Mikkelsen L, Brandsborg E, Marcotte H. Our gut microbiota: a long walk to homeostasis. Benef Microbes 2018; 9:3-20. [DOI: 10.3920/bm2017.0066] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The microbiome of the human gastrointestinal tract (GIT) consists of billions of bacteria, fungi and viruses, of which bacteria play the most important role in nutrition, immune development, production of vitamins and maintaining a well-balanced (homeostatic) microbial population. Many papers have been published on the microbiota in the human GIT, but little is known about the first group of bacteria that colonises an infant. The intestinal tract of an unborn is, despite general belief, not sterile, but contains bacteria that have been transferred from the mother. This opens a new research field and may change our understanding about the role bacteria play in early life, the selection of strains with probiotic properties and the treatment of diseases related to bacterial infections. Differences in bacterial populations isolated from meconia may provide answers to the prevention of certain forms of diabetes. More research is now focusing on the effect that a genetically diverse group, versus a much simpler microbial population, may have on the development of a homeostatic gut microbiome. The effect different bacterial species have on the gut-associated lymphoid tissue and cascade of immune responses has been well researched, but we still fail in identifying the ideal group of intestinal bacteria and if we do, it will certainly not be possible to maintain homeostasis with so many challenges the gut faces. Changes in diet, antibiotics, food preservatives and stress are some of the factors we would like to control, but more than often fail to do so. The physiology and genetics of the GIT changes with age and so the microbiome. This review summarises factors involved in the regulation of a gut microbiome.
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Affiliation(s)
- L.M.T. Dicks
- Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch 7600, South Africa
| | - J. Geldenhuys
- Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch 7600, South Africa
| | | | - E. Brandsborg
- Bifodan A/S, Bogbinderivej 6, 3390 Hundested, Denmark
| | - H. Marcotte
- Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital, Huddinge 141 86, Sweden
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15
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Acuña-Amador L, Primot A, Cadieu E, Roulet A, Barloy-Hubler F. Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains. BMC Genomics 2018; 19:54. [PMID: 29338683 PMCID: PMC5771137 DOI: 10.1186/s12864-017-4429-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/29/2017] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Without knowledge of their genomic sequences, it is impossible to make functional models of the bacteria that make up human and animal microbiota. Unfortunately, the vast majority of publicly available genomes are only working drafts, an incompleteness that causes numerous problems and constitutes a major obstacle to genotypic and phenotypic interpretation. In this work, we began with an example from the class Bacteroidia in the phylum Bacteroidetes, which is preponderant among human orodigestive microbiota. We successfully identify the genetic loci responsible for assembly breaks and misassemblies and demonstrate the importance and usefulness of long-read sequencing and curated reannotation. RESULTS We showed that the fragmentation in Bacteroidia draft genomes assembled from massively parallel sequencing linearly correlates with genomic repeats of the same or greater size than the reads. We also demonstrated that some of these repeats, especially the long ones, correspond to misassembled loci in three reference Porphyromonas gingivalis genomes marked as circularized (thus complete or finished). We prove that even at modest coverage (30X), long-read resequencing together with PCR contiguity verification (rrn operons and an integrative and conjugative element or ICE) can be used to identify and correct the wrongly combined or assembled regions. Finally, although time-consuming and labor-intensive, consistent manual biocuration of three P. gingivalis strains allowed us to compare and correct the existing genomic annotations, resulting in a more accurate interpretation of the genomic differences among these strains. CONCLUSIONS In this study, we demonstrate the usefulness and importance of long-read sequencing in verifying published genomes (even when complete) and generating assemblies for new bacterial strains/species with high genomic plasticity. We also show that when combined with biological validation processes and diligent biocurated annotation, this strategy helps reduce the propagation of errors in shared databases, thus limiting false conclusions based on incomplete or misleading information.
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Affiliation(s)
- Luis Acuña-Amador
- Institut de Génétique et Développement de Rennes, CNRS, UMR6290, Université de Rennes 1, Rennes, France.,Laboratorio de Investigación en Bacteriología Anaerobia, Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Aline Primot
- Institut de Génétique et Développement de Rennes, CNRS, UMR6290, Université de Rennes 1, Rennes, France
| | - Edouard Cadieu
- Institut de Génétique et Développement de Rennes, CNRS, UMR6290, Université de Rennes 1, Rennes, France
| | - Alain Roulet
- GenoToul Genome & Transcriptome (GeT-PlaGe), INRA, US1426, Castanet-Tolosan, France
| | - Frédérique Barloy-Hubler
- Institut de Génétique et Développement de Rennes, CNRS, UMR6290, Université de Rennes 1, Rennes, France.
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16
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Turroni F, Milani C, Duranti S, Ferrario C, Lugli GA, Mancabelli L, van Sinderen D, Ventura M. Bifidobacteria and the infant gut: an example of co-evolution and natural selection. Cell Mol Life Sci 2018; 75:103-118. [PMID: 28983638 PMCID: PMC11105234 DOI: 10.1007/s00018-017-2672-0] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 09/29/2017] [Indexed: 12/16/2022]
Abstract
Throughout the human life, the gut microbiota interacts with us in a number of different ways, thereby influencing our health status. The acquisition of such an interactive gut microbiota commences at birth. Medical and environmental factors including diet, antibiotic exposure and mode of delivery are major factors that shape the composition of the microbial communities in the infant gut. Among the most abundant members of the infant microbiota are species belonging to the Bifidobacterium genus, which are believed to confer beneficial effects upon their host. Bifidobacteria may be acquired directly from the mother by vertical transmission and their persistence in the infant gut is associated with their saccharolytic activity toward glycans that are abundant in the infant gut. Here, we discuss the establishment of the infant gut microbiota and the contribution of bifidobacteria to this early life microbial consortium.
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Affiliation(s)
- Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Chiara Ferrario
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.
- Microbiome Research Hub, University of Parma, Parma, Italy.
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17
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Bottacini F, Zomer A, Milani C, Ferrario C, Lugli GA, Egan M, Ventura M, van Sinderen D. Global transcriptional landscape and promoter mapping of the gut commensal Bifidobacterium breve UCC2003. BMC Genomics 2017; 18:991. [PMID: 29281966 PMCID: PMC5746004 DOI: 10.1186/s12864-017-4387-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 12/15/2017] [Indexed: 12/16/2022] Open
Abstract
Background Bifidobacterium breve represents a common member of the infant gut microbiota and its presence in the gut has been associated with host well being. For this reason it is relevant to investigate and understand the molecular mechanisms underlying the establishment, persistence and activities of this gut commensal in the host environment. Results The assessment of vegetative promoters in the bifidobacterial prototype Bifidobacterium breve UCC2003 was performed employing a combination of RNA tiling array analysis and cDNA sequencing. Canonical −10 (TATAAT) and −35 (TTGACA) sequences were identified upstream of transcribed genes or operons, where deviations from this consensus correspond to transcription level variations. A Random Forest analysis assigned the −10 region of B. breve promoters as the element most impacting on the level of transcription, followed by the spacer length and the 5’-UTR length of transcripts. Furthermore, our transcriptome study also identified rho-independent termination as the most common and effective termination signal of highly and moderately transcribed operons in B. breve. Conclusion The present study allowed us to identify genes and operons that are actively transcribed in this organism during logarithmic growth, and link promoter elements with levels of transcription of essential genes in this organism. As homologs of many of our identified genes are present across the whole genus Bifidobacterium, our dataset constitutes a transcriptomic reference to be used for future investigations of gene expression in members of this genus. Electronic supplementary material The online version of this article (10.1186/s12864-017-4387-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Francesca Bottacini
- APC Microbiome Institute and School of Microbiology, University College Cork, Cork, Ireland
| | - Aldert Zomer
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemical Sciences, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Chiara Ferrario
- Laboratory of Probiogenomics, Department of Chemical Sciences, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemical Sciences, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Muireann Egan
- APC Microbiome Institute and School of Microbiology, University College Cork, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemical Sciences, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, University College Cork, Cork, Ireland.
