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Jiang CS, Li CY, Gu CT. Bifidobacterium apis sp. nov., isolated from the gut of honeybee ( Apis mellifera). Int J Syst Evol Microbiol 2024; 74. [PMID: 38661726 DOI: 10.1099/ijsem.0.006358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024] Open
Abstract
A novel bifidobacterium (designated F753-1T) was isolated from the gut of honeybee (Apis mellifera). Strain F753-1T was characterized using a polyphasic taxonomic approach. Strain F753-1T was phylogenetically related to the type strains of Bifidobacterium mizhiensis, Bifidobacterium asteroides, Bifidobacterium choladohabitans, Bifidobacterium mellis, Bifidobacterium apousia and Bifidobacterium polysaccharolyticum, having 98.4-99.8 % 16S rRNA gene sequence similarities. The phylogenomic tree indicated that strain F753-1T was most closely related to the type strains of B. mellis and B. choladohabitans. Strain F753-1T had the highest average nucleotide identity (94.1-94.5 %) and digital DNA-DNA hybridization (56.3 %) values with B. mellis Bin7NT. Acid production from amygdalin, d-fructose, gentiobiose, d-mannose, maltose, sucrose and d-xylose, activity of α-galactosidase, pyruvate utilization and hydrolysis of hippurate could differentiate strain F753-1T from B. mellis CCUG 66113T and B. choladohabitans JCM 34586T. Based upon the data obtained in the present study, a novel species, Bifidobacterium apis sp. nov., is proposed, and the type strain is F753-1T (=CCTCC AB 2023227T=JCM 36562T=LMG 33388T).
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Affiliation(s)
- Cheng-Shan Jiang
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, PR China
| | - Chun Yan Li
- College of Food Science, Northeast Agricultural University, Harbin 150030, PR China
| | - Chun Tao Gu
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, PR China
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2
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Laursen MF, Sakanaka M, von Burg N, Mörbe U, Andersen D, Moll JM, Pekmez CT, Rivollier A, Michaelsen KF, Mølgaard C, Lind MV, Dragsted LO, Katayama T, Frandsen HL, Vinggaard AM, Bahl MI, Brix S, Agace W, Licht TR, Roager HM. Bifidobacterium species associated with breastfeeding produce aromatic lactic acids in the infant gut. Nat Microbiol 2021; 6:1367-1382. [PMID: 34675385 PMCID: PMC8556157 DOI: 10.1038/s41564-021-00970-4] [Citation(s) in RCA: 152] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 08/26/2021] [Indexed: 12/12/2022]
Abstract
Breastfeeding profoundly shapes the infant gut microbiota, which is critical for early life immune development, and the gut microbiota can impact host physiology in various ways, such as through the production of metabolites. However, few breastmilk-dependent microbial metabolites mediating host-microbiota interactions are currently known. Here, we demonstrate that breastmilk-promoted Bifidobacterium species convert aromatic amino acids (tryptophan, phenylalanine and tyrosine) into their respective aromatic lactic acids (indolelactic acid, phenyllactic acid and 4-hydroxyphenyllactic acid) via a previously unrecognized aromatic lactate dehydrogenase (ALDH). The ability of Bifidobacterium species to convert aromatic amino acids to their lactic acid derivatives was confirmed using monocolonized mice. Longitudinal profiling of the faecal microbiota composition and metabolome of Danish infants (n = 25), from birth until 6 months of age, showed that faecal concentrations of aromatic lactic acids are correlated positively with the abundance of human milk oligosaccharide-degrading Bifidobacterium species containing the ALDH, including Bifidobacterium longum, B. breve and B. bifidum. We further demonstrate that faecal concentrations of Bifidobacterium-derived indolelactic acid are associated with the capacity of these samples to activate in vitro the aryl hydrocarbon receptor (AhR), a receptor important for controlling intestinal homoeostasis and immune responses. Finally, we show that indolelactic acid modulates ex vivo immune responses of human CD4+ T cells and monocytes in a dose-dependent manner by acting as an agonist of both the AhR and hydroxycarboxylic acid receptor 3 (HCA3). Our findings reveal that breastmilk-promoted Bifidobacterium species produce aromatic lactic acids in the gut of infants and suggest that these microbial metabolites may impact immune function in early life.
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Affiliation(s)
- Martin F Laursen
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Mikiyasu Sakanaka
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
- Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Ishikawa, Japan
| | - Nicole von Burg
- Mucosal Immunology Group, Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Urs Mörbe
- Mucosal Immunology Group, Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Daniel Andersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Janne Marie Moll
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Ceyda T Pekmez
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg C, Denmark
| | - Aymeric Rivollier
- Mucosal Immunology Group, Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Kim F Michaelsen
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg C, Denmark
| | - Christian Mølgaard
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg C, Denmark
| | - Mads Vendelbo Lind
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg C, Denmark
| | - Lars O Dragsted
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg C, Denmark
| | - Takane Katayama
- Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Ishikawa, Japan
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Henrik L Frandsen
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Martin I Bahl
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Susanne Brix
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - William Agace
- Mucosal Immunology Group, Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark
- Immunology Section, BMC D14, Department of Experimental Medicine, Lund University, Lund, Sweden
| | - Tine R Licht
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark.
| | - Henrik M Roager
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark.
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg C, Denmark.
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Xiao Y, Zhao J, Zhang H, Zhai Q, Chen W. Mining genome traits that determine the different gut colonization potential of Lactobacillus and Bifidobacterium species. Microb Genom 2021; 7:000581. [PMID: 34100697 PMCID: PMC8461469 DOI: 10.1099/mgen.0.000581] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 04/12/2021] [Indexed: 12/11/2022] Open
Abstract
Although the beneficial effects of probiotics are likely to be associated with their ability to colonize the gut, little is known about the characteristics of good colonizers. In a systematic analysis of the comparative genomics, we tried to elucidate the genomic contents that account for the distinct host adaptability patterns of Lactobacillus and Bifidobacterium species. The Bifidobacterium species, with species-level phylogenetic structures affected by recombination among strains, broad mucin-foraging activity, and dietary-fibre-degrading ability, represented niche conservatism and tended to be host-adapted. The Lactobacillus species stretched across three lifestyles, namely free-living, nomadic and host-adapted, as characterized by the variations of bacterial occurrence time, guanine-cytosine (GC) content and genome size, evolution event frequency, and the presence of human-adapted bacterial genes. The numbers and activity of host-adapted factors, such as bile salt hydrolase and intestinal tissue-anchored elements, were distinctly distributed among the three lifestyles. The strains of the three lifestyles could be separated with such a collection of colonization-related genomic content (genes, genome size and GC content). Thus, our work provided valuable information for rational selection and gut engraftment prediction of probiotics. Here, we have found many interesting predictive results for bacterial gut fitness, which will be validated in vitro and in vivo.
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Affiliation(s)
- Yue Xiao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- Yangzhou Institute of Food Biotechnology, Jiangnan University, Yangzhou, Jiangsu 225004, PR China
- Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi 214122, PR China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, PR China
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Modesto M, Satti M, Watanabe K, Huang CH, Liou JS, Tamura T, Saito S, Mori K, Huang L, Sandri C, Spiezio C, Sgorbati B, Scarafile D, Cammà C, Ancora M, Patavino C, Arita M, Mattarelli P. Bifidobacteria in two-toed sloths ( Choloepus didactylus): phylogenetic characterization of the novel taxon Bifidobacterium choloepi sp. nov. Int J Syst Evol Microbiol 2021; 70:6115-6125. [PMID: 33052806 DOI: 10.1099/ijsem.0.004506] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Seven bifidobacterial strains were isolated from the faeces of two adult males of the two-toed sloth (Choloepus didactylus) housed in Parco Natura Viva, in Italy. Comparative sequence analysis of 16S rRNA and of five housekeeping (hsp60, rpoB, clpC, dnaJ, dnaG) genes revealed that these strains were classified into two clusters. On the basis of 16S rRNA gene sequence similarity, the type strain of Bifidobacterium catenulatum subsp. kashiwanohense DSM 21854T (95.4 %) was the closest neighbour to strain in Cluster I (BRDM 6T), whereas the type strain of Bifidobacterium dentium DSM 20436T (values were in the range of 98‒99.8 %) was the closest neighbour to the other six strains in Cluster II. The average nucleotide identity (ANI) values of BRDM 6T and of strains in Cluster II with the closely related type strains were 76.0 and 98.9 % (mean value) respectively. Therefore, genotyping based on the genome sequence of the strain BRDM 6T combined with phenotypic analyses clearly revealed that the strain BRDM 6T represents a novel species for which the names Bifidobacterium choloepi sp. nov. (BRDM 6T=NBRC 114053T=BCRC 81222T) is proposed.
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Affiliation(s)
- Monica Modesto
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Maria Satti
- Department of Genetics, SOKENDAI University (National Institute of Genetics), Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Koichi Watanabe
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan, ROC
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan, ROC
| | - Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan, ROC
| | - Jong-Shian Liou
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan, ROC
| | - Tomohiko Tamura
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Satomi Saito
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Koji Mori
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Lina Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan, ROC
| | - Camillo Sandri
- Department of Animal Health Care and Management, Parco Natura Viva - Garda Zoological Park, Bussolengo, Verona, Italy
| | - Caterina Spiezio
- Department of Animal Health Care and Management, Parco Natura Viva - Garda Zoological Park, Bussolengo, Verona, Italy
| | - Barbara Sgorbati
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Donatella Scarafile
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Cesare Cammà
- National Reference Center for Whole Genome Sequencing of microbial pathogens: database and bioinformatic analysis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Campo Boario, 64100, Teramo, Italy
| | - Massimo Ancora
- National Reference Center for Whole Genome Sequencing of microbial pathogens: database and bioinformatic analysis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Campo Boario, 64100, Teramo, Italy
| | - Claudio Patavino
- National Reference Center for Whole Genome Sequencing of microbial pathogens: database and bioinformatic analysis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Campo Boario, 64100, Teramo, Italy
| | - Masanori Arita
- Bioinformation and DDBJ Center, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Paola Mattarelli
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
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Janczy A, Aleksandrowicz-Wrona E, Kochan Z, Małgorzewicz S. Impact of diet and synbiotics on selected gut bacteria and intestinal permeability in individuals with excess body weight - A Prospective, Randomized Study. Acta Biochim Pol 2020; 67:571-578. [PMID: 33326198 DOI: 10.18388/abp.2020_5443] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/20/2020] [Indexed: 11/10/2022]
Abstract
Overweight and obese individuals may have leaky intestinal barrier and microbiome dysbiosis. The aim of this study was to determine whether body mass reduction with diet and synbiotics in an adult person with excess body mass has an influence on the gut microbiota and zonulin concentration. The study was a single blinded trial. 60 persons with excess body mass were examined. Based on randomization, patients were qualified either to the intervention group (Synbiotic group) or to the control group (Placebo group). Anthropometric measurements, microbiological assessment of faecal samples and zonulin concentration in the stool were performed before and after observation. After 3-months, an increase in the variety of intestinal bacteria (increase in the Shannon-Weaver index and the Simpson index) and a decrease in concentration of zonulin in faecal samples were observed in the Synbiotic group. Also, statistically significant correlation between zonulin and Bifidobacterium spp. (Spearman test, R=-0.51; p=0.0040) was noticed. There were no significant relationships between the body mass, BMI and changes in the intestinal microbiota or zonulin concentrations. The use of diet and synbiotics improved the condition of the microbiota and intestinal barrier in patients in the Synbiotic group.
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Affiliation(s)
- Agata Janczy
- Department of Nutritional Biochemistry, Medical University of Gdansk, Gdańsk, Poland
| | | | - Zdzisław Kochan
- Department of Nutritional Biochemistry, Medical University of Gdansk, Gdańsk, Poland
| | - Sylwia Małgorzewicz
- Department of Clinical Nutrition, Medical University of Gdansk, Gdańsk, Poland
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Mattison CP, Aryana KJ, Clermont K, Prestenburg E, Lloyd SW, Grimm CC, Wasserman RL. Microbiological, Physicochemical, and Immunological Analysis of a Commercial Cashew Nut-Based Yogurt. Int J Mol Sci 2020; 21:ijms21218267. [PMID: 33158240 PMCID: PMC7663355 DOI: 10.3390/ijms21218267] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/27/2020] [Accepted: 10/28/2020] [Indexed: 11/16/2022] Open
Abstract
Nut-based milks and yogurts are gaining popularity, but may not offer the same benefits as dairy yogurts to consumers. Cashew nuts often cause severe allergic reactions, and cashew nut allergens are stable to several types of processing. To compare its characteristics to dairy yogurt and characterize the effects of fermentation on the Ana o 1-3 cashew nut allergens, a commercial yogurt made from cashew nuts (Cashewgurt) was evaluated for microbiological, physiochemical, and immunological properties. Average counts for lactobacilli and Streptococcus thermophilus were greater than 10 million colony forming units per milliliter, indicating the capacity to provide a health benefit. Cashewgurt pH and viscosity values were comparable to cow milk yogurts, and it was off white in color. SDS-PAGE analysis indicated a clear reduction in Ana o 1 and 2, and immuno-assay with polyclonal anti-cashew IgG antibody and cashew-allergic IgE indicated an overall reduction in allergen content. In contrast, SDS-PAGE, mass spectrometry, immunoblot, and ELISA all revealed that Ana o 3 was relatively unaffected by the fermentation process. In conclusion, Ana o 1 and Ana o 2 are sensitive to degradation, while Ana o 3 survives lactic acid bacterial fermentation during yogurt production. The analysis presented here indicates that cashew nut yogurt is not suitable for those with cashew nut allergy.