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18
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Omics of bifidobacteria: research and insights into their health-promoting activities. Biochem J 2017; 474:4137-4152. [PMID: 29212851 DOI: 10.1042/bcj20160756] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 10/10/2017] [Accepted: 11/06/2017] [Indexed: 12/17/2022]
Abstract
Members of the genus Bifidobacterium include gut commensals that are particularly abundant among the microbial communities residing in the gut of healthy breast-fed infants, where their presence has been linked to many beneficial host effects. Next-generation DNA sequencing and comparative and functional genome methodologies have been shown to be particularly useful in exploring the diversity of this genus. These combined approaches have allowed the identification of genetic features related to bifidobacterial establishment in the gut, involving host-microbe as well as microbe-microbe interactions. Among these, proteinaceous structures, which protrude from the bacterial surface, i.e. pili or fimbriae, and exopolysaccharidic cell surface layers or capsules represent crucial features that assist in their colonization and persistence in the gut. As bifidobacteria are colonizers of the large intestine, they have to be able to cope with various sources of osmotic, oxidative, bile and acid stress during their transit across the gastric barrier and the small intestine. Bifidobacterial genomes thus encode various survival mechanisms, such as molecular chaperones and efflux pumps, to overcome such challenges. Bifidobacteria represent part of an anaerobic gut community, and feed on nondigestible carbohydrates through a specialized fermentative metabolic pathway, which in turn produces growth substrates for other members of the gut community. Conversely, bifidobacteria may also be dependent on other (bifido)bacteria to access host- and diet-derived glycans, and these complex co-operative interactions, based on resource sharing and cross-feeding strategies, represent powerful driving forces that shape gut microbiota composition.
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19
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Hidalgo-Cantabrana C, Delgado S, Ruiz L, Ruas-Madiedo P, Sánchez B, Margolles A. Bifidobacteria and Their Health-Promoting Effects. Microbiol Spectr 2017; 5:10.1128/microbiolspec.bad-0010-2016. [PMID: 28643627 PMCID: PMC11687494 DOI: 10.1128/microbiolspec.bad-0010-2016] [Citation(s) in RCA: 244] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Indexed: 12/28/2022] Open
Abstract
Bifidobacteria are members of the intestinal microbiota of mammals and other animals, and some strains are able to exert health-promoting effects. The genus Bifidobacterium belongs to the Actinobacteria phylum. Firmicutes, Bacteroidetes, and Actinobacteria constitute the most abundant phyla in the human intestinal microbiota, Firmicutes and Bacteroidetes being predominant in adults, and Actinobacteria in breast-fed infants, where bifidobacteria can reach levels higher than 90% of the total bacterial population. They are among the first microbial colonizers of the intestines of newborns, and play key roles in the development of their physiology, including maturation of the immune system and use of dietary components. Indeed, some nutrients, such as human milk oligosaccharides, are important drivers of bifidobacterial development. Some Bifidobacterium strains are considered probiotic microorganisms because of their beneficial effects, and they have been included as bioactive ingredients in functional foods, mainly dairy products, as well as in food supplements and pharma products, alone, or together with, other microbes or microbial substrates. Well-documented scientific evidence of their activities is currently available for bifidobacteria-containing preparations in some intestinal and extraintestinal pathologies. In this review, we focus on the role of bifidobacteria as members of the human intestinal microbiota and their use as probiotics in the prevention and treatment of disease.
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Affiliation(s)
- Claudio Hidalgo-Cantabrana
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Paseo Río Linares s/n 33300, Villaviciosa, Asturias, Spain
| | - Susana Delgado
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Paseo Río Linares s/n 33300, Villaviciosa, Asturias, Spain
| | - Lorena Ruiz
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Paseo Río Linares s/n 33300, Villaviciosa, Asturias, Spain
| | - Patricia Ruas-Madiedo
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Paseo Río Linares s/n 33300, Villaviciosa, Asturias, Spain
| | - Borja Sánchez
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Paseo Río Linares s/n 33300, Villaviciosa, Asturias, Spain
| | - Abelardo Margolles
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Paseo Río Linares s/n 33300, Villaviciosa, Asturias, Spain
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20
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Abstract
The microbiome comprises all the microbes living in and on the human body. Human cells are greatly outnumbered by bacterial cells; thus human health depends on the health of the microbial ecosystem. For the immature preterm infant, the microbiome also influences intestinal and immune system development. This has implications for short term morbidities such as neonatal necrotizing enterocolitis and sepsis, but also long term health outcomes. Optimization of the preterm infant microbiome is a growing topic of interest. The microbial world is not one of good versus evil, but rather one of community; thus optimization includes not only minimizing pathogens, but also enhancing beneficial organisms. Options for optimization include judicious antibiotic use, administration of supplements such as prebiotics or probiotics, and transfaunation procedures such as fecal microbial transplant or microbial ecosystem therapeutics. Potential for benefit as well as risk for each of these options will be discussed.
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Affiliation(s)
| | - Elaine O. Petrof
- Queen's University, Department of Medicine, Kingston General Hospital, Kingston, ON, Canada
| | - Erika C. Claud
- University of Chicago, Chicago, IL, USA,Corresponding author. Address: University of Chicago, 5841 S. Maryland Ave. MC6060, Chicago, IL 60637, USA. Tel.: +1 773-702-6210; fax: +1 773-702-0764. (E.C. Claud)
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21
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Ku S, Park MS, Ji GE, You HJ. Review on Bifidobacterium bifidum BGN4: Functionality and Nutraceutical Applications as a Probiotic Microorganism. Int J Mol Sci 2016; 17:ijms17091544. [PMID: 27649150 PMCID: PMC5037818 DOI: 10.3390/ijms17091544] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 09/01/2016] [Accepted: 09/08/2016] [Indexed: 01/20/2023] Open
Abstract
Bifidobacterium bifidum BGN4 is a probiotic strain that has been used as a major ingredient to produce nutraceutical products and as a dairy starter since 2000. The various bio-functional effects and potential for industrial application of B. bifidum BGN4 has been characterized and proven by in vitro (i.e., phytochemical bio-catalysis, cell adhesion and anti-carcinogenic effects on cell lines, and immunomodulatory effects on immune cells), in vivo (i.e., suppressed allergic responses in mouse model and anti-inflammatory bowel disease), and clinical studies (eczema in infants and adults with irritable bowel syndrome). Recently, the investigation of the genome sequencing was finished and this data potentially clarifies the biochemical characteristics of B. bifidum BGN4 that possibly illustrate its nutraceutical functionality. However, further systematic research should be continued to gain insight for academic and industrial applications so that the use of B. bifidum BGN4 could be expanded to result in greater benefit. This review deals with multiple studies on B. bifidum BGN4 to offer a greater understanding as a probiotic microorganism available in functional food ingredients. In particular, this work considers the potential for commercial application, physiological characterization and exploitation of B. bifidum BGN4 as a whole.
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Affiliation(s)
- Seockmo Ku
- Department of Food and Nutrition, Research Institute of Human Ecology, Seoul National University, Seoul 151-742, Korea.
- Laboratory of Renewable Resources Engineering, Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907-2022, USA.
| | - Myeong Soo Park
- Department of Hotel Culinary Arts, Yeonsung University, Anyang 430-749, Korea.
| | - Geun Eog Ji
- Department of Food and Nutrition, Research Institute of Human Ecology, Seoul National University, Seoul 151-742, Korea.