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Affiliation(s)
- Christopher P. Mattison
- Southern Regional Research Center, United States Department of Agriculture, Agricultural Research Service, New Orleans, LA 70124, USA; (K.C.); (E.P.); (S.W.L.); (C.C.G.)
- Correspondence: ; Tel.: +1-(504)-286-4392; Fax: +1-(504)-286-4419
| | - Kayanush J. Aryana
- School of Nutrition and Food Science, Louisiana State University Agricultural Center, 115 Dairy Science Building, Baton Rouge, LA 70803, USA;
| | - Kristen Clermont
- Southern Regional Research Center, United States Department of Agriculture, Agricultural Research Service, New Orleans, LA 70124, USA; (K.C.); (E.P.); (S.W.L.); (C.C.G.)
- Oak Ridge Institute for Science and Education, U.S. Department of Energy, Oak Ridge, TN 37831-0117, USA
| | - Eric Prestenburg
- Southern Regional Research Center, United States Department of Agriculture, Agricultural Research Service, New Orleans, LA 70124, USA; (K.C.); (E.P.); (S.W.L.); (C.C.G.)
- Oak Ridge Institute for Science and Education, U.S. Department of Energy, Oak Ridge, TN 37831-0117, USA
| | - Steven W. Lloyd
- Southern Regional Research Center, United States Department of Agriculture, Agricultural Research Service, New Orleans, LA 70124, USA; (K.C.); (E.P.); (S.W.L.); (C.C.G.)
| | - Casey C. Grimm
- Southern Regional Research Center, United States Department of Agriculture, Agricultural Research Service, New Orleans, LA 70124, USA; (K.C.); (E.P.); (S.W.L.); (C.C.G.)
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7
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Traversi D, Rabbone I, Scaioli G, Vallini C, Carletto G, Racca I, Ala U, Durazzo M, Collo A, Ferro A, Carrera D, Savastio S, Cadario F, Siliquini R, Cerutti F. Risk factors for type 1 diabetes, including environmental, behavioural and gut microbial factors: a case-control study. Sci Rep 2020; 10:17566. [PMID: 33067559 PMCID: PMC7568546 DOI: 10.1038/s41598-020-74678-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 09/30/2020] [Indexed: 12/12/2022] Open
Abstract
Type 1 diabetes (T1D) is a common autoimmune disease that is characterized by insufficient insulin production. The onset of T1D is the result of gene-environment interactions. Sociodemographic and behavioural factors may contribute to T1D, and the gut microbiota is proposed to be a driving factor of T1D. An integrated preventive strategy for T1D is not available at present. This case-control study attempted to estimate the exposure linked to T1D to identify significant risk factors for healthy children. Forty children with T1D and 56 healthy controls were included in this study. Anthropometric, socio-economic, nutritional, behavioural, and clinical data were collected. Faecal bacteria were investigated by molecular methods. The findings showed, in multivariable model, that the risk factors for T1D include higher Firmicutes levels (OR 7.30; IC 2.26-23.54) and higher carbohydrate intake (OR 1.03; IC 1.01-1.05), whereas having a greater amount of Bifidobacterium in the gut (OR 0.13; IC 0.05 - 0.34) was a protective factor for T1D. These findings may facilitate the development of preventive strategies for T1D, such as performing genetic screening, characterizing the gut microbiota, and managing nutritional and social factors.
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Affiliation(s)
- Deborah Traversi
- Department of Public Health and Pediatrics, University of Turin, Piazza Polonia 94, 10126, Torino, Italy.
- Department of Public Health and Pediatrics, Hygiene Unit, University of the Study of Turin, via Santena 5 bis, 10126, Torino, Italy.
| | - Ivana Rabbone
- S.S.V.D. Endocrinology and Diabetology, O.I.R.M., Azienda Ospedaliera Città Della Salute E Della Scienza, Turin, Italy
- Department of Health Science, University of Eastern Piedmont Amadeo Avogadro - Azienda Ospedaliero Universitaria Maggiore Della Carità - Novara, Novara, Italy
| | - Giacomo Scaioli
- Department of Public Health and Pediatrics, University of Turin, Piazza Polonia 94, 10126, Torino, Italy
- Department of Public Health and Pediatrics, Hygiene Unit, University of the Study of Turin, via Santena 5 bis, 10126, Torino, Italy
| | - Camilla Vallini
- S.S.V.D. Endocrinology and Diabetology, O.I.R.M., Azienda Ospedaliera Città Della Salute E Della Scienza, Turin, Italy
| | - Giulia Carletto
- Department of Public Health and Pediatrics, University of Turin, Piazza Polonia 94, 10126, Torino, Italy
- Department of Public Health and Pediatrics, Hygiene Unit, University of the Study of Turin, via Santena 5 bis, 10126, Torino, Italy
| | - Irene Racca
- Department of Public Health and Pediatrics, University of Turin, Piazza Polonia 94, 10126, Torino, Italy
| | - Ugo Ala
- Department of Veterinary Sciences, University of Turin, Torino, Italy
| | - Marilena Durazzo
- S.C.U. Medicina Interna 3, Azienda Ospedaliera Città Della Salute e Della Scienza Di Torino, Torino, Italy
| | - Alessandro Collo
- S.C.U. Medicina Interna 3, Azienda Ospedaliera Città Della Salute e Della Scienza Di Torino, Torino, Italy
- Dietetic and Clinical Nutrition Department, Azienda Ospedaliero Universitaria Maggiore Della Carità, Novara, Italy
| | - Arianna Ferro
- S.C.U. Medicina Interna 3, Azienda Ospedaliera Città Della Salute e Della Scienza Di Torino, Torino, Italy
| | - Deborah Carrera
- Paediatric Endocrinology, Azienda Ospedaliero Universitaria Maggiore Della Carità - Novara, Novara, Italy
| | - Silvia Savastio
- Paediatric Endocrinology, Azienda Ospedaliero Universitaria Maggiore Della Carità - Novara, Novara, Italy
| | - Francesco Cadario
- Paediatric Endocrinology, Azienda Ospedaliero Universitaria Maggiore Della Carità - Novara, Novara, Italy
| | - Roberta Siliquini
- Department of Public Health and Pediatrics, University of Turin, Piazza Polonia 94, 10126, Torino, Italy
- Department of Public Health and Pediatrics, Hygiene Unit, University of the Study of Turin, via Santena 5 bis, 10126, Torino, Italy
| | - Franco Cerutti
- Department of Public Health and Pediatrics, University of Turin, Piazza Polonia 94, 10126, Torino, Italy
- S.S.V.D. Endocrinology and Diabetology, O.I.R.M., Azienda Ospedaliera Città Della Salute E Della Scienza, Turin, Italy
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8
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Chen C, Li T, Chen G, Chen D, Peng Y, Hu B, Sun Y, Zeng X. Commensal Relationship of Three Bifidobacterial Species Leads to Increase of Bifidobacterium in Vitro Fermentation of Sialylated Immunoglobulin G by Human Gut Microbiota. J Agric Food Chem 2020; 68:9110-9119. [PMID: 32806107 DOI: 10.1021/acs.jafc.0c03628] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Sialylated immunoglobulin G (IgG) is an important immunoglobulin in breast milk, but its effect on adult gut microbiota is not yet clear due to digestion by pepsin. Based on our previous IgG protecting study, effects of sialylated IgG on gut microbiota were investigated by in vitro anaerobic fermentation in the present study. It was found that the addition of sialylated IgG could significantly promote the growth of Bifidobacterium. Meanwhile, three bifidobacterial species B. bifidum CCX 19061, Bembidion breve CCX 19041, and B. longum subsp. infantis CCX 19042 were isolated. Furthermore, B. breve CCX 19041 and B. longum subsp. infantis CCX 19042 showed co-culture growth property with B. bifidum CCX 19061 in a sialylated IgG-based medium, which was also supported by changes of free monosaccharides and N-glycan structure. These findings suggest that the increase of Bifidobacterium in vitro fermentation is attributed to the commensal relationship of the three bifidobacterial species by utilizing sugars released from sialylated IgG.
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Affiliation(s)
- Chunxu Chen
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
- College of Food Engineering, Anhui Science and Technology University, Fengyang 233100, Anhui, China
| | - Tianhui Li
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Guijie Chen
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Dan Chen
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Yujia Peng
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Bing Hu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Yi Sun
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Xiaoxiong Zeng
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
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9
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Abstract
BACKGROUND The assembly of animal microbiomes is influenced by multiple environmental factors and host genetics, although the relative importance of these factors remains unclear. Bifidobacteria (genus Bifidobacterium, phylum Actinobacteria) are common first colonizers of gut microbiomes in humans and inhabit other mammals, social insects, food, and sewages. In humans, the presence of bifidobacteria in the gut has been correlated with health-promoting benefits. Here, we compared the genome sequences of a subset of the over 400 Bifidobacterium strains publicly available to investigate the adaptation of bifidobacteria diversity. We tested 1) whether bifidobacteria show a phylogenetic signal with their isolation sources (hosts and environments) and 2) whether key traits encoded by the bifidobacteria genomes depend on the host or environment from which they were isolated. We analyzed Bifidobacterium genomes available in the PATRIC and NCBI repositories and identified the hosts and/or environment from which they were isolated. A multilocus phylogenetic analysis was conducted to compare the genetic relatedness the strains harbored by different hosts and environments. Furthermore, we examined differences in genomic traits and genes related to amino acid biosynthesis and degradation of carbohydrates. RESULTS We found that bifidobacteria diversity appears to have evolved with their hosts as strains isolated from the same host were non-randomly associated with their phylogenetic relatedness. Moreover, bifidobacteria isolated from different sources displayed differences in genomic traits such as genome size and accessory gene composition and on particular traits related to amino acid production and degradation of carbohydrates. In contrast, when analyzing diversity within human-derived bifidobacteria, we observed no phylogenetic signal or differences on specific traits (amino acid biosynthesis genes and CAZymes). CONCLUSIONS Overall, our study shows that bifidobacteria diversity is strongly adapted to specific hosts and environments and that several genomic traits were associated with their isolation sources. However, this signal is not observed in human-derived strains alone. Looking into the genomic signatures of bifidobacteria strains in different environments can give insights into how this bacterial group adapts to their environment and what types of traits are important for these adaptations.
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Affiliation(s)
- Cynthia I Rodriguez
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA.
| | - Jennifer B H Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA
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10
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Lawley B, Otal A, Moloney-Geany K, Diana A, Houghton L, Heath ALM, Taylor RW, Tannock GW. Fecal Microbiotas of Indonesian and New Zealand Children Differ in Complexity and Bifidobacterial Taxa during the First Year of Life. Appl Environ Microbiol 2019; 85:e01105-19. [PMID: 31375480 PMCID: PMC6752005 DOI: 10.1128/aem.01105-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/22/2019] [Indexed: 02/07/2023] Open
Abstract
The biological succession that occurs during the first year of life in the gut of infants in Western countries is broadly predictable in terms of the increasing complexity of the composition of microbiotas. Less information is available about microbiotas in Asian countries, where environmental, nutritional, and cultural influences may differentially affect the composition and development of the microbial community. We compared the fecal microbiotas of Indonesian (n = 204) and New Zealand (NZ) (n = 74) infants 6 to 7 months and 12 months of age. Comparisons were made by analysis of 16S rRNA gene sequences and derivation of community diversity metrics, relative abundances of bacterial families, enterotypes, and cooccurrence correlation networks. Abundances of Bifidobacterium longum subsp. infantis and B. longum subsp. longum were determined by quantitative PCR. All observations supported the view that the Indonesian and NZ infant microbiotas developed in complexity over time, but the changes were much greater for NZ infants. B. longum subsp. infantis dominated the microbiotas of Indonesian children, whereas B. longum subsp. longum was dominant in NZ children. Network analysis showed that the niche model (in which trophic adaptation results in preferential colonization) of the assemblage of microbiotas was supported in Indonesian infants, whereas the neutral (stochastic) model was supported by the development of the microbiotas of NZ infants. The results of the study show that the development of the fecal microbiota is not the same for infants in all countries, and they point to the necessity of obtaining a better understanding of the factors that control the colonization of the gut in early life.IMPORTANCE This study addresses the microbiology of a natural ecosystem (the infant bowel) for children in a rural setting in Indonesia and in an urban environment in New Zealand. Analysis of DNA sequences generated from the microbial community (microbiota) in the feces of the infants during the first year of life showed marked differences in the composition and complexity of the bacterial collections. The differences were most likely due to differences in the prevalence and duration of breastfeeding of infants in the two countries. These kinds of studies are essential for developing concepts of microbial ecology related to the influence of nutrition and environment on the development of the gut microbiota and for determining the long-term effects of microbiological events in early life on human health and well-being.