- Research Center, BIFIDO Co., Ltd., Hongcheon 250-804, Korea.
| | - Hyun Ju You
- Department of Food and Nutrition, Research Institute of Human Ecology, Seoul National University, Seoul 151-742, Korea.
- Institute of Health and Environment, Graduate School of Public Health, Seoul National University, Seoul 151-742, Korea.
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22
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Zhang G, Gao B, Adeolu M, Khadka B, Gupta RS. Phylogenomic Analyses and Comparative Studies on Genomes of the Bifidobacteriales: Identification of Molecular Signatures Specific for the Order Bifidobacteriales and Its Different Subclades. Front Microbiol 2016; 7:978. [PMID: 27446019 PMCID: PMC4921777 DOI: 10.3389/fmicb.2016.00978] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/07/2016] [Indexed: 11/24/2022] Open
Abstract
The order Bifidobacteriales comprises a diverse variety of species found in the gastrointestinal tract of humans and other animals, some of which are opportunistic pathogens, whereas a number of others exhibit health-promoting effects. However, currently very few biochemical or molecular characteristics are known which are specific for the order Bifidobacteriales, or specific clades within this order, which distinguish them from other bacteria. This study reports the results of detailed comparative genomic and phylogenetic studies on 62 genome-sequenced species/strains from the order Bifidobacteriales. In a robust phylogenetic tree for the Bifidobacteriales constructed based on 614 core proteins, a number of well-resolved clades were observed including a clade separating the Scarodvia-related genera (Scardovia clade) from the genera Bifidobacterium and Gardnerella, as well as a number of previously reported clusters of Bifidobacterium spp. In parallel, our comparative analyses of protein sequences from the Bifidobacteriales genomes have identified numerous molecular markers that are specific for this group of bacteria. Of these markers, 32 conserved signature indels (CSIs) in widely distributed proteins and 10 signature proteins are distinctive characteristics of all sequenced Bifidobacteriales species and provide novel and highly specific means for distinguishing these bacteria. In addition, multiple other molecular signatures are specific for the following clades of Bifidobacteriales: (i) 5 CSIs specific for a clade comprising of the Scardovia-related genera; (ii) 3 CSIs and 2 CSPs specific for a clade consisting of the Bifidobacterium and Gardnerella spp.; (iii) multiple other signatures demarcating a number of clusters of the B. asteroides-and B. longum- related species. The described molecular markers provide novel and reliable means for distinguishing the Bifidobacteriales and a number of their clades in molecular terms and for the classification of these bacteria. The Bifidobacteriales-specific CSIs, found in important proteins, are predicted to play important roles in modifying the cellular functions of the affected proteins. Hence, biochemical studies on the cellular functions of these CSIs could lead to discovery of novel characteristics of either all Bifidobacteriales, or specific groups of bacteria within this order. Some of the functions affected/modified by these genetic changes could also be important for the probiotic/pathogenic activities of the bifidobacteria.
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Affiliation(s)
- Grace Zhang
- Department of Biochemistry and Biomedical Sciences, McMaster University Hamilton, ON, Canada
| | - Beile Gao
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou, China
| | - Mobolaji Adeolu
- Department of Biochemistry and Biomedical Sciences, McMaster University Hamilton, ON, Canada
| | - Bijendra Khadka
- Department of Biochemistry and Biomedical Sciences, McMaster University Hamilton, ON, Canada
| | - Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University Hamilton, ON, Canada
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23
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Barka EA, Vatsa P, Sanchez L, Gaveau-Vaillant N, Jacquard C, Meier-Kolthoff JP, Klenk HP, Clément C, Ouhdouch Y, van Wezel GP. Taxonomy, Physiology, and Natural Products of Actinobacteria. Microbiol Mol Biol Rev 2016; 80:1-43. [PMID: 26609051 PMCID: PMC4711186 DOI: 10.1128/mmbr.00019-15] [Citation(s) in RCA: 1008] [Impact Index Per Article: 112.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Actinobacteria are Gram-positive bacteria with high G+C DNA content that constitute one of the largest bacterial phyla, and they are ubiquitously distributed in both aquatic and terrestrial ecosystems. Many Actinobacteria have a mycelial lifestyle and undergo complex morphological differentiation. They also have an extensive secondary metabolism and produce about two-thirds of all naturally derived antibiotics in current clinical use, as well as many anticancer, anthelmintic, and antifungal compounds. Consequently, these bacteria are of major importance for biotechnology, medicine, and agriculture. Actinobacteria play diverse roles in their associations with various higher organisms, since their members have adopted different lifestyles, and the phylum includes pathogens (notably, species of Corynebacterium, Mycobacterium, Nocardia, Propionibacterium, and Tropheryma), soil inhabitants (e.g., Micromonospora and Streptomyces species), plant commensals (e.g., Frankia spp.), and gastrointestinal commensals (Bifidobacterium spp.). Actinobacteria also play an important role as symbionts and as pathogens in plant-associated microbial communities. This review presents an update on the biology of this important bacterial phylum.
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Affiliation(s)
- Essaid Ait Barka
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UFR Sciences, UPRES EA 4707, Université de Reims Champagne-Ardenne, Reims, France
| | - Parul Vatsa
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UFR Sciences, UPRES EA 4707, Université de Reims Champagne-Ardenne, Reims, France
| | - Lisa Sanchez
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UFR Sciences, UPRES EA 4707, Université de Reims Champagne-Ardenne, Reims, France
| | - Nathalie Gaveau-Vaillant
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UFR Sciences, UPRES EA 4707, Université de Reims Champagne-Ardenne, Reims, France
| | - Cedric Jacquard
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UFR Sciences, UPRES EA 4707, Université de Reims Champagne-Ardenne, Reims, France
| | | | - Hans-Peter Klenk
- School of Biology, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Christophe Clément
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UFR Sciences, UPRES EA 4707, Université de Reims Champagne-Ardenne, Reims, France
| | - Yder Ouhdouch
- Faculté de Sciences Semlalia, Université Cadi Ayyad, Laboratoire de Biologie et de Biotechnologie des Microorganismes, Marrakesh, Morocco
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Sylvius Laboratories, Leiden University, Leiden, The Netherlands
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Khoroshkin MS, Leyn SA, Van Sinderen D, Rodionov DA. Transcriptional Regulation of Carbohydrate Utilization Pathways in the Bifidobacterium Genus. Front Microbiol 2016; 7:120. [PMID: 26903998 PMCID: PMC4746261 DOI: 10.3389/fmicb.2016.00120] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 01/22/2016] [Indexed: 12/21/2022] Open
Abstract
Bifidobacteria, which represent common commensals of mammalian gut, are believed to have positive effects on human health. The influence of certain non-digestible carbohydrates (and their use as so-called prebiotics) on growth and metabolic activity of bifidobacteria is of increasing interest; however, mechanisms of transcriptional control of carbohydrate metabolism are poorly understood in these species. We used a comparative genomics approach to reconstruct carbohydrate utilization pathways and transcriptional regulons in 10 Bifidobacterium genomes. Analysis of regulatory gene regions revealed candidate DNA motifs and reconstructed regulons for 268 transcription factors from the LacI, ROK, DeoR, AraC, GntR, and TetR families that form 64 orthologous groups of regulators. Most of the reconstructed regulons are local and control specific catabolic pathways for host- and diet-derived glycans and monosaccharides. Mosaic distributions of many of these local regulators across Bifidobacterium species correlate with distribution of corresponding catabolic pathways. In contrast, the maltose, galactose, sucrose, and fructose regulons, as well as a novel global LacI-family regulator that is predicted to control the central carbohydrate metabolism and arabinose catabolism genes, are universally present in all 10 studied bifidobacteria. A novel group of TetR-family regulators presumably controls the glucoside and galactoside utilization pathways. Paralogs of the ribose repressor RbsR control the pyrimidine nucleoside utilization genes. Multiple paralogs of the maltose regulator MalR co-regulate large sets of genes involved in maltodextrin utilization. The inferred metabolic regulons provide new insights on diverse carbohydrate utilization networks in bifidobacteria that can be employed in metabolic modeling, phenotype prediction and the rational development of novel prebiotics.
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Affiliation(s)
- Matvei S Khoroshkin
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences Moscow, Russia
| | - Semen A Leyn
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences Moscow, Russia
| | - Douwe Van Sinderen
- School of Microbiology and Alimentary Pharmabiotic Centre Microbiome Institute, University College Cork Cork, Ireland
| | - Dmitry A Rodionov
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of SciencesMoscow, Russia; Sanford Burnham Prebys Medical Discovery InstituteLa Jolla, CA, USA
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Thakur K, Tomar SK, De S. Lactic acid bacteria as a cell factory for riboflavin production. Microb Biotechnol 2015; 9:441-51. [PMID: 26686515 PMCID: PMC4919986 DOI: 10.1111/1751-7915.12335] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 09/29/2015] [Accepted: 10/12/2015] [Indexed: 11/30/2022] Open
Abstract
Consumers are increasingly becoming aware of their health and nutritional requirements, and in this context, vitamins produced in situ by microbes may suit their needs and expectations. B groups vitamins are essential components of cellular metabolism and among them riboflavin is one of the vital vitamins required by bacteria, plants, animals and humans. Here, we focus on the importance of microbial production of riboflavin over chemical synthesis. In addition, genetic abilities for riboflavin biosynthesis by lactic acid bacteria are discussed. Genetically modified strains by employing genetic engineering and chemical analogues have been developed to enhance riboflavin production. The present review attempts to collect the currently available information on riboflavin production by microbes in general, while placing greater emphasis on food grade lactic acid bacteria and human gut commensals. For designing riboflavin‐enriched functional foods, proper selection and exploitation of riboflavin‐producing lactic acid bacteria is essential. Moreover, eliminating the in situ vitamin fortification step will decrease the cost of food production.
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Affiliation(s)
- Kiran Thakur
- Division of Dairy Microbiology, National Dairy Research Institute, Karnal, Haryana, India
| | - Sudhir Kumar Tomar
- Division of Dairy Microbiology, National Dairy Research Institute, Karnal, Haryana, India
| | - Sachinandan De
- Animal Biotechnology Centre, National Dairy Research Institute, Karnal, Haryana, India
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26
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Bifidobacteria exhibit social behavior through carbohydrate resource sharing in the gut. Sci Rep 2015; 5:15782. [PMID: 26506949 PMCID: PMC4623478 DOI: 10.1038/srep15782] [Citation(s) in RCA: 210] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 10/02/2015] [Indexed: 12/14/2022] Open
Abstract
Bifidobacteria are common and frequently dominant members of the gut microbiota of
many animals, including mammals and insects. Carbohydrates are considered key carbon
sources for the gut microbiota, imposing strong selective pressure on the complex
microbial consortium of the gut. Despite its importance, the genetic traits that
facilitate carbohydrate utilization by gut microbiota members are still poorly
characterized. Here, genome analyses of 47 representative Bifidobacterium
(sub)species revealed the genes predicted to be required for the degradation and
internalization of a wide range of carbohydrates, outnumbering those found in many
other gut microbiota members. The glycan-degrading abilities of bifidobacteria are
believed to reflect available carbon sources in the mammalian gut. Furthermore,
transcriptome profiling of bifidobacterial genomes supported the involvement of
various chromosomal loci in glycan metabolism. The widespread occurrence of
bifidobacterial saccharolytic features is in line with metagenomic and
metatranscriptomic datasets obtained from human adult/infant faecal samples, thereby
supporting the notion that bifidobacteria expand the human glycobiome. This study
also underscores the hypothesis of saccharidic resource sharing among bifidobacteria
through species-specific metabolic specialization and cross feeding, thereby forging
trophic relationships between members of the gut microbiota.
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27
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O'Callaghan A, Bottacini F, O'Connell Motherway M, van Sinderen D. Pangenome analysis of Bifidobacterium longum and site-directed mutagenesis through by-pass of restriction-modification systems. BMC Genomics 2015; 16:832. [PMID: 26489930 PMCID: PMC4618763 DOI: 10.1186/s12864-015-1968-4] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 09/30/2015] [Indexed: 12/16/2022] Open
Abstract
Background Bifidobacterial genome analysis has provided insights as to how these gut commensals adapt to and persist in the human GIT, while also revealing genetic diversity among members of a given bifidobacterial (sub)species. Bifidobacteria are notoriously recalcitrant to genetic modification, which prevents exploration of their genomic functions, including those that convey (human) health benefits. Methods PacBio SMRT sequencing was used to determine the whole genome seqeunces of two B. longum subsp. longum strains. The B. longum pan-genome was computed using PGAP v1.2 and the core B. longum phylogenetic tree was constructed using a maximum-likelihood based approach in PhyML v3.0. M.blmNCII was cloned in E. coli and an internal fragment if arfBarfB was cloned into pORI19 for insertion mutagenesis. Results In this study we present the complete genome sequences of two Bifidobacterium longum subsp. longum strains. Comparative analysis with thirty one publicly available B. longum genomes allowed the definition of the B. longum core and dispensable genomes. This analysis also highlighted differences in particular metabolic abilities between members of the B. longum subspecies infantis, longum and suis. Furthermore, phylogenetic analysis of the B. longum core genome indicated the existence of a novel subspecies. Methylome data, coupled to the analysis of restriction-modification systems, allowed us to substantially increase the genetic accessibility of B. longum subsp. longum NCIMB 8809 to a level that was shown to permit site-directed mutagenesis. Conclusions Comparative genomic analysis of thirty three B. longum representatives revealed a closed pan-genome for this bifidobacterial species. Phylogenetic analysis of the B. longum core genome also provides evidence for a novel fifth B. longum subspecies. Finally, we improved genetic accessibility for the strain B. longum subsp. longum NCIMB 8809, which allowed the generation of a mutant of this strain. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1968-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- A O'Callaghan
- APC Microbiome Institute & School of Microbiology, University College Cork, Western Road, Cork, Ireland.
| | - F Bottacini
- APC Microbiome Institute & School of Microbiology, University College Cork, Western Road, Cork, Ireland.
| | - M O'Connell Motherway
- APC Microbiome Institute & School of Microbiology, University College Cork, Western Road, Cork, Ireland.
| | - D van Sinderen
- APC Microbiome Institute & School of Microbiology, University College Cork, Western Road, Cork, Ireland.