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Affiliation(s)
- Blair Lawley
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Anna Otal
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Kit Moloney-Geany
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Aly Diana
- Department of Human Nutrition, University of Otago, Dunedin, New Zealand
| | - Lisa Houghton
- Department of Human Nutrition, University of Otago, Dunedin, New Zealand
- Microbiome Otago, University of Otago, Dunedin, New Zealand
| | - Anne-Louise M Heath
- Department of Human Nutrition, University of Otago, Dunedin, New Zealand
- Microbiome Otago, University of Otago, Dunedin, New Zealand
| | - Rachael W Taylor
- Microbiome Otago, University of Otago, Dunedin, New Zealand
- Department of Medicine, University of Otago, Dunedin, New Zealand
| | - Gerald W Tannock
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Microbiome Otago, University of Otago, Dunedin, New Zealand
- Riddet Centre of Research Excellence, Massey University, Palmerston North, New Zealand
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11
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Brown CJ, Mtui D, Oswald BP, Van Leuven JT, Vallender EJ, Schultz‐Darken N, Ross CN, Tardif SD, Austad SN, Forney LJ. Comparative genomics of Bifidobacterium species isolated from marmosets and humans. Am J Primatol 2019; 81:e983. [PMID: 31062394 PMCID: PMC6900142 DOI: 10.1002/ajp.22983] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 03/08/2019] [Accepted: 04/14/2019] [Indexed: 12/15/2022]
Abstract
The genus Bifidobacterium is purported to have beneficial consequences for human health and is a major component of many gastrointestinal probiotics. Although species of Bifidobacterium are generally at low relative frequency in the adult human gastrointestinal tract, they can constitute high proportions of the gastrointestinal communities of adult marmosets. To identify genes that might be important for the maintenance of Bifidobacterium in adult marmosets, ten strains of Bifidobacterium were isolated from the feces of seven adult marmosets, and their genomes were sequenced. There were six B. reuteri strains, two B. callitrichos strains, one B. myosotis sp. nov. and one B. tissieri sp. nov. among our isolates. Phylogenetic analysis showed that three of the four species we isolated were most closely related to B. bifidum, B. breve and B. longum, which are species found in high abundance in human infants. There were 1357 genes that were shared by at least one strain of B. reuteri, B. callitrichos, B. breve, and B. longum, and 987 genes that were found in all strains of the four species. There were 106 genes found in B. reuteri and B. callitrichos but not in human bifidobacteria, and several of these genes were involved in nutrient uptake. These pathways for nutrient uptake appeared to be specific to Bifidobacterium from New World monkeys. Additionally, the distribution of Bifidobacterium in fecal samples from captive adult marmosets constituted as much as 80% of the gut microbiome, although this was variable between individuals and colonies. We suggest that nutrient transporters may be important for the maintenance of Bifidobacterium during adulthood in marmosets.
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Affiliation(s)
- Celeste J. Brown
- Department of Biological ScienceUniversity of IdahoMoscowIdaho
- Center for Modeling Complex InteractionsUniversity of IdahoMoscowIdaho
- Institute for Bioinformatics and Evolutionary StudiesUniversity of IdahoMoscowIdaho
| | - Dorah Mtui
- Department of Biological ScienceUniversity of IdahoMoscowIdaho
| | - Benjamin P. Oswald
- Department of Biological ScienceUniversity of IdahoMoscowIdaho
- Institute for Bioinformatics and Evolutionary StudiesUniversity of IdahoMoscowIdaho
| | | | - Eric J. Vallender
- New England Primate Research CenterHarvard Medical SchoolSouthboroughMassachusetts
| | - Nancy Schultz‐Darken
- Wisconsin National Primate Research CenterUniversity of WisconsinMadisonWisconsin
| | - Corinna N. Ross
- Southwest National Primate Research CenterTexas Biomedical Research InstituteSan AntonioTexas
- Department of Science and MathematicsTexas A&M UniversitySan AntonioTexas
| | - Suzette D. Tardif
- Southwest National Primate Research CenterTexas Biomedical Research InstituteSan AntonioTexas
| | - Steven N. Austad
- Department of Cellular and Structural BiologyUniversity of Texas Health Science Center at San AntonioSan AntonioTexas
| | - Larry J. Forney
- Department of Biological ScienceUniversity of IdahoMoscowIdaho
- Institute for Bioinformatics and Evolutionary StudiesUniversity of IdahoMoscowIdaho
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12
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Tuomisto S, Huhtala H, Martiskainen M, Goebeler S, Lehtimäki T, Karhunen PJ. Age-dependent association of gut bacteria with coronary atherosclerosis: Tampere Sudden Death Study. PLoS One 2019; 14:e0221345. [PMID: 31437200 PMCID: PMC6705803 DOI: 10.1371/journal.pone.0221345] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 08/05/2019] [Indexed: 12/22/2022] Open
Abstract
Background The gut microbiome is thought to remain stable into old age. Gut bacteria and their translocation may play a role in the development of coronary heart disease (CHD) by modulating cholesterol levels and immune responses, as well as by producing toxic metabolites and bacterial endotoxins. The association of changes in the gut microbiome with the severity of coronary atherosclerosis and the ability of gut bacteria themselves to translocate into coronary plaques has not been studied. Materials and methods As a part of the Tampere Sudden Death Study, we measured age-dependent changes in the relative ratios of major intestinal bacterial communities (Bacteroides species [spp.], the Clostridium leptum group, the Clostridium coccoides group, Bifidobacterium spp., Enterobactericeae, Lactobacillus spp.) and Streptococcus spp. in both feces and coronary plaques of the same male autopsy cases (n = 67, age range 44–95) using real-time quantitative PCR (qPCR). The area of coronary atherosclerotic lesions were measured by computer-assisted morphometry. Fecal bacterial DNA measurements from healthy volunteers served as a control for gut bacterial analyses of autopsy cases. The relative amount of bacterial DNA in a sample was determined with the comparative Cq method. Results The relative ratios of fecal Lactobacillus spp., Bifidobacterium spp., the Clostridium coccoides group, and Bacteroides spp. did not differ between controls and autopsy cases and showed no age-dependence. In contrast, the ratios of the Clostridium leptum group, Enterobactericeae, and Streptococcus spp. increased with age. Elevated relative ratios of fecal Enterobactericeae associated with a larger coronary plaque fibrotic area (p = 0.001), and the Clostridium leptum group with a larger calcification area (p = 0.015). Intestinal bacterial DNA could be amplified in 67.6% of the coronary plaques, the most common being Streptococcus spp. (41.0%), followed by Enterobactericeae (12.1%), Clostridium leptum (2.4%), and Lactobacillus spp. (2.4%). The percentages of Streptococcus spp. DNA decreased, and those of Enterobactericeae increased in coronary plaques along with age. Conclusions DNA of the Clostridium leptum group and pathogenic Enterobactericeae increase in the gut microbiome with age and can be detected in the same individual’s coronary plaques along with pathogenic Streptococcus spp., associating with more severe coronary atherosclerosis.
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Affiliation(s)
- Sari Tuomisto
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Fimlab Laboratories Ltd, Pirkanmaa Hospital District, Tampere, Finland
- * E-mail:
| | - Heini Huhtala
- Faculty of Social Sciences, Tampere University, Tampere, Finland
| | - Mika Martiskainen
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- National Institute for Health and Welfare, Tampere, Finland
| | | | - Terho Lehtimäki
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Fimlab Laboratories Ltd, Pirkanmaa Hospital District, Tampere, Finland
| | - Pekka J. Karhunen
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Fimlab Laboratories Ltd, Pirkanmaa Hospital District, Tampere, Finland
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13
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Abstract
The structure and distribution of genomic diversity in natural microbial communities is largely unexplored. Here, we used shotgun metagenomics to assess the diversity of the honey bee gut microbiota, a community consisting of few bacterial phylotypes. Our results show that most phylotypes are composed of sequence-discrete populations, which co-exist in individual bees and show age-specific abundance profiles. In contrast, strains present within these sequence-discrete populations were found to segregate into individual bees. Consequently, despite a conserved phylotype composition, each honey bee harbors a distinct community at the functional level. While ecological differentiation seems to facilitate coexistence at higher taxonomic levels, our findings suggest that, at the level of strains, priority effects during community assembly result in individualized profiles, despite the social lifestyle of the host. Our study underscores the need to move beyond phylotype-level characterizations to understand the function of this community, and illustrates its potential for strain-level analysis.
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Affiliation(s)
- Kirsten M Ellegaard
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland.
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland.
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14
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Kim HJ, Shin SI, Lee SJ, Moon TW, Lee CJ. Screening and selection of Bifidobacterium strains isolated from human feces capable of utilizing resistant starch. J Sci Food Agric 2018; 98:5901-5907. [PMID: 30009448 DOI: 10.1002/jsfa.9260] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 07/10/2018] [Accepted: 07/12/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Resistant starch (RS) has been studied for its ability to serve as a substrate for the microbiota present in the human large intestine and for its beneficial physiological effects. The aim of this study was to screen and select novel strains of lactic acid bacteria (LAB) in the genus Bifidobacterium isolated from human fecal samples for further application as probiotics relying on their utilization of RS3, a prebiotic. RESULTS LAB were isolated from human fecal samples, based on their ability to utilize RS3 as a carbon source. Consequently, two LAB were identified as Bifidobacterium adolescentis based on morphological, physiological and biochemical properties, and molecular biological analysis. The RS3-utilizing ability of these isolates was shown by the rapid decrease in pH of RS3-MRS media and by the pinhole traces on the surface of RS3 particles. Isolated B. adolescentis JSC2 was shown to be negative for β-glucuronidase, suggesting that it would be safe for human use, and was found to be tolerant towards the acidic, bile-salt environment. CONCLUSION This synbiotics approach of B. adolescentis JCS2, an RS-utilizing probiotics, coupled with RS utilization, is expected to enhance RS utilization in the food industry and be beneficial for the promotion of human health. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Hyun-Joong Kim
- Department of Food Science and Biotechnology, Institute of Life Sciences and Resources, Kyung Hee University, Yongin, Republic of Korea
| | - Sang Ick Shin
- R&D Center, Korea Yakult Co. Ltd., Yongin, Republic of Korea
| | - Sang-Jun Lee
- Department of Food Nutrition, Chungkang College of Cultural Industries, Icheon, Republic of Korea
| | - Tae Wha Moon
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Chang Joo Lee
- Department of Food Science and Biotechnology, Wonkwang University, Iksan, Republic of Korea
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15
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Korpela K, Salonen A, Vepsäläinen O, Suomalainen M, Kolmeder C, Varjosalo M, Miettinen S, Kukkonen K, Savilahti E, Kuitunen M, de Vos WM. Probiotic supplementation restores normal microbiota composition and function in antibiotic-treated and in caesarean-born infants. Microbiome 2018; 6:182. [PMID: 30326954 PMCID: PMC6192119 DOI: 10.1186/s40168-018-0567-4] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 09/28/2018] [Indexed: 05/17/2023]
Abstract
BACKGROUND Infants born by caesarean section or receiving antibiotics are at increased risk of developing metabolic, inflammatory and immunological diseases, potentially due to disruption of normal gut microbiota at a critical developmental time window. We investigated whether probiotic supplementation could ameliorate the effects of antibiotic use or caesarean birth on infant microbiota in a double blind, placebo-controlled randomized clinical trial. Mothers were given a multispecies probiotic, consisting of Bifidobacterium breve Bb99 (Bp99 2 × 108 cfu) Propionibacterium freundenreichii subsp. shermanii JS (2 × 109cfu), Lactobacillus rhamnosus Lc705 (5 × 109 cfu) and Lactobacillus rhamnosus GG (5 × 109 cfu) (N = 168 breastfed and 31 formula-fed), or placebo supplement (N = 201 breastfed and 22 formula-fed) during pregnancy, and the infants were given the same supplement. Faecal samples of the infants were collected at 3 months and analyzed using taxonomic, metagenomic and metaproteomic approaches. RESULTS The probiotic supplement had a strong overall impact on the microbiota composition, but the effect depended on the infant's diet. Only breastfed infants showed the expected increase in bifidobacteria and reduction in Proteobacteria and Clostridia. In the placebo group, both birth mode and antibiotic use were significantly associated with altered microbiota composition and function, particularly reduced Bifidobacterium abundance. In the probiotic group, the effects of antibiotics and birth mode were either completely eliminated or reduced. CONCLUSIONS The results indicate that it is possible to correct undesired changes in microbiota composition and function caused by antibiotic treatments or caesarean birth by supplementing infants with a probiotic mixture together with at least partial breastfeeding. TRIAL REGISTRATION clinicaltrials.gov NCT00298337 . Registered March 2, 2006.