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Duranti S, Milani C, Lugli GA, Turroni F, Mancabelli L, Sanchez B, Ferrario C, Viappiani A, Mangifesta M, Mancino W, Gueimonde M, Margolles A, van Sinderen D, Ventura M. Insights from genomes of representatives of the human gut commensal Bifidobacterium bifidum. Environ Microbiol 2015; 17:2515-31. [PMID: 25523018 DOI: 10.1111/1462-2920.12743] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 11/25/2014] [Accepted: 12/03/2014] [Indexed: 11/27/2022]
Abstract
Bifidobacteria are bacterial gut commensals of mammals, birds and social insects that are perceived to influence the metabolism/physiology of their host. In this context, members of the Bifidobacterium bifidum species are believed to significantly contribute to the overall microbiota of the human gut at infant stage. However, the molecular reasons for their adaptation to this environment are poorly understood. In this study, we analysed the pan-genome of B. bifidum species by decoding genomes of 15 B. bifidum strains, which highlighted the existence of a conserved gene uniquely present in this bifidobacterial taxon, underscoring a nutrient acquisition strategy that targets host-derived glycans, such as those present in mucin. Growth experiments and corresponding transcriptomic analyses confirmed the in silico data and supported these intriguing and unique host glycan-specific saccharolytic features. The ubiquity of the genetic features of B. bifidum for the breakdown of host glycans was confirmed by interrogating metagenomic datasets, thereby supporting the notion that metabolic access to host-derived glycans is a potent evolutionary force that has shaped B. bifidum genomes and consequently the ecology of the infant intestinal microbiota.
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Affiliation(s)
- Sabrina Duranti
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Francesca Turroni
- Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Borja Sanchez
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, Consejo Superior de Investigaciones Científicas, CSIC, Villaviciosa, Asturias, Spain
| | - Chiara Ferrario
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Alice Viappiani
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Marta Mangifesta
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Walter Mancino
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Miguel Gueimonde
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, Consejo Superior de Investigaciones Científicas, CSIC, Villaviciosa, Asturias, Spain
| | - Abelardo Margolles
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, Consejo Superior de Investigaciones Científicas, CSIC, Villaviciosa, Asturias, Spain
| | - Douwe van Sinderen
- Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
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Comparative genomic analysis of 45 type strains of the genus Bifidobacterium: a snapshot of its genetic diversity and evolution. PLoS One 2015; 10:e0117912. [PMID: 25658111 PMCID: PMC4319941 DOI: 10.1371/journal.pone.0117912] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Accepted: 12/30/2014] [Indexed: 01/08/2023] Open
Abstract
Bifidobacteria are well known for their human health-promoting effects and are therefore widely applied in the food industry. Members of the Bifidobacterium genus were first identified from the human gastrointestinal tract and were then found to be widely distributed across various ecological niches. Although the genetic diversity of Bifidobacterium has been determined based on several marker genes or a few genomes, the global diversity and evolution scenario for the entire genus remain unresolved. The present study comparatively analyzed the genomes of 45 type strains. We built a robust genealogy for Bifidobacterium based on 402 core genes and defined its root according to the phylogeny of the tree of bacteria. Our results support that all human isolates are of younger lineages, and although species isolated from bees dominate the more ancient lineages, the bee was not necessarily the original host for bifidobacteria. Moreover, the species isolated from different hosts are enriched with specific gene sets, suggesting host-specific adaptation. Notably, bee-specific genes are strongly associated with respiratory metabolism and are potential in helping those bacteria adapt to the oxygen-rich gut environment in bees. This study provides a snapshot of the genetic diversity and evolution of Bifidobacterium, paving the way for future studies on the taxonomy and functional genomics of the genus.
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30
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Abstract
OBJECTIVES The benefits of human milk for preterm infants are mainly the result of its nutritional characteristics and the presence of biologically active compounds. Among these compounds, glycosaminoglycans (GAGs) play an emerging leading role. When mother's milk is unavailable or in short supply, pasteurised donor milk represents an important nutritional alternative. The aim of this study was to evaluate the effect of Holder pasteurisation on the concentration of different GAGs in preterm human milk. METHODS Milk samples collected from 9 mothers having delivered preterm were divided into 2 parts. One part of each sample was immediately frozen (-80°C), whereas the other part was pasteurised with the Holder method before being frozen at -80°C. Specific analytical procedures were applied to evaluate the amount, composition, and structure of main human milk GAGs. RESULTS No significative differences were measured between not-treated and pasteurised samples for total GAGs content, relative percentages of chondroitin sulfate and heparan sulfate, and main parameters related to galactosaminoglycans structure, even if a slight decrease of total GAGs content of ∼18% was observed in treated samples. CONCLUSIONS Our results indicate that the Holder pasteurisation does not significatively affect the concentration of the main human milk GAGs.
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31
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Egan M, O'Connell Motherway M, van Sinderen D. A GntR-type transcriptional repressor controls sialic acid utilization in Bifidobacterium breve UCC2003. FEMS Microbiol Lett 2014; 362:fnu056. [PMID: 25688064 DOI: 10.1093/femsle/fnu056] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Bifidobacterium breve strains are numerically prevalent among the gut microbiota of healthy, breast-fed infants. The metabolism of sialic acid, a ubiquitous monosaccharide in the infant and adult gut, by B. breve UCC2003 is dependent on a large gene cluster, designated the nan/nag cluster. This study describes the transcriptional regulation of the nan/nag cluster and thus sialic acid metabolism in B. breve UCC2003. Insertion mutagenesis and transcriptome analysis revealed that the nan/nag cluster is regulated by a GntR family transcriptional repressor, designated NanR. Crude cell extract of Escherichia coli EC101 in which the nanR gene had been cloned and overexpressed was shown to bind to two promoter regions within this cluster, each of which containing an imperfect inverted repeat that is believed to act as the NanR operator sequence. Formation of the DNA-NanR complex is prevented in the presence of sialic acid, which we had previously shown to induce transcription of this gene cluster.
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Affiliation(s)
- Muireann Egan
- School of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Western Road, Cork, Ireland
| | - Mary O'Connell Motherway
- School of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Western Road, Cork, Ireland
| | - Douwe van Sinderen
- School of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Western Road, Cork, Ireland
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32
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Egan M, Motherway MO, Kilcoyne M, Kane M, Joshi L, Ventura M, van Sinderen D. Cross-feeding by Bifidobacterium breve UCC2003 during co-cultivation with Bifidobacterium bifidum PRL2010 in a mucin-based medium. BMC Microbiol 2014; 14:282. [PMID: 25420416 PMCID: PMC4252021 DOI: 10.1186/s12866-014-0282-7] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 11/03/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bifidobacteria constitute a specific group of commensal bacteria that commonly inhabit the mammalian gastrointestinal tract. Bifidobacterium breve UCC2003 was previously shown to utilize a variety of plant/diet/host-derived carbohydrates, including cellodextrin, starch and galactan, as well as the mucin and HMO-derived monosaccharide, sialic acid. In the current study, we investigated the ability of this strain to utilize parts of a host-derived source of carbohydrate, namely the mucin glycoprotein, when grown in co-culture with the mucin-degrading Bifidobacterium bifidum PRL2010. RESULTS B. breve UCC2003 was shown to exhibit growth properties in a mucin-based medium, but only when grown in the presence of B. bifidum PRL2010, which is known to metabolize mucin. A combination of HPAEC-PAD and transcriptome analyses identified some of the possible monosaccharides and oligosaccharides which support this enhanced co-cultivation growth/viability phenotype. CONCLUSION This study describes the potential existence of a gut commensal relationship between two bifidobacterial species. We demonstrate the in vitro ability of B. breve UCC2003 to cross-feed on sugars released by the mucin-degrading activity of B. bifidum PRL2010, thus advancing our knowledge on the metabolic adaptability which allows the former strain to colonize the (infant) gut by its extensive metabolic abilities to (co-)utilize available carbohydrate sources.
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Affiliation(s)
- Muireann Egan
- School of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland.
| | - Mary O'Connell Motherway
- School of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland.
| | - Michelle Kilcoyne
- Glycoscience Group, National Centre for Biomedical Engineering Science, National University of Ireland, Galway, Ireland.
- Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland.
| | - Marian Kane
- Glycoscience Group, National Centre for Biomedical Engineering Science, National University of Ireland, Galway, Ireland.
| | - Lokesh Joshi
- Glycoscience Group, National Centre for Biomedical Engineering Science, National University of Ireland, Galway, Ireland.
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy.
| | - Douwe van Sinderen
- School of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland.
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Turroni F, Duranti S, Bottacini F, Guglielmetti S, Van Sinderen D, Ventura M. Bifidobacterium bifidum as an example of a specialized human gut commensal. Front Microbiol 2014; 5:437. [PMID: 25191315 PMCID: PMC4140077 DOI: 10.3389/fmicb.2014.00437] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 08/01/2014] [Indexed: 12/12/2022] Open
Abstract
Bifidobacteria are considered dominant and for this reason key members of the human gut microbiota, particularly during the first one to two years following birth. A substantial proportion of the bifidobacterial population in the intestine of infants belong to the Bifidobacterium bifidum taxon, whose members have been shown to display remarkable physiological and genetic features involving adhesion to epithelia, as well as utilization of host-derived glycans. Here, we reviewed the current knowledge on the genetic features and associated adaptations of B. bifidum to the human gut.
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Affiliation(s)
- Francesca Turroni
- Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland Cork, Ireland
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma Parma, Italy
| | - Francesca Bottacini
- Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland Cork, Ireland
| | - Simone Guglielmetti
- Department of Food, Environmental and Nutritional Sciences, University of Milan Milan, Italy
| | - Douwe Van Sinderen
- Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma Parma, Italy
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Werning ML, Pérez-Ramos A, Fernández de Palencia P, Mohedano ML, Dueñas MT, Prieto A, López P. A specific immunological method to detect and quantify bacterial 2-substituted (1,3)-β-D-glucan. Carbohydr Polym 2014; 113:39-45. [PMID: 25256456 DOI: 10.1016/j.carbpol.2014.06.072] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 06/25/2014] [Accepted: 06/27/2014] [Indexed: 10/25/2022]
Abstract
Exopolysaccharides synthesized by lactic acid bacteria have prebiotic properties and contribute to the rheology and texture of fermented foods. Here, we have standardized an immunological method for the specific detection of 2-substituted (1,3)-β-D-glucans. The method allows direct detection and quantification of this exopolysaccharide in culture supernatants containing other mono- and poly-saccharides. Moreover, it allows specific detection of the biomolecules synthesized in vitro in enzymatic reactions. Thus, this method allows the fast identification of producing bacteria, as well as biochemical characterization of the glycosyltransferases responsible for their synthesis.
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Affiliation(s)
- María Laura Werning
- Centro de Investigaciones Biológicas, C.S.I.C., Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Adrián Pérez-Ramos
- Centro de Investigaciones Biológicas, C.S.I.C., Ramiro de Maeztu 9, 28040 Madrid, Spain
| | | | - María Luz Mohedano
- Centro de Investigaciones Biológicas, C.S.I.C., Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - María Teresa Dueñas
- Departamento de Química Aplicada, Facultad de Ciencias Químicas, Box 1072, 20080 San Sebastian, Spain
| | - Alicia Prieto
- Centro de Investigaciones Biológicas, C.S.I.C., Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Paloma López
- Centro de Investigaciones Biológicas, C.S.I.C., Ramiro de Maeztu 9, 28040 Madrid, Spain.
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35
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Metabolism of sialic acid by Bifidobacterium breve UCC2003. Appl Environ Microbiol 2014; 80:4414-26. [PMID: 24814790 DOI: 10.1128/aem.01114-14] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Bifidobacteria constitute a specific group of commensal bacteria that inhabit the gastrointestinal tracts of humans and other mammals. Bifidobacterium breve UCC2003 has previously been shown to utilize several plant-derived carbohydrates that include cellodextrins, starch, and galactan. In the present study, we investigated the ability of this strain to utilize the mucin- and human milk oligosaccharide (HMO)-derived carbohydrate sialic acid. Using a combination of transcriptomic and functional genomic approaches, we identified a gene cluster dedicated to the uptake and metabolism of sialic acid. Furthermore, we demonstrate that B. breve UCC2003 can cross feed on sialic acid derived from the metabolism of 3'-sialyllactose, an abundant HMO, by another infant gut bifidobacterial strain, Bifidobacterium bifidum PRL2010.
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36
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Ventura M, Turroni F, Lugli GA, van Sinderen D. Bifidobacteria and humans: our special friends, from ecological to genomics perspectives. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2014; 94:163-168. [PMID: 23963950 DOI: 10.1002/jsfa.6356] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 08/02/2013] [Accepted: 08/20/2013] [Indexed: 06/02/2023]
Abstract
Bifidobacteria are widely used as health-promoting microorganisms in many functional foods. However, the molecular mechanisms as to how these bacteria positively impact on host health are far from completely understood. For this reason these bacteria constitute a growing area of scientific interest with respect to their genomics, molecular biology and genetics. Genome sequencing of an increasing number of strains of bifidobacteria has provided access to the complete genetic make-up of many representative members of these bacteria. The aim of this review is to highlight the genetic and functional features of bifidobacteria residing in the human gastrointestinal tract using genomic and ecology-based information.
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Affiliation(s)
- Marco Ventura
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy
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The quest for a unified view of bacterial land colonization. ISME JOURNAL 2014; 8:1358-69. [PMID: 24451209 PMCID: PMC4069389 DOI: 10.1038/ismej.2013.247] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 11/15/2013] [Accepted: 12/12/2013] [Indexed: 12/13/2022]
Abstract
Exploring molecular mechanisms underlying bacterial water-to-land transition represents a critical start toward a better understanding of the functioning and stability of the terrestrial ecosystems. Here, we perform comprehensive analyses based on a large variety of bacteria by integrating taxonomic, phylogenetic and metagenomic data, in the quest for a unified view that elucidates genomic, evolutionary and ecological dynamics of the marine progenitors in adapting to nonaquatic environments. We hypothesize that bacterial land colonization is dominated by a single-gene sweep, that is, the emergence of dnaE2 derived from an early duplication event of the primordial dnaE, followed by a series of niche-specific genomic adaptations, including GC content increase, intensive horizontal gene transfer and constant genome expansion. In addition, early bacterial radiation may be stimulated by an explosion of land-borne hosts (for example, plants and animals) after initial land colonization events.
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Turroni F, Ventura M, Buttó LF, Duranti S, O’Toole PW, Motherway MO, van Sinderen D. Molecular dialogue between the human gut microbiota and the host: a Lactobacillus and Bifidobacterium perspective. Cell Mol Life Sci 2014; 71:183-203. [PMID: 23516017 PMCID: PMC11113728 DOI: 10.1007/s00018-013-1318-0] [Citation(s) in RCA: 228] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 02/13/2013] [Accepted: 03/04/2013] [Indexed: 02/06/2023]
Abstract
The human gut represents a highly complex ecosystem, which is densely colonized by a myriad of microorganisms that influence the physiology, immune function and health status of the host. Among the many members of the human gut microbiota, there are microorganisms that have co-evolved with their host and that are believed to exert health-promoting or probiotic effects. Probiotic bacteria isolated from the gut and other environments are commercially exploited, and although there is a growing list of health benefits provided by the consumption of such probiotics, their precise mechanisms of action have essentially remained elusive. Genomics approaches have provided exciting new opportunities for the identification of probiotic effector molecules that elicit specific responses to influence the physiology and immune function of their human host. In this review, we describe the current understanding of the intriguing relationships that exist between the human gut and key members of the gut microbiota such as bifidobacteria and lactobacilli, discussed here as prototypical groups of probiotic microorganisms.