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Affiliation(s)
- Katri Korpela
- Immunobiology Research Programme, Department of Bacteriology and Immunology, University of Helsinki, Helsinki, Finland
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Anne Salonen
- Immunobiology Research Programme, Department of Bacteriology and Immunology, University of Helsinki, Helsinki, Finland
| | - Outi Vepsäläinen
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Marjo Suomalainen
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Carolin Kolmeder
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Sini Miettinen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Kaarina Kukkonen
- Skin and Allergy Hospital, Department of Paediatrics, Helsinki University Hospital, Helsinki, Finland
| | - Erkki Savilahti
- Children’s Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Mikael Kuitunen
- Children’s Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Willem M de Vos
- Immunobiology Research Programme, Department of Bacteriology and Immunology, University of Helsinki, Helsinki, Finland
- Laboratory of Microbiology, Wageningen University, Wageningen, the Netherlands
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16
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Stewart CJ, Ajami NJ, O'Brien JL, Hutchinson DS, Smith DP, Wong MC, Ross MC, Lloyd RE, Doddapaneni H, Metcalf GA, Muzny D, Gibbs RA, Vatanen T, Huttenhower C, Xavier RJ, Rewers M, Hagopian W, Toppari J, Ziegler AG, She JX, Akolkar B, Lernmark A, Hyoty H, Vehik K, Krischer JP, Petrosino JF. Temporal development of the gut microbiome in early childhood from the TEDDY study. Nature 2018; 562:583-588. [PMID: 30356187 PMCID: PMC6415775 DOI: 10.1038/s41586-018-0617-x] [Citation(s) in RCA: 981] [Impact Index Per Article: 163.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 08/30/2018] [Indexed: 12/16/2022]
Abstract
The development of the microbiome from infancy to childhood is dependent on a range of factors, with microbial-immune crosstalk during this time thought to be involved in the pathobiology of later life diseases1-9 such as persistent islet autoimmunity and type 1 diabetes10-12. However, to our knowledge, no studies have performed extensive characterization of the microbiome in early life in a large, multi-centre population. Here we analyse longitudinal stool samples from 903 children between 3 and 46 months of age by 16S rRNA gene sequencing (n = 12,005) and metagenomic sequencing (n = 10,867), as part of the The Environmental Determinants of Diabetes in the Young (TEDDY) study. We show that the developing gut microbiome undergoes three distinct phases of microbiome progression: a developmental phase (months 3-14), a transitional phase (months 15-30), and a stable phase (months 31-46). Receipt of breast milk, either exclusive or partial, was the most significant factor associated with the microbiome structure. Breastfeeding was associated with higher levels of Bifidobacterium species (B. breve and B. bifidum), and the cessation of breast milk resulted in faster maturation of the gut microbiome, as marked by the phylum Firmicutes. Birth mode was also significantly associated with the microbiome during the developmental phase, driven by higher levels of Bacteroides species (particularly B. fragilis) in infants delivered vaginally. Bacteroides was also associated with increased gut diversity and faster maturation, regardless of the birth mode. Environmental factors including geographical location and household exposures (such as siblings and furry pets) also represented important covariates. A nested case-control analysis revealed subtle associations between microbial taxonomy and the development of islet autoimmunity or type 1 diabetes. These data determine the structural and functional assembly of the microbiome in early life and provide a foundation for targeted mechanistic investigation into the consequences of microbial-immune crosstalk for long-term health.
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Affiliation(s)
- Christopher J Stewart
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK.
| | - Nadim J Ajami
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Jacqueline L O'Brien
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Diane S Hutchinson
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Daniel P Smith
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Matthew C Wong
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Matthew C Ross
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Richard E Lloyd
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | | | - Ginger A Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Tommi Vatanen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Marian Rewers
- Barbara Davis Center for Childhood Diabetes, University of Colorado, Aurora, CO, USA
| | | | - Jorma Toppari
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, University of Turku, Turku, Finland
- Department of Pediatrics, Turku University Hospital, Turku, Finland
| | - Anette-G Ziegler
- Institute of Diabetes Research, Helmholtz Zentrum München, Munich, Germany
- Forschergruppe Diabetes, Technische Universität München, Klinikum Rechts der Isar, Munich, Germany
- Forschergruppe Diabetes e.V. at Helmholtz Zentrum München, Munich, Germany
| | - Jin-Xiong She
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Beena Akolkar
- National Institute of Diabetes & Digestive & Kidney Diseases, Bethesda, MD, USA
| | - Ake Lernmark
- Department of Clinical Sciences, Lund University/CRC, Skane University Hospital, Malmö, Sweden
| | - Heikki Hyoty
- Department of Virology, Faculty of Medicine and Biosciences, University of Tampere, Tampere, Finland
- Fimlab Laboratories, Pirkanmaa Hospital District, Tampere, Finland
| | - Kendra Vehik
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Jeffrey P Krischer
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
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17
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Lundgren SN, Madan JC, Emond JA, Morrison HG, Christensen BC, Karagas MR, Hoen AG. Maternal diet during pregnancy is related with the infant stool microbiome in a delivery mode-dependent manner. Microbiome 2018; 6:109. [PMID: 29973274 PMCID: PMC6033232 DOI: 10.1186/s40168-018-0490-8] [Citation(s) in RCA: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/30/2018] [Indexed: 05/21/2023]
Abstract
BACKGROUND The gut microbiome has an important role in infant health and immune development and may be affected by early-life exposures. Maternal diet may influence the infant gut microbiome through vertical transfer of maternal microbes to infants during vaginal delivery and breastfeeding. We aimed to examine the association of maternal diet during pregnancy with the infant gut microbiome 6 weeks post-delivery in mother-infant dyads enrolled in the New Hampshire Birth Cohort Study. Infant stool samples were collected from 145 infants, and maternal prenatal diet was assessed using a food frequency questionnaire. We used targeted sequencing of the 16S rRNA V4-V5 hypervariable region to characterize infant gut microbiota. To account for differences in baseline and trajectories of infant gut microbial profiles, we stratified analyses by delivery mode. RESULTS We identified three infant gut microbiome clusters, characterized by increased abundance of Bifidobacterium, Streptococcus and Clostridium, and Bacteroides, respectively, overall and in the vaginally delivered infant stratum. In the analyses stratified to infants born vaginally and adjusted for other potential confounders, maternal fruit intake was associated with infant gut microbial community structure (PERMANOVA, p < 0.05). In multinomial logistic regression analyses, increased fruit intake was associated with an increased odds of belonging to the high Streptococcus/Clostridium group among infants born vaginally (OR (95% CI) = 2.73 (1.36, 5.46)). In infants delivered by Cesarean section, we identified three clusters that differed slightly from vaginally delivered infants, which were characterized by a high abundance of Bifidobacterium, high Clostridium and low Streptococcus and Ruminococcus genera, and high abundance of the family Enterobacteriaceae. Maternal dairy intake was associated with an increased odds of infants belonging to the high Clostridium cluster in infants born by Cesarean section (OR (95% CI) = 2.36 (1.05, 5.30)). Linear models suggested additional associations between maternal diet and infant intestinal microbes in both delivery mode strata. CONCLUSIONS Our data indicate that maternal diet influences the infant gut microbiome and that these effects differ by delivery mode.
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Affiliation(s)
- Sara N. Lundgren
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
| | - Juliette C. Madan
- Division of Neonatology, Department of Pediatrics, Children’s Hospital at Dartmouth, Hanover, NH USA
- Children’s Environmental Health & Disease Prevention Research Center at Dartmouth, Lebanon, NH USA
| | - Jennifer A. Emond
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH USA
| | - Hilary G. Morrison
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA USA
| | - Brock C. Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
- Center for Molecular Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
| | - Margaret R. Karagas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
- Children’s Environmental Health & Disease Prevention Research Center at Dartmouth, Lebanon, NH USA
- Center for Molecular Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
| | - Anne G. Hoen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
- Children’s Environmental Health & Disease Prevention Research Center at Dartmouth, Lebanon, NH USA
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH USA
- Center for Molecular Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
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Anderson KE, Ricigliano VA, Mott BM, Copeland DC, Floyd AS, Maes P. The queen's gut refines with age: longevity phenotypes in a social insect model. Microbiome 2018; 6:108. [PMID: 29914555 PMCID: PMC6006926 DOI: 10.1186/s40168-018-0489-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 05/29/2018] [Indexed: 05/10/2023]
Abstract
BACKGROUND In social insects, identical genotypes can show extreme lifespan variation providing a unique perspective on age-associated microbial succession. In honey bees, short- and long-lived host phenotypes are polarized by a suite of age-associated factors including hormones, nutrition, immune senescence, and oxidative stress. Similar to other model organisms, the aging gut microbiota of short-lived (worker) honey bees accrue Proteobacteria and are depleted of Lactobacillus and Bifidobacterium, consistent with a suite of host senescence markers. In contrast, long-lived (queen) honey bees maintain youthful cellular function with much lower expression of oxidative stress genes, suggesting a very different host environment for age-associated microbial succession. RESULTS We sequenced the microbiota of 63 honey bee queens exploring two chronological ages and four alimentary tract niches. To control for genetic and environmental variation, we quantified carbonyl accumulation in queen fat body tissue as a proxy for biological aging. We compared our results to the age-specific microbial succession of worker guts. Accounting for queen source variation, two or more bacterial species per niche differed significantly by queen age. Biological aging in queens was correlated with microbiota composition highlighting the relationship of microbiota with oxidative stress. Queens and workers shared many major gut bacterial species, but differ markedly in community structure and age succession. In stark contrast to aging workers, carbonyl accumulation in queens was significantly associated with increased Lactobacillus and Bifidobacterium and depletion of various Proteobacteria. CONCLUSIONS We present a model system linking changes in gut microbiota to diet and longevity, two of the most confounding variables in human microbiota research. The pattern of age-associated succession in the queen microbiota is largely the reverse of that demonstrated for workers. The guts of short-lived worker phenotypes are progressively dominated by three major Proteobacteria, but these same species were sparse or significantly depleted in long-lived queen phenotypes. More broadly, age-related changes in the honey bee microbiota reflect the regulatory anatomy of reproductive host metabolism. Our synthesis suggests that the evolution of colony-level reproductive physiology formed the context for host-microbial interactions and age-related succession of honey bee microbiota.