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Affiliation(s)
- Francesca Turroni
- Alimentary Pharmabiotic Centre, Department of Microbiology Biosciences Institute, University College Cork, National University of Ireland, Western Road, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Genetics, Biology of Microorganisms, Anthropology and Evolution, University of Parma, Parma, Italy
| | - Ludovica F. Buttó
- Alimentary Pharmabiotic Centre, Department of Microbiology Biosciences Institute, University College Cork, National University of Ireland, Western Road, Cork, Ireland
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Genetics, Biology of Microorganisms, Anthropology and Evolution, University of Parma, Parma, Italy
| | - Paul W. O’Toole
- Alimentary Pharmabiotic Centre, Department of Microbiology Biosciences Institute, University College Cork, National University of Ireland, Western Road, Cork, Ireland
| | - Mary O’Connell Motherway
- Alimentary Pharmabiotic Centre, Department of Microbiology Biosciences Institute, University College Cork, National University of Ireland, Western Road, Cork, Ireland
| | - Douwe van Sinderen
- Alimentary Pharmabiotic Centre, Department of Microbiology Biosciences Institute, University College Cork, National University of Ireland, Western Road, Cork, Ireland
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39
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Bifidobacterium bifidum PRL2010 modulates the host innate immune response. Appl Environ Microbiol 2013; 80:730-40. [PMID: 24242237 DOI: 10.1128/aem.03313-13] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Here, we describe data obtained from transcriptome profiling of human cell lines and intestinal cells of a murine model upon exposure and colonization, respectively, with Bifidobacterium bifidum PRL2010. Significant changes were detected in the transcription of genes that are known to be involved in innate immunity. Furthermore, results from enzyme-linked immunosorbent assays (ELISAs) showed that exposure to B. bifidum PRL2010 causes enhanced production of interleukin 6 (IL-6) and IL-8 cytokines, presumably through NF-κB activation. The obtained global transcription profiles strongly suggest that Bifidobacterium bifidum PRL2010 modulates the innate immune response of the host.
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40
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Comparative genomics of Bifidobacterium animalis subsp. lactis reveals a strict monophyletic bifidobacterial taxon. Appl Environ Microbiol 2013; 79:4304-15. [PMID: 23645200 DOI: 10.1128/aem.00984-13] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Strains of Bifidobacterium animalis subsp. lactis are extensively exploited by the food industry as health-promoting bacteria, although the genetic variability of members belonging to this taxon has so far not received much scientific attention. In this article, we describe the complete genetic makeup of the B. animalis subsp. lactis Bl12 genome and discuss the genetic relatedness of this strain with other sequenced strains belonging to this taxon. Moreover, a detailed comparative genomic analysis of B. animalis subsp. lactis genomes was performed, which revealed a closely related and isogenic nature of all currently available B. animalis subsp. lactis strains, thus strongly suggesting a closed pan-genome structure of this bacterial group.
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41
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Coppa GV, Gabrielli O, Zampini L, Bertino E, Volpi N. Human milk glycosaminoglycans as possible bioactive substances for the breastfed newborn. Breastfeed Med 2013; 8:227. [PMID: 23249131 DOI: 10.1089/bfm.2012.0052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Giovanni V. Coppa
- Department of Clinical Sciences, Polytechnic University of the Marche, Ancona, Italy
| | - Orazio Gabrielli
- Department of Clinical Sciences, Polytechnic University of the Marche, Ancona, Italy
| | - Lucia Zampini
- Department of Clinical Sciences, Polytechnic University of the Marche, Ancona, Italy
| | - Enrico Bertino
- Neonatal Intensive Care Unit, Department of Pediatrics, University of Turin, Turin, Italy
| | - Nicola Volpi
- Department of Life Sciences, University of Modena & Reggio Emilia, Modena, Italy
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42
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Lewis ZT, Bokulich NA, Kalanetra KM, Ruiz-Moyano S, Underwood MA, Mills DA. Use of bifidobacterial specific terminal restriction fragment length polymorphisms to complement next generation sequence profiling of infant gut communities. Anaerobe 2013; 19:62-9. [PMID: 23261904 PMCID: PMC4764513 DOI: 10.1016/j.anaerobe.2012.12.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 12/05/2012] [Indexed: 02/06/2023]
Abstract
Bifidobacteria are intestinal anaerobes often associated with gut health. Specific bifidobacterial species are particularly common in the gastrointestinal tract of breast-fed infants. Current short read next-generation sequencing approaches to profile fecal microbial ecologies do not discriminate bifidobacteria to the species level. Here we describe a low-cost terminal restriction fragment length polymorphism (TRFLP) procedure to distinguish between the common infant-associated bifidobacterial species. An empirical database of TRF sizes was created from both common reference strains and well-identified isolates from infant feces. Species-specific quantitative PCR validated bifidobacterial-specific TRFLP profiles from infant feces. These results indicate that bifidobacterial-specific TRFLP is a useful method to monitor intestinal bifidobacterial populations from infant fecal samples. When used alongside next generation sequencing methods that detect broader population levels at lower resolution, this high-throughput, low-cost tool can help clarify the role of bifidobacteria in health and disease.
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Affiliation(s)
- Zachery T Lewis
- Department of Viticulture and Enology, University of California, Davis, CA 95616, USA
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43
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Coppa GV, Gabrielli O, Bertino E, Zampini L, Galeazzi T, Padella L, Santoro L, Marchesiello RL, Galeotti F, Maccari F, Volpi N. Human milk glycosaminoglycans: the state of the art and future perspectives. Ital J Pediatr 2013; 39:2. [PMID: 23321150 PMCID: PMC3564826 DOI: 10.1186/1824-7288-39-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 01/10/2013] [Indexed: 11/12/2022] Open
Abstract
Recently, a complete characterization and detailed evaluation of the glycosaminoglycans of human milk were performed. The total glycosaminoglycans content in milk from healthy mothers having delivered term or preterm newborns showed a constant pattern which was essentially composed of two main polysaccharides: chondroitin sulfate (60-70%) and heparin (30-40%). Moreover, considerable variations of glycosaminoglycans concentration were found during the first month of lactation, the highest values being present in colostrum compared to mature milk. Metabolism and potential biological functions of human milk glycosaminoglycans are hypothesized and future studies are encouraged.
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Affiliation(s)
- Giovanni Valentino Coppa
- Pediatric Division, Department of Clinical Sciences, Polytechnic University of Marche, Ospedali Riuniti, Presidio Salesi, Via Toti 4, Ancona, 60121, Italy.
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44
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Bifidobacterial succession and correlation networks in a large unselected cohort of mothers and their children. Appl Environ Microbiol 2012; 79:497-507. [PMID: 23124244 DOI: 10.1128/aem.02359-12] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Bifidobacteria are a major microbial component of infant gut microbiota, which is believed to promote health benefits for the host and stimulate maturation of the immune system. Despite their perceived importance, very little is known about the natural development of and possible correlations between bifidobacteria in human populations. To address this knowledge gap, we analyzed stool samples from a randomly selected healthy cohort of 87 infants and their mothers with >90% of vaginal delivery and nearly 100% breast-feeding at 4 months. Fecal material was sampled during pregnancy, at 3 and 10 days, at 4 months, and at 1 and 2 years after birth. Stool samples were predicted to be rich in the species Bifidobacterium adolescentis, B. bifidum, B. dentium, B. breve, and B. longum. Due to high variation, we did not identify a clear age-related structure at the individual level. Within the population as a whole, however, there were clear age-related successions. Negative correlations between the B. longum group and B. adolescentis were detected in adults and in 1- and 2-year-old children, whereas negative correlations between B. longum and B. breve were characteristic for newborns and 4-month-old infants. The highly structured age-related development of and correlation networks between bifidobacterial species during the first 2 years of life mirrors their different or competing nutritional requirements, which in turn may be associated with specific biological functions in the development of healthy gut.