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Affiliation(s)
- Kirk E. Anderson
- USDA-ARS Carl Hayden Bee Research Center, 2000 E. Allen Rd, Tucson, AZ 85719 USA
- Department of Entomology and Center for Insect Science, University of Arizona, Tucson, AZ 85721 USA
| | | | - Brendon M. Mott
- USDA-ARS Carl Hayden Bee Research Center, 2000 E. Allen Rd, Tucson, AZ 85719 USA
| | - Duan C. Copeland
- Department of Microbiology, School of Animal & Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721 USA
| | - Amy S. Floyd
- Department of Entomology and Center for Insect Science, University of Arizona, Tucson, AZ 85721 USA
| | - Patrick Maes
- Department of Entomology and Center for Insect Science, University of Arizona, Tucson, AZ 85721 USA
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Jin W, Li Y, Cheng Y, Mao S, Zhu W. The bacterial and archaeal community structures and methanogenic potential of the cecal microbiota of goats fed with hay and high-grain diets. Antonie Van Leeuwenhoek 2018; 111:2037-2049. [PMID: 29774508 DOI: 10.1007/s10482-018-1096-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 05/08/2018] [Indexed: 11/26/2022]
Abstract
The cecum plays an important role in the feed fermentation of ruminants. However, information is very limited regarding the cecal microbiota and their methane production. In the present study, the cecal content from twelve local Chinese goats, fed with either a hay diet (0% grain) or a high-grain diet (71.5% grain), were used to investigate the bacterial and archaeal community and their methanogenic potential. Microbial community analysis was determined using high-throughput sequencing of 16S rRNA genes and real-time PCR, and the methanogenesis potential was assessed by in vitro fermentation with ground corn or hay as substrates. Compared with the hay group, the high-grain diet significantly increased the length and weight of the cecum, the proportions of starch and crude protein, the concentrations of volatile fatty acids and ammonia nitrogen, but decreased the pH values (P < 0.05). The high-grain diet significantly increased the abundances of bacteria and archaea (P < 0.05) and altered their community. For the bacterial community, the genera Bifidobacterium, Prevotella, and Treponema were significantly increased in the high-grain group (P < 0.05), while Akkermansia, Oscillospira, and Coprococcus were significantly decreased (P < 0.05). For the archaeal community, Methanosphaera stadtmanae was significantly increased in the high-grain group (P < 0.05), while Methanosphaera sp. ISO3-F5 was significantly decreased (P < 0.05). In the in vitro fermentation with grain as substrate, the cecal microorganisms from the high-grain group produced a significantly higher amount of methane and volatile fatty acids (P < 0.05), and produced significantly lower amount of lactate (P < 0.05). Conclusively, high-grain diet led to more fermentable substrates flowing into the hindgut of goats, resulting in an enhancement of microbial fermentation and methane production in the cecum.
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Affiliation(s)
- Wei Jin
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yin Li
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanfen Cheng
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Shengyong Mao
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, 210095, China
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20
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Freitas AC, Hill JE. Bifidobacteria isolated from vaginal and gut microbiomes are indistinguishable by comparative genomics. PLoS One 2018; 13:e0196290. [PMID: 29684056 PMCID: PMC5912743 DOI: 10.1371/journal.pone.0196290] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 04/10/2018] [Indexed: 12/13/2022] Open
Abstract
Bifidobacteria colonize the human gastrointestinal tract, vagina, oral cavity and breast milk. They influence human physiology and nutrition through health-promoting effects, play an important role as primary colonizers of the newborn gut, and contribute to vaginal microbiome homeostasis by producing lactic acid. Nevertheless, the mechanisms by which bifidobacteria are transmitted from mother to infant remains in discussion. Moreover, studies have suggested that Bifidobacterium spp. have specializations for gut colonization, but comparisons of strains of the same bifidobacteria species from different body sites are lacking. Here, our objective was to compare the genomes of Bifidobacterium breve (n = 17) and Bifidobacterium longum (n = 26) to assess whether gut and vaginal isolates of either species were distinguishable based on genome content. Comparison of the general genome features showed that vaginal and gut isolates did not differ in size, GC content, number of genes and CRISPR, either for B. breve or B. longum. Average nucleotide identity and whole genome phylogeny analysis revealed that vaginal and gut isolates did not cluster separately. Vaginal and gut isolates also had a similar COG (Cluster of Orthologous Group) category distribution. Differences in the accessory genomes between vaginal and gut strains were observed, but were not sufficient to distinguish isolates based on their origin. The results of this study support the hypothesis that the vaginal and gut microbiomes are colonized by a shared community of Bifidobacterium, and further emphasize the potential importance of the maternal vaginal microbiome as a source of infant gut microbiota.
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Affiliation(s)
- Aline C. Freitas
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Janet E. Hill
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- * E-mail:
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罗 月, 刘 斐, 陈 慕, 唐 文, 杨 月, 谭 细, 周 宏. [A machine learning model based on initial gut microbiome data for predicting changes of Bifidobacterium after prebiotics consumption]. Nan Fang Yi Ke Da Xue Xue Bao 2018; 38:251-260. [PMID: 29643029 PMCID: PMC6744178 DOI: 10.3969/j.issn.1673-4254.2018.03.03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Indexed: 06/08/2023]
Abstract
OBJECTIVE To investigate the effects of prebiotics supplementation for 9 days on gut microbiota structure and function and establish a machine learning model based on the initial gut microbiota data for predicting the variation of Bifidobacterium after prebiotic intake. METHODS With a randomized double-blind self-controlled design, 35 healthy volunteers were asked to consume fructo-oligosaccharides (FOS) or galacto-oligosaccharides (GOS) for 9 days (16 g per day). 16S rRNA gene high-throughput sequencing was performed to investigate the changes of gut microbiota after prebiotics intake. PICRUSt was used to infer the differences between the functional modules of the bacterial communities. Random forest model based on the initial gut microbiota data was used to identify the changes in Bifidobacterium after 5 days of prebiotic intake and then to build a continuous index to predict the changes of Bifidobacterium. The data of fecal samples collected after 9 days of GOS intervention were used to validate the model. RESULTS Fecal samples analysis with QIIME revealed that FOS intervention for 5 days reduced the intestinal flora alpha diversity, which rebounded on day 9; in GOS group, gut microbiota alpha diversity decreased progressively during the intervention. Neither FOS nor GOS supplement caused significant changes in β diversity of gut microbiota. The area under the curve (AUC) of the prediction model was 89.6%. The continuous index could successfully predict the changes in Bifidobacterium (R=0.45, P=0.01), and the prediction accuracy was verified by the validation model (R=0.62, P=0.01). CONCLUSION Short-term prebiotics intervention can significantly decrease α-diversity of the intestinal flora. The machine learning model based on initial gut microbiota data can accurately predict the changes in Bifidobacterium, which sheds light on personalized nutrition intervention and precise modulation of the intestinal flora.
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Affiliation(s)
- 月梅 罗
- 南方医科大学公共卫生学院环境卫生学系,广东 广州 510515Department of Environmental Health, School of Public Health, Southern Medical University, Guangzhou 510515, China
- 南方医科大学珠江医院检验医学部器官衰竭 研究国家重点实验室,广东 广州 510515State Key Laboratory of Organ Failure Research, Division of Laboratory Medicine, Guangzhou 510515, China
| | - 斐童 刘
- 南方医科大学公共卫生学院环境卫生学系,广东 广州 510515Department of Environmental Health, School of Public Health, Southern Medical University, Guangzhou 510515, China
- 南方医科大学珠江医院检验医学部器官衰竭 研究国家重点实验室,广东 广州 510515State Key Laboratory of Organ Failure Research, Division of Laboratory Medicine, Guangzhou 510515, China
| | - 慕璇 陈
- 南方医科大学珠江医院检验医学部器官衰竭 研究国家重点实验室,广东 广州 510515State Key Laboratory of Organ Failure Research, Division of Laboratory Medicine, Guangzhou 510515, China
| | - 文丽 唐
- 南方医科大学珠江医院检验医学部器官衰竭 研究国家重点实验室,广东 广州 510515State Key Laboratory of Organ Failure Research, Division of Laboratory Medicine, Guangzhou 510515, China
| | - 月莲 杨
- 南方医科大学珠江医院检验医学部器官衰竭 研究国家重点实验室,广东 广州 510515State Key Laboratory of Organ Failure Research, Division of Laboratory Medicine, Guangzhou 510515, China
- 南方医科大学 南方医科大学珠江医院老年病科,广东 广州 510515Department of Geriatrics, Guangzhou 510515, China
| | - 细兰 谭
- 南方医科大学公共卫生学院环境卫生学系,广东 广州 510515Department of Environmental Health, School of Public Health, Southern Medical University, Guangzhou 510515, China
- 南方医科大学珠江医院检验医学部器官衰竭 研究国家重点实验室,广东 广州 510515State Key Laboratory of Organ Failure Research, Division of Laboratory Medicine, Guangzhou 510515, China
- 南方医科大学珠江医院感染科,广东 广州 510282Department of Infectious Diseases4, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - 宏伟 周
- 南方医科大学公共卫生学院环境卫生学系,广东 广州 510515Department of Environmental Health, School of Public Health, Southern Medical University, Guangzhou 510515, China
- 南方医科大学珠江医院检验医学部器官衰竭 研究国家重点实验室,广东 广州 510515State Key Laboratory of Organ Failure Research, Division of Laboratory Medicine, Guangzhou 510515, China
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Douillard FP, Mora D, Eijlander RT, Wels M, de Vos WM. Comparative genomic analysis of the multispecies probiotic-marketed product VSL#3. PLoS One 2018; 13:e0192452. [PMID: 29451876 PMCID: PMC5815585 DOI: 10.1371/journal.pone.0192452] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 01/23/2018] [Indexed: 02/07/2023] Open
Abstract
Several probiotic-marketed formulations available for the consumers contain live lactic acid bacteria and/or bifidobacteria. The multispecies product commercialized as VSL#3 has been used for treating various gastro-intestinal disorders. However, like many other products, the bacterial strains present in VSL#3 have only been characterized to a limited extent and their efficacy as well as their predicted mode of action remain unclear, preventing further applications or comparative studies. In this work, the genomes of all eight bacterial strains present in VSL#3 were sequenced and characterized, to advance insights into the possible mode of action of this product and also to serve as a basis for future work and trials. Phylogenetic and genomic data analysis allowed us to identify the 7 species present in the VSL#3 product as specified by the manufacturer. The 8 strains present belong to the species Streptococcus thermophilus, Lactobacillus acidophilus, Lactobacillus paracasei, Lactobacillus plantarum, Lactobacillus helveticus, Bifidobacterium breve and B. animalis subsp. lactis (two distinct strains). Comparative genomics revealed that the draft genomes of the S. thermophilus and L. helveticus strains were predicted to encode most of the defence systems such as restriction modification and CRISPR-Cas systems. Genes associated with a variety of potential probiotic functions were also identified. Thus, in the three Bifidobacterium spp., gene clusters were predicted to encode tight adherence pili, known to promote bacteria-host interaction and intestinal barrier integrity, and to impact host cell development. Various repertoires of putative signalling proteins were predicted to be encoded by the genomes of the Lactobacillus spp., i.e. surface layer proteins, LPXTG-containing proteins, or sortase-dependent pili that may interact with the intestinal mucosa and dendritic cells. Taken altogether, the individual genomic characterization of the strains present in the VSL#3 product confirmed the product specifications, determined its coding capacity as well as identified potential probiotic functions.
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Affiliation(s)
- François P. Douillard
- Research Program Unit Immunobiology, Medicum, University of Helsinki, Helsinki, Finland
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Diego Mora
- Department of Food, Environmental, and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
| | | | | | - Willem M. de Vos
- Research Program Unit Immunobiology, Medicum, University of Helsinki, Helsinki, Finland
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- * E-mail:
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Xiong W, Wang Y, Sun Y, Ma L, Zeng Q, Jiang X, Li A, Zeng Z, Zhang T. Antibiotic-mediated changes in the fecal microbiome of broiler chickens define the incidence of antibiotic resistance genes. Microbiome 2018; 6:34. [PMID: 29439741 PMCID: PMC5811963 DOI: 10.1186/s40168-018-0419-2] [Citation(s) in RCA: 154] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 01/30/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND Antimicrobial agents have been widely used in animal farms to prevent and treat animal diseases and to promote growth. Antimicrobial agents may change the bacterial community and enhance the resistome in animal feces. We used metagenome-wide analysis to investigate the changes in bacterial community, variations in antibiotic resistance genes (ARGs), and their bacterial hosts in the feces of broiler chickens over a full-treatment course of chlortetracycline at low and therapeutic dose levels. RESULTS The effects of chlortetracycline on resistome were dependent on the specific ARG subtypes and not simply the overall community-level ARGs. Therapeutic dose of chlortetracycline promoted the abundance of tetracycline resistance genes (tetA and tetW) and inhibited multidrug resistance genes (mdtA, mdtC, mdtK, ompR, and TolC). The therapeutic dose of chlortetracycline led to loss of Proteobacteria mainly due to the decrease of Escherichia/Shigella (from 72 to 58%). Inhibition of Escherichia by chlortetracycline was the primary reason for the decrease of genes resistant to multiple drugs in the therapeutic dose group. The ARG host Bifidobacterium were enriched due to tetW harbored by Bifidobacterium under chlortetracycline treatment. Escherichia was always the major host for multidrug resistance genes, whereas the primary host was changed from Escherichia to Klebsiella for aminoglycoside resistance genes with the treatment of therapeutic dose of chlortetracycline. CONCLUSIONS We provided the first metagenomic insights into antibiotic-mediated alteration of ARG-harboring bacterial hosts at community-wide level in chicken feces. These results indicated that the changes in the structure of antibiotic-induced feces microbial communities accompany changes in the abundance of bacterial hosts carrying specific ARGs in the feces microbiota. These findings will help to optimize therapeutic schemes for the effective treatment of antibiotic resistant pathogens in poultry farms. Resistome variations in faecal microbiome of chickens exposed to chlortetracycline.