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45
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Exploration of the genomic diversity and core genome of the Bifidobacterium adolescentis phylogenetic group by means of a polyphasic approach. Appl Environ Microbiol 2012; 79:336-46. [PMID: 23064340 DOI: 10.1128/aem.02467-12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the current work, we describe genome diversity and core genome sequences among representatives of three bifidobacterial species, i.e., Bifidobacterium adolescentis, Bifidobacterium catenulatum, and Bifidobacterium pseudocatenulatum, by employing a polyphasic approach involving analysis of 16S rRNA gene and 16S-23S internal transcribed spacer (ITS) sequences, pulsed-field gel electrophoresis (PFGE), and comparative genomic hybridization (CGH) assays.
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46
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LeBlanc JG, Milani C, de Giori GS, Sesma F, van Sinderen D, Ventura M. Bacteria as vitamin suppliers to their host: a gut microbiota perspective. Curr Opin Biotechnol 2012; 24:160-8. [PMID: 22940212 DOI: 10.1016/j.copbio.2012.08.005] [Citation(s) in RCA: 920] [Impact Index Per Article: 70.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 07/30/2012] [Accepted: 08/15/2012] [Indexed: 02/07/2023]
Abstract
Food-related lactic acid bacteria (LAB) as well as human gut commensals such as bifidobacteria can de novo synthesize and supply vitamins. This is important since humans lack the biosynthetic capacity for most vitamins and these must thus be provided exogenously. Although vitamins are present in a variety of foods, deficiencies still occur, mainly due to malnutrition as a result of insufficient food intake and because of poor eating habits. Fermented milks with high levels of B-group vitamins (such as folate and riboflavin) can be produced by LAB-promoted and possibly bifidobacteria-promoted biosynthesis. Moreover, certain strains of LAB produce the complex vitamin cobalamin (or vitamin B12). In this review, fermented foods with elevated levels of B-group vitamins produced by LAB used as starter cultures will be covered. In addition, genetic abilities for vitamin biosynthesis by selected human gut commensals will be discussed.
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Affiliation(s)
- Jean Guy LeBlanc
- Centro de Referencia para Lactobacilos (CERELA-CONICET) Chacabuco 145, (T4000ILC) Tucumán, Argentina
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47
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A two-component regulatory system controls autoregulated serpin expression in Bifidobacterium breve UCC2003. Appl Environ Microbiol 2012; 78:7032-41. [PMID: 22843530 DOI: 10.1128/aem.01776-12] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
This work reports on the identification and molecular characterization of a two-component regulatory system (2CRS), encoded by serRK, which is believed to control the expression of the ser(2003) locus in Bifidobacterium breve UCC2003. The ser(2003) locus consists of two genes, Bbr_1319 (sagA) and Bbr_1320 (serU), which are predicted to encode a hypothetical membrane-associated protein and a serpin-like protein, respectively. The response regulator SerR was shown to bind to the promoter region of ser(2003), and the probable recognition sequence of SerR was determined by a combinatorial approach of in vitro site-directed mutagenesis coupled to transcriptional fusion and electrophoretic mobility shift assays (EMSAs). The importance of the serRK 2CRS in the response of B. breve to protease-mediated induction was confirmed by generating a B. breve serR insertion mutant, which was shown to exhibit altered ser(2003) transcriptional induction patterns compared to the parent strain, UCC2003. Interestingly, the analysis of a B. breve serU mutant revealed that the SerRK signaling pathway appears to include a SerU-dependent autoregulatory loop.
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48
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Analysis of predicted carbohydrate transport systems encoded by Bifidobacterium bifidum PRL2010. Appl Environ Microbiol 2012; 78:5002-12. [PMID: 22562993 DOI: 10.1128/aem.00629-12] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Bifidobacterium bifidum PRL2010 genome encodes a relatively small set of predicted carbohydrate transporters. Growth experiments and transcriptome analyses of B. bifidum PRL2010 revealed that carbohydrate utilization in this microorganism appears to be restricted to a relatively low number of carbohydrates.
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49
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Ott L, McKenzie A, Baltazar MT, Britting S, Bischof A, Burkovski A, Hoskisson PA. Evaluation of invertebrate infection models for pathogenic corynebacteria. ACTA ACUST UNITED AC 2012; 65:413-21. [PMID: 22443092 DOI: 10.1111/j.1574-695x.2012.00963.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 03/08/2012] [Accepted: 03/09/2012] [Indexed: 02/02/2023]
Abstract
For several pathogenic bacteria, model systems for host-pathogen interactions were developed, which provide the possibility of quick and cost-effective high throughput screening of mutant bacteria for genes involved in pathogenesis. A number of different model systems, including amoeba, nematodes, insects, and fish, have been introduced, and it was observed that different bacteria respond in different ways to putative surrogate hosts, and distinct model systems might be more or less suitable for a certain pathogen. The aim of this study was to develop a suitable invertebrate model for the human and animal pathogens Corynebacterium diphtheriae, Corynebacterium pseudotuberculosis, and Corynebacterium ulcerans. The results obtained in this study indicate that Acanthamoeba polyphaga is not optimal as surrogate host, while both Caenorhabtitis elegans and Galleria larvae seem to offer tractable models for rapid assessment of virulence between strains. Caenorhabtitis elegans gives more differentiated results and might be the best model system for pathogenic corynebacteria, given the tractability of bacteria and the range of mutant nematodes available to investigate the host response in combination with bacterial virulence. Nevertheless, Galleria will also be useful in respect to innate immune responses to pathogens because insects offer a more complex cell-based innate immune system compared with the simple innate immune system of C. elegans.
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Affiliation(s)
- Lisa Ott
- Lehrstuhl für Mikrobiologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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50
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Gao B, Gupta RS. Phylogenetic framework and molecular signatures for the main clades of the phylum Actinobacteria. Microbiol Mol Biol Rev 2012; 76:66-112. [PMID: 22390973 PMCID: PMC3294427 DOI: 10.1128/mmbr.05011-11] [Citation(s) in RCA: 168] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The phylum Actinobacteria harbors many important human pathogens and also provides one of the richest sources of natural products, including numerous antibiotics and other compounds of biotechnological interest. Thus, a reliable phylogeny of this large phylum and the means to accurately identify its different constituent groups are of much interest. Detailed phylogenetic and comparative analyses of >150 actinobacterial genomes reported here form the basis for achieving these objectives. In phylogenetic trees based upon 35 conserved proteins, most of the main groups of Actinobacteria as well as a number of their superageneric clades are resolved. We also describe large numbers of molecular markers consisting of conserved signature indels in protein sequences and whole proteins that are specific for either all Actinobacteria or their different clades (viz., orders, families, genera, and subgenera) at various taxonomic levels. These signatures independently support the existence of different phylogenetic clades, and based upon them, it is now possible to delimit the phylum Actinobacteria (excluding Coriobacteriia) and most of its major groups in clear molecular terms. The species distribution patterns of these markers also provide important information regarding the interrelationships among different main orders of Actinobacteria. The identified molecular markers, in addition to enabling the development of a stable and reliable phylogenetic framework for this phylum, also provide novel and powerful means for the identification of different groups of Actinobacteria in diverse environments. Genetic and biochemical studies on these Actinobacteria-specific markers should lead to the discovery of novel biochemical and/or other properties that are unique to different groups of Actinobacteria.
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Affiliation(s)
- Beile Gao
- Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, Ontario, Canada
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