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Affiliation(s)
- Wenguang Xiong
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs (SCAU) and Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642 China
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yulin Wang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yongxue Sun
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs (SCAU) and Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642 China
| | - Liping Ma
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Qinglin Zeng
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs (SCAU) and Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642 China
| | - Xiaotao Jiang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Andong Li
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Zhenling Zeng
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs (SCAU) and Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642 China
| | - Tong Zhang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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Metwally AA, Yang J, Ascoli C, Dai Y, Finn PW, Perkins DL. MetaLonDA: a flexible R package for identifying time intervals of differentially abundant features in metagenomic longitudinal studies. Microbiome 2018; 6:32. [PMID: 29439731 PMCID: PMC5812052 DOI: 10.1186/s40168-018-0402-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/12/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Microbial longitudinal studies are powerful experimental designs utilized to classify diseases, determine prognosis, and analyze microbial systems dynamics. In longitudinal studies, only identifying differential features between two phenotypes does not provide sufficient information to determine whether a change in the relative abundance is short-term or continuous. Furthermore, sample collection in longitudinal studies suffers from all forms of variability such as a different number of subjects per phenotypic group, a different number of samples per subject, and samples not collected at consistent time points. These inconsistencies are common in studies that collect samples from human subjects. RESULTS We present MetaLonDA, an R package that is capable of identifying significant time intervals of differentially abundant microbial features. MetaLonDA is flexible such that it can perform differential abundance tests despite inconsistencies associated with sample collection. Extensive experiments on simulated datasets quantitatively demonstrate the effectiveness of MetaLonDA with significant improvement over alternative methods. We applied MetaLonDA to the DIABIMMUNE cohort ( https://pubs.broadinstitute.org/diabimmune ) substantiating significant early lifetime intervals of exposure to Bacteroides and Bifidobacterium in Finnish and Russian infants. Additionally, we established significant time intervals during which novel differentially relative abundant microbial genera may contribute to aberrant immunogenicity and development of autoimmune disease. CONCLUSION MetaLonDA is computationally efficient and can be run on desktop machines. The identified differentially abundant features and their time intervals have the potential to distinguish microbial biomarkers that may be used for microbial reconstitution through bacteriotherapy, probiotics, or antibiotics. Moreover, MetaLonDA can be applied to any longitudinal count data such as metagenomic sequencing, 16S rRNA gene sequencing, or RNAseq. MetaLonDA is publicly available on CRAN ( https://CRAN.R-project.org/package=MetaLonDA ).
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Affiliation(s)
- Ahmed A. Metwally
- Department of Bioengineering, University of Illinois at Chicago, Chicago, 60607 IL USA
- Department of Medicine, University of Illinois at Chicago, Chicago, 60612 IL USA
- Department of Computer Science, University of Illinois at Chicago, Chicago, 60607 IL USA
| | - Jie Yang
- Department of Mathematics, Statistics, and Computer Science, University of Illinois at Chicago, Chicago, 60607 IL USA
| | - Christian Ascoli
- Department of Medicine, University of Illinois at Chicago, Chicago, 60612 IL USA
| | - Yang Dai
- Department of Bioengineering, University of Illinois at Chicago, Chicago, 60607 IL USA
| | - Patricia W. Finn
- Department of Medicine, University of Illinois at Chicago, Chicago, 60612 IL USA
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, 60612 IL USA
| | - David L. Perkins
- Department of Bioengineering, University of Illinois at Chicago, Chicago, 60607 IL USA
- Department of Medicine, University of Illinois at Chicago, Chicago, 60612 IL USA
- Department of Surgery, University of Illinois at Chicago, Chicago, 60612 IL USA
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25
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Dahl C, Stanislawski M, Iszatt N, Mandal S, Lozupone C, Clemente JC, Knight R, Stigum H, Eggesbø M. Gut microbiome of mothers delivering prematurely shows reduced diversity and lower relative abundance of Bifidobacterium and Streptococcus. PLoS One 2017; 12:e0184336. [PMID: 29069100 PMCID: PMC5656300 DOI: 10.1371/journal.pone.0184336] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 08/22/2017] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVE Preterm birth is the main reason for neonatal deaths worldwide. We investigate whether maternal gut microbiota may play a previously overlooked role. METHODS The Norwegian Microbiota Study (NoMIC) is a case control study on preterm birth (<259 days of gestation, calculated primarily based on the last menstrual period), including two consecutively born term infants per infant born prematurely. Eligible mothers were fluent in Norwegian and recruited from the maternity ward at a county hospital in Eastern Norway in the period 2002-2005. Fecal samples were collected at day 4 postpartum, and analyzed using 16S ribosomal RNA gene sequencing. We used samples from 121 mothers giving birth vaginally. Measures of alpha diversity (Shannon, Phylogenetic Diversity and Observed Operational Taxonomic Units) and microbiome composition were combined with information from the Medical Birth Registry, pregnancy journals, and questionnaires. RESULTS The association between maternal gut diversity and preterm delivery was examined using logistic regression. One IQR increase in Shannon diversity was significantly associated with 38% lower odds of spontaneous preterm birth, (95% confident interval (CI): 1%, 61%), and the association was stronger when adjusting for maternal age, marital status, ethnicity, parity, BMI, education, antibiotic use, pets in the household, income and smoking (48% lower odds, 95% CI: 4.2%, 72%). Mothers delivering prematurely also had lower abundance of OTUs belonging to Bifidobacterium and Streptococcus, and of the Clostridiales order. CONCLUSION Analysis of maternal gut microbiota using next-generation sequencing shows that low gut diversity, with a distinct microbial composition, is associated with spontaneous preterm delivery.
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Affiliation(s)
- Cecilie Dahl
- Department of Environmental Exposure and Epidemiology, Norwegian Institute of Public Health, Oslo, Norway
| | - Maggie Stanislawski
- University of Colorado School of Medicine, Colorado, United States of America
| | - Nina Iszatt
- Department of Environmental Exposure and Epidemiology, Norwegian Institute of Public Health, Oslo, Norway
| | | | - Catherine Lozupone
- University of Colorado School of Medicine, Colorado, United States of America
| | - Jose C. Clemente
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics & Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States of America
- Department of Medicine, Division of Clinical Immunology and Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, United States of America
| | - Rob Knight
- Departments of Pediatrics and Computer Science & Engineering, University of California San Diego, San Diego, United States of America
| | - Hein Stigum
- Department of Non-Communicable Diseases, Norwegian Institute of Public Health, Oslo, Norway
| | - Merete Eggesbø
- Department of Environmental Exposure and Epidemiology, Norwegian Institute of Public Health, Oslo, Norway
- * E-mail:
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Golubeva AV, Joyce SA, Moloney G, Burokas A, Sherwin E, Arboleya S, Flynn I, Khochanskiy D, Moya-Pérez A, Peterson V, Rea K, Murphy K, Makarova O, Buravkov S, Hyland NP, Stanton C, Clarke G, Gahan CGM, Dinan TG, Cryan JF. Microbiota-related Changes in Bile Acid & Tryptophan Metabolism are Associated with Gastrointestinal Dysfunction in a Mouse Model of Autism. EBioMedicine 2017; 24:166-178. [PMID: 28965876 PMCID: PMC5652137 DOI: 10.1016/j.ebiom.2017.09.020] [Citation(s) in RCA: 209] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 09/01/2017] [Accepted: 09/15/2017] [Indexed: 01/24/2023] Open
Abstract
Autism spectrum disorder (ASD) is one of the most prevalent neurodevelopmental conditions worldwide. There is growing awareness that ASD is highly comorbid with gastrointestinal distress and altered intestinal microbiome, and that host-microbiome interactions may contribute to the disease symptoms. However, the paucity of knowledge on gut-brain axis signaling in autism constitutes an obstacle to the development of precision microbiota-based therapeutics in ASD. To this end, we explored the interactions between intestinal microbiota, gut physiology and social behavior in a BTBR T+Itpr3tf/J mouse model of ASD. Here we show that a reduction in the relative abundance of very particular bacterial taxa in the BTBR gut - namely, bile-metabolizing Bifidobacterium and Blautia species, - is associated with deficient bile acid and tryptophan metabolism in the intestine, marked gastrointestinal dysfunction, as well as impaired social interactions in BTBR mice. Together these data support the concept of targeted manipulation of the gut microbiota for reversing gastrointestinal and behavioral symptomatology in ASD, and offer specific plausible targets in this endeavor.
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Affiliation(s)
- Anna V Golubeva
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Susan A Joyce
- APC Microbiome Institute, University College Cork, Cork, Ireland; School of Biochemistry & Cell Biology, University College Cork, Cork, Ireland
| | - Gerard Moloney
- Department of Anatomy & Neuroscience, University College Cork, Cork, Ireland
| | | | - Eoin Sherwin
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Silvia Arboleya
- APC Microbiome Institute, University College Cork, Cork, Ireland; Teagasc Food Research Centre, Moorepark Fermoy, County Cork, Ireland
| | - Ian Flynn
- Department of Anatomy & Neuroscience, University College Cork, Cork, Ireland
| | | | | | | | - Kieran Rea
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Kiera Murphy
- Teagasc Food Research Centre, Moorepark Fermoy, County Cork, Ireland
| | - Olga Makarova
- Research Institute of Human Morphology, Moscow, Russia; Lomonosov Moscow State University, Moscow, Russia
| | - Sergey Buravkov
- Research Institute of Human Morphology, Moscow, Russia; Lomonosov Moscow State University, Moscow, Russia
| | - Niall P Hyland
- APC Microbiome Institute, University College Cork, Cork, Ireland; Department of Pharmacology & Therapeutics, University College Cork, Cork, Ireland
| | - Catherine Stanton
- APC Microbiome Institute, University College Cork, Cork, Ireland; Teagasc Food Research Centre, Moorepark Fermoy, County Cork, Ireland; Department of Psychiatry & Neurobehavioural Sciences, University College Cork, Cork, Ireland
| | - Gerard Clarke
- APC Microbiome Institute, University College Cork, Cork, Ireland; Department of Psychiatry & Neurobehavioural Sciences, University College Cork, Cork, Ireland
| | - Cormac G M Gahan
- APC Microbiome Institute, University College Cork, Cork, Ireland; School of Microbiology, University College Cork, Cork, Ireland
| | - Timothy G Dinan
- APC Microbiome Institute, University College Cork, Cork, Ireland; Department of Psychiatry & Neurobehavioural Sciences, University College Cork, Cork, Ireland
| | - John F Cryan
- APC Microbiome Institute, University College Cork, Cork, Ireland; Department of Anatomy & Neuroscience, University College Cork, Cork, Ireland.
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Stanislawski MA, Dabelea D, Wagner BD, Sontag MK, Lozupone CA, Eggesbø M. Pre-pregnancy weight, gestational weight gain, and the gut microbiota of mothers and their infants. Microbiome 2017; 5:113. [PMID: 28870230 PMCID: PMC5584478 DOI: 10.1186/s40168-017-0332-0] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 08/23/2017] [Indexed: 05/16/2023]
Abstract
BACKGROUND Recent evidence supports that the maternal gut microbiota impacts the initial infant gut microbiota. Since the gut microbiota may play a causal role in the development of obesity, it is important to understand how pre-pregnancy weight and gestational weight gain (GWG) impact the gut microbiota of mothers at the time of delivery and their infants in early life. In this study, we performed 16S rRNA gene sequencing on gut microbiota samples from 169 women 4 days after delivery and from the 844 samples of their infants at six timepoints during the first 2 years of life. We categorized the women (1) according to pre-pregnancy body mass index into overweight/obese (OW/OB, BMI ≥ 25) or non-overweight/obese (BMI < 25) and (2) into excessive and non-excessive GWG in the subset of mothers of full-term singleton infants (N = 116). We compared alpha diversity and taxonomic composition of the maternal and infant samples by exposure groups. We also compared taxonomic similarity between maternal and infant gut microbiota. RESULTS Maternal OW/OB was associated with lower maternal alpha diversity. Maternal pre-pregnancy OW/OB and excessive GWG were associated with taxonomic differences in the maternal gut microbiota, including taxa from the highly heritable family Christensenellaceae, the genera Lachnospira, Parabacteroides, Bifidobacterium, and Blautia. These maternal characteristics were not associated with overall differences in the infant gut microbiota over the first 2 years of life. However, the presence of specific OTUs in maternal gut microbiota at the time of delivery did significantly increase the odds of presence in the infant gut at age 4-10 days for many taxa, and these included some lean-associated taxa. CONCLUSIONS Our results show differences in maternal gut microbiota composition at the time of delivery by pre-pregnancy weight and GWG, but these changes were only associated with limited compositional differences in the early life gut microbiota of their infants. Further work is needed to determine the degree to which these maternal microbiota differences at time of birth with OW/OB and GWG may affect the health of the infant over time and by what mechanism.
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Affiliation(s)
- Maggie A. Stanislawski
- Colorado School of Public Health, Colorado, Aurora USA
- VA Eastern Colorado Health Care System, Denver, CO USA
| | - Dana Dabelea
- Colorado School of Public Health, Colorado, Aurora USA
- University of Colorado School of Medicine, Colorado, Aurora USA
| | | | | | | | - Merete Eggesbø
- Department of Environmental Exposure and Epidemiology, Norwegian Institute of Public Health, PO Box 4404, Oslo, Norway
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Wang SY, Yu XH, Li M, Li SS, Miao JJ, Yu Q, He F. [A Preliminary Analysis of Bifidobacterial Species Dependent Influence on the Health of the Elderly]. Sichuan Da Xue Xue Bao Yi Xue Ban 2017; 48:745-749. [PMID: 29130669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
OBJECTIVE To analyze the species dependent effect of bifidobacteria to the heath of the middle and elderly. METHODS Total 148 healthy volunteers living in Chengdu with 5074 years old were recruited in 2015. The blood samples were collected from them and analyzed physiologically and immunologically. The fecal bifidobacterial were also analyzed by realtime fluorescence quantitative PCR (qPCR) using 16S rRNA targeting designed gene and species specific primers. RESULTS Bifidobacterium can be detected in feces of the elderly,the detection rate was 100%,10⁸/g fecal. Especially,more species predominated in the infants were found the tested subjects. Bifidobacterium was positively associated with urea nitrogen ( r=0.214, P<0.05). B. adolescentis was negatively associated with body mass index (BMI) ( r=-0.311, P<0.05),while B.catenulatum was positive to BMI ( r=0.167, P<0.05). B.breve and high density lipoproteincholesterol (HDLC) were negatively correlated ( r=-0.247, P<0.05). Bifidobacterium infantis and HDLC were positively correlated ( r=0.350, P<0.05). Among tested immune parameters,only B.bifidum was found to be positive associated with IgA ( r=0.365, P<0.05). CONCLUSION Bifidobacterium might affect the host physiologically and immunology in the species dependent manner. Keeping intestinal bifidobacteria in the ideal species composition might be one of effective ways to slow immune senescence,and promote the health of the elderly.
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Affiliation(s)
- Shu-Yue Wang
- Department of Nutrition,Food Safety and Toxiology,West China School of Public Health,Sichuan University,Chengdu 610041,China
| | - Xiao-Hong Yu
- Department of Nutrition,Food Safety and Toxiology,West China School of Public Health,Sichuan University,Chengdu 610041,China
| | - Ming Li
- Department of Nutrition,Food Safety and Toxiology,West China School of Public Health,Sichuan University,Chengdu 610041,China
| | - Shan-Shan Li
- Department of Nutrition,Food Safety and Toxiology,West China School of Public Health,Sichuan University,Chengdu 610041,China
| | - Jun-Jie Miao
- Department of Sanitary Inspection,School of Public Health,Hebei Medical University,Shijiazhuang 050017,China
| | - Qian Yu
- Department of Public Health Laboratory Sciences,West China School of Public Health,Sichuan University,Chengdu 610041,China
| | - Fang He
- Department of Nutrition,Food Safety and Toxiology,West China School of Public Health,Sichuan University,Chengdu 610041,China
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Suriano F, Bindels LB, Verspreet J, Courtin CM, Verbeke K, Cani PD, Neyrinck AM, Delzenne NM. Fat binding capacity and modulation of the gut microbiota both determine the effect of wheat bran fractions on adiposity. Sci Rep 2017; 7:5621. [PMID: 28717237 PMCID: PMC5514075 DOI: 10.1038/s41598-017-05698-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 06/02/2017] [Indexed: 12/18/2022] Open
Abstract
The aim of this study was to determine the impact of different wheat bran fractions on the gut microbiota and fat binding capacity to explain their differential effects on metabolic and inflammatory disorders induced by a western diet (WD) in mice. Wheat bran derived arabinoxylan oligosaccharides (AXOS), a crude fraction of wheat bran (WB), or the same wheat bran with reduced particle size (WBs) were added to the WD of mice for 8 weeks. AXOS shifted the gut microbiota composition, blunted Clostridium and Turicibacter genera and strongly promoted Bifidobacterium and Butyricicoccus genera, independently of changes in gut antimicrobial peptide expression. AXOS was the most efficient to reduce adiposity. Only WB fraction promoted fat excretion and differed from the other fractions by the capacity to increase the Akkermansia genus and to counteract gut interleukin 1 beta (IL1β) overexpression. Strikingly, WBs promoted steatosis and adipose tissue inflammation, despite its ability -like WB- to increase bacterial diversity. In conclusion, wheat bran fractions differently affect metabolic and inflammatory disorders associated with WD feeding, depending on their particle size, their fat binding capacity and their influence on the gut microbiota. Those results might be useful to take into account in nutritional advices to control obesity.
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Affiliation(s)
- Francesco Suriano
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université catholique de Louvain, B-1200, Brussels, Belgium
| | - Laure B Bindels
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université catholique de Louvain, B-1200, Brussels, Belgium
| | - Joran Verspreet
- Laboratory of Food Chemistry and Biochemistry, Leuven Food Science and Nutrition, Research Center (LFoRCe). KU Leuven, B-3001, Leuven, Belgium
| | - Christophe M Courtin
- Laboratory of Food Chemistry and Biochemistry, Leuven Food Science and Nutrition, Research Center (LFoRCe). KU Leuven, B-3001, Leuven, Belgium
| | - Kristin Verbeke
- Translational Research Center for Gastrointestinal Disorders and Leuven Food Science and Nutrition Center, KU Leuven, B-3000, Leuven, Belgium
| | - Patrice D Cani
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université catholique de Louvain, B-1200, Brussels, Belgium
- Walloon Excellence in Life Sciences and BIOtechnology (WELBIO), Louvain Drug Research Institute, UCL, B-1200, Brussels, Belgium
| | - Audrey M Neyrinck
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université catholique de Louvain, B-1200, Brussels, Belgium
| | - Nathalie M Delzenne
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université catholique de Louvain, B-1200, Brussels, Belgium.
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30
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Kato K, Odamaki T, Mitsuyama E, Sugahara H, Xiao JZ, Osawa R. Age-Related Changes in the Composition of Gut Bifidobacterium Species. Curr Microbiol 2017; 74:987-995. [PMID: 28593350 PMCID: PMC5486783 DOI: 10.1007/s00284-017-1272-4] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 05/27/2017] [Indexed: 12/18/2022]
Abstract
Bifidobacteria are one of the major components in human microbiota that are suggested to function in maintaining human health. The colonization and cell number of Bifidobacterium species in human intestine vary with ageing. However, sequential changes of Bifidobacterium species ranging from newborns to centenarians remain unresolved. Here, we investigated the gut compositional changes of Bifidobacterium species over a wide range of ages. Faecal samples of 441 healthy Japanese subjects between the ages of 0 and 104 years were analysed using real-time PCR with species-specific primers. B. longum group was widely detected from newborns to centenarians, with the highest detection rate. B. breve was detected in approximately 70% of children under 3 years old. B. adolescentis and B. catenulatum groups were predominant after weaning. B. bifidum was detected at almost all ages. The detection rate of B. dentium was higher in the elderly than in other ages. B. animalis ssp. lactis was detected in 11.4% of the subjects and their ages were restricted. B. gallinarum goup was detected in only nine subjects, while B. minimum and B. mongoliense were undetected at any age. The presence of certain Bifidobacterium groups was associated with significantly higher numbers of other Bifidobacterium species/subspecies. Inter-species correlations were found among each species, exception for B. animalis ssp. lactis. These results revealed the patterns and transition points with respect to compositional changes of Bifidobacterium species that occur with ageing, and the findings indicate that there may be symbiotic associations between some of these species in the gut microbiota.
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Affiliation(s)
- Kumiko Kato
- Next Generation Science Institute R&D Division, Morinaga Milk Industry Co., Ltd., 5-1-83, Higashihara, Zama-city, Kanagawa, 252-8583, Japan.
| | - Toshitaka Odamaki
- Next Generation Science Institute R&D Division, Morinaga Milk Industry Co., Ltd., 5-1-83, Higashihara, Zama-city, Kanagawa, 252-8583, Japan
| | - Eri Mitsuyama
- Next Generation Science Institute R&D Division, Morinaga Milk Industry Co., Ltd., 5-1-83, Higashihara, Zama-city, Kanagawa, 252-8583, Japan
| | - Hirosuke Sugahara
- Next Generation Science Institute R&D Division, Morinaga Milk Industry Co., Ltd., 5-1-83, Higashihara, Zama-city, Kanagawa, 252-8583, Japan
| | - Jin-Zhong Xiao
- Next Generation Science Institute R&D Division, Morinaga Milk Industry Co., Ltd., 5-1-83, Higashihara, Zama-city, Kanagawa, 252-8583, Japan
| | - Ro Osawa
- Department of Bioresource Science, Graduate School of Agricultural Science, Kobe University, Kobe, Hyogo, Japan
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Pidgorskyi VS, Kovalenko NK, Garmasheva IL. Taxonomic Research, Biological Properties and Biosynthetic Activity of Lactic Acid Bacteria and Bifdobacteria Isolated from Various Natural Ecological Niches. Mikrobiol Z 2016; 78:8-18. [PMID: 30141879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Lactic acid bacteria (LAB) and bifdobacteria play an important role in human health and have wide application in food industry. LAB propagation and high quantity of them in natural substrates testifes that many species of these microorganisms have adapted to the environmental conditions, and specifc ecological niches. Lactic acid bacteria isolated from different ecological niches were identifed using phenotypic and molecular–genetic methods. The species of Lactobacillus plantarum, Enterococcus faecium, E. durans, E. hirae, E. faecalis were identifed among LAB. Bifdobacteria were majorly represented by Bifdobacterium infantis, B. breve, B. animalis, B. bifdum and B. dentium species. The intraspecifc heterogeneity of LAB and bifdobacteria strains isolated from distal part of intestinal tract of people belonging to various age group was investigated. The role of teichoic acids in adhesion of the studied LAB strains to human’s buccal epithelium was evaluated. Different biological activities, such as gastric juice resistance, tolerance to bile acids, adhesive properties to macroorganism’s epithelial cells, sensitivity to clinically signifcant antibiotics were studied. All of these properties make specifc LAB and bifdobacteria strains to be promising for probiotics and functional foods creation.
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Fernández-Navarro T, Salazar N, Gutiérrez-Díaz I, Sánchez B, Rúas-Madiedo P, de Los Reyes-Gavilán CG, Margolles A, Gueimonde M, González S. Bioactive compounds from regular diet and faecal microbial metabolites. Eur J Nutr 2016; 57:487-497. [PMID: 27744545 DOI: 10.1007/s00394-016-1332-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 10/11/2016] [Indexed: 12/17/2022]
Abstract
PURPOSE Short-chain fatty acids (SCFAs) formation by intestinal bacteria is regulated by many different factors, among which dietary fibre is currently receiving most attention. However, since fibre-rich foods are usually good dietary sources of phenolic compounds, which are also known to affect the microbiota, authors hypothesize that the regular intake of these bioactive compounds could be associated with a modulation of faecal SCFA production by the intestinal microbiota. METHODS In this work, food intake was recorded by means of a validated Food Frequency Questionnaire. Fibres were determined using Marlett food composition tables, and phenolic compounds were obtained from Phenol-Explorer Database. Analysis of SCFA was performed by gas chromatography-flame ionization/mass spectrometry and quantification of microbial populations in faeces by quantitative PCR. RESULTS Klason lignin and its food contributors, as predictors of faecal butyrate production, were directly associated with Bacteroides and Bifidobacterium levels, as well as lignans with Bacteroides. Also, anthocyanidins, provided by strawberries, were associated with faecal propionate and inversely related to Lactobacillus group. CONCLUSIONS These results support the hypothesis we put forward regarding the association between some vegetable foods (strawberries, pasta, lentils, lettuce and olive oil) and faecal SCFA. More studies are needed in order to elucidate whether these associations have been mediated by the bacterial modulatory effect of the bioactive compounds, anthocyanins, lignans or Klason lignin, present in foodstuffs.
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Affiliation(s)
- Tania Fernández-Navarro
- Department of Functional Biology, University of Oviedo, C/Julián Clavería s/n, 33006, Oviedo, Asturias, Spain
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain
| | - Nuria Salazar
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain
| | - Isabel Gutiérrez-Díaz
- Department of Functional Biology, University of Oviedo, C/Julián Clavería s/n, 33006, Oviedo, Asturias, Spain
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain
| | - Borja Sánchez
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain
| | - Patricia Rúas-Madiedo
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain
| | - Clara G de Los Reyes-Gavilán
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain
| | - Abelardo Margolles
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain
| | - Miguel Gueimonde
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain
| | - Sonia González
- Department of Functional Biology, University of Oviedo, C/Julián Clavería s/n, 33006, Oviedo, Asturias, Spain.
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Fisinin VI, Il'ina LA, Iyldyrym EA, Nikonov IN, Filippova VA, Laptev GY, Novikova NI, Grozina AA, Lenkova TN, Manukya VA, Egorov IA. Broiler Cecal Microbiocenoses Depending on Mixed Fodder. Mikrobiologiia 2016; 85:472-480. [PMID: 28853779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Molecular genetic techniques (NGS sequencing and quantitative PCR) were used to determine the composition of the cecal bacterial community of broiler chickens fed with different mixed fodder. The Cecal microbiome exhibited taxonomic diversity, with both typical inhabitants of avian intestine belonging to the families Clostridiaceae, Eubacteriaceae, and Lactobacillaceae and to the phylum Bacteroidetes, and new un- identified taxa, as well as bacteria of the families Lachnospiraceae and Ruminococcaceae, which were previ- ously considered restricted to the rumen microflora. Contrary to traditional concepts, enterococci and bi- fidobacteria were among the minor components of the community, lactate-fermenting species were absent, and typical avian pathogens of the genus Staphylococcus were detected but seldom. Members of the family Suterellaceae and the genus Gallibacterium, which are responsible for avian respiratory infections, were also detected. Significant fluctuations of abundance and composition of microbial groups within the cecal com- munity and of the parameters of broiler productivity were found to occur depending on the feed allowance. Cellulose content in the feed had the most pronounced effect on the composition aid structure of bacterial communities. Decreased cellulose content resulted in a decrease of bacterial abundance by-aii order of mag- nitude and in increased ratios of members of the phylum Bacteroidetes and the family Clostridiaceae, which possess the enzymes degrading starch polysadcharides. Abundance of the normal inhabitants of avian intes- tine belonging to the genus Ldctobacillus and the order Bacillales decreased, while the share of Escherichia and members of the family Sutterellaceae increased, including some species capable of causing dysbiotic changes in avian intestine. No significant change in abundance of cellulolytics of the families Ruminococca- ceae, Lachnospiraceae, and Eubacteriaceae was observed.
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Michelini S, Modesto M, Filippini G, Spiezio C, Sandri C, Biavati B, Pisi A, Mattarelli P. Bifidobacterium aerophilum sp. nov., Bifidobacterium avesanii sp. nov. and Bifidobacterium ramosum sp. nov.: Three novel taxa from the faeces of cotton-top tamarin (Saguinus oedipus L.). Syst Appl Microbiol 2016; 39:229-236. [PMID: 27236565 DOI: 10.1016/j.syapm.2016.04.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 04/12/2016] [Accepted: 04/14/2016] [Indexed: 01/08/2023]
Abstract
Forty-five microorganisms were isolated on bifidobacteria selective medium from one faecal sample of an adult subject of the cotton-top tamarin (Saguinus oedipus L.). All isolates were Gram-positive, catalase-negative, anaerobic, fructose-6-phosphate phosphoketolase positive, and asporogenous rod-shaped bacteria. In this study, only eight out of the forty-five strains were characterized more deeply, whereas the others are still currently under investigation. They were grouped by BOX-PCR into three clusters: Cluster I (TRE 17(T), TRE 7, TRE 26, TRE 32, TRE 33, TRE I), Cluster II (TRE C(T)), and Cluster III (TRE M(T)). Comparative analysis of 16S rRNA gene sequences confirmed the results from the cluster analysis and revealed relatively low level similarities to each other (mean value 95%) and to members of the genus Bifidobacterium. All eight isolates showed the highest level of 16S rRNA gene sequence similarities with Bifidobacterium scardovii DSM 13734(T) (mean value 96.6%). Multilocus sequence analysis (MLSA) of five housekeeping genes (hsp60, rpoB, clpC, dnaJ and dnaG) supported their independent phylogenetic position to each other and to related species of Bifidobacterium. The G+C contents were 63.2%, 65.9% and 63.0% for Cluster I, Cluster II and Cluster III, respectively. Peptidoglycan types were A3α l-Lys-l-Thr-l-Ala, A4β l-Orn (Lys)-d-Ser-d-Glu and A3β l-Orn-l-Ser-l-Ala in Clusters I, II and III, respectively. Based on the data provided, each cluster represented a novel taxon for which the names Bifidobacterium aerophilum sp. nov. (TRE 17(T)=DSM 100689=JCM 30941; TRE 26=DSM 100690=JCM 30942), Bifidobacterium avesanii sp. nov. (TRE C(T)=DSM 100685=JCM 30943) and Bifidobacterium ramosum sp. nov. (TRE M=DSM 100688=JCM 30944) are proposed.
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Affiliation(s)
| | - Monica Modesto
- Department of Agricultural Sciences, University of Bologna, Italy.
| | | | - Caterina Spiezio
- Natura Viva Garda Zoological Park S.r.l., Bussolengo, Verona, Italy.
| | - Camillo Sandri
- Natura Viva Garda Zoological Park S.r.l., Bussolengo, Verona, Italy.
| | - Bruno Biavati
- Institute of Earth Systems, Division of Rural Sciences & Food Systems, University of Malta, Msida, Malta.
| | - Annamaria Pisi
- Department of Agricultural Sciences, University of Bologna, Italy.
| | - Paola Mattarelli
- Department of Agricultural Sciences, University of Bologna, Italy.
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Abstract
Human intestinal flora comprises thousands of bacterial species. Growth and composition of intestinal microbiota is dependent on various parameters, including immune mechanisms, dietary factors and intestinal motility. Patients with spinal cord injury (SCI) frequently display neurogenic bowel dysfunction due to the absence of central nervous system control over the gastrointestinal system. Considering the bowel dysfunction and altered colonic transit time in patients with SCI, we hypothesized the presence of a significant change in the composition of their gut microbiome. The objective of this study was to characterize the gut microbiota in adult SCI patients with different types of bowel dysfunction. We tested our hypothesis on 30 SCI patients (15 upper motor neuron [UMN] bowel syndrome, 15 lower motor neuron [LMN] bowel syndrome) and 10 healthy controls using the 16S rRNA sequencing. Gut microbial patterns were sampled from feces. Independent of study groups, gut microbiota of the participants were dominated by Blautia, Bifidobacterium, Faecalibacterium and Ruminococcus. When we compared all study groups, Roseburia, Pseudobutyrivibrio, Dialister, Marvinbryantia and Megamonas appeared as the genera that were statistically different between groups. In comparison to the healthy group, total bacterial counts of Pseudobutyrivibrio, Dialister and Megamonas genera were significantly lower in UMN bowel dysfunction group. The total bacterial count of Marvinbryantia genus was significantly lower in UMN bowel dysfunction group when compared to the LMN group. Total bacterial counts of Roseburia, Pseudobutyrivibrio and Megamonas genera were significantly lower in LMN bowel dysfunction group when compared to healthy groups. Our results demonstrate for the first time that butyrate-producing members are specifically reduced in SCI patients when compared to healthy subjects. The results of this study would be of interest since to our knowledge, microbiome-associated studies targeting SCI patients are non-existent and the results might help explain possible implications of gut microbiome in SCI.
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Affiliation(s)
- Bilgi Gungor
- Department of Molecular Biology and Genetics, Middle East Technical University, Ankara, Turkey
| | - Emre Adiguzel
- Department of PMR, Gulhane Military Medical Academy, Turkish Armed Forces Rehabilitation Center, Ankara,Turkey
| | - Ihsan Gursel
- THORLAB, Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Bilge Yilmaz
- Department of PMR, Gulhane Military Medical Academy, Turkish Armed Forces Rehabilitation Center, Ankara,Turkey
- * E-mail: (MG); (BY)
| | - Mayda Gursel
- Department of Molecular Biology and Genetics, Middle East Technical University, Ankara, Turkey
- * E-mail: (MG); (BY)
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El Enshasy H, Malik K, Malek RA, Othman NZ, Elsayed EA, Wadaan M. Anaerobic Probiotics: The Key Microbes for Human Health. Adv Biochem Eng Biotechnol 2016. [PMID: 26907552 DOI: 10.1007/10-2015-5008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Human gastrointestinal microbiota (HGIM) incorporate a large number of microbes from different species. Anaerobic bacteria are the dominant organisms in this microbial consortium and play a crucial role in human health. In addition to their functional role as the main source of many essential metabolites for human health, they are considered as biotherapeutic agents in the regulation of different human metabolites. They are also important in the prevention and in the treatment of different physical and mental diseases. Bifidobacteria are the dominant anaerobic bacteria in HGIM and are widely used in the development of probiotic products for infants, children and adults. To develop bifidobacteria-based bioproducts, therefore, it is necessary to develop a large-scale biomass production platform based on a good understanding of the ideal medium and bioprocessing parameters for their growth and viability. In addition, high cell viability should be maintained during downstream processing and storage of probiotic cell powder or the final formulated product. In this work we review the latest information about the biology, therapeutic activities, cultivation and industrial production of bifidobacteria.
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Affiliation(s)
- Hesham El Enshasy
- Institute of Bioproduct Development (IBD), Universiti Teknologi Malaysia (UTM), Skudai, Johor Bahru, Malaysia.
- City of Scientific Research and Technology Applications, New Burg Al Arab, Alexandria, Egypt.
| | - Khairuddin Malik
- Institute of Bioproduct Development (IBD), Universiti Teknologi Malaysia (UTM), Skudai, Johor Bahru, Malaysia
| | - Roslinda Abd Malek
- Institute of Bioproduct Development (IBD), Universiti Teknologi Malaysia (UTM), Skudai, Johor Bahru, Malaysia
| | - Nor Zalina Othman
- Institute of Bioproduct Development (IBD), Universiti Teknologi Malaysia (UTM), Skudai, Johor Bahru, Malaysia
| | - Elsayed Ahmed Elsayed
- Bioproducts Research Chair, Faculty of Science, King Saud University, Riyadh, Saudi Arabia
- Natural and Microbial Products Department, National Research Centre, Dokki, Cairo, Egypt
| | - Mohammad Wadaan
- Bioproducts Research Chair, Faculty of Science, King Saud University, Riyadh, Saudi Arabia
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Srutkova D, Schwarzer M, Hudcovic T, Zakostelska Z, Drab V, Spanova A, Rittich B, Kozakova H, Schabussova I. Bifidobacterium longum CCM 7952 Promotes Epithelial Barrier Function and Prevents Acute DSS-Induced Colitis in Strictly Strain-Specific Manner. PLoS One 2015. [PMID: 26218526 PMCID: PMC4517903 DOI: 10.1371/journal.pone.0134050] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Reduced microbial diversity has been associated with inflammatory bowel disease (IBD) and probiotic bacteria have been proposed for its prevention and/or treatment. Nevertheless, comparative studies of strains of the same subspecies for specific health benefits are scarce. Here we compared two Bifidobacterium longum ssp. longum strains for their capacity to prevent experimental colitis. METHODS Immunomodulatory properties of nine probiotic bifidobacteria were assessed by stimulation of murine splenocytes. The immune responses to B. longum ssp. longum CCM 7952 (Bl 7952) and CCDM 372 (Bl 372) were further characterized by stimulation of bone marrow-derived dendritic cell, HEK293/TLR2 or HEK293/NOD2 cells. A mouse model of dextran sulphate sodium (DSS)-induced colitis was used to compare their beneficial effects in vivo. RESULTS The nine bifidobacteria exhibited strain-specific abilities to induce cytokine production. Bl 372 induced higher levels of both pro- and anti-inflammatory cytokines in spleen and dendritic cell cultures compared to Bl 7952. Both strains engaged TLR2 and contain ligands for NOD2. In a mouse model of DSS-induced colitis, Bl 7952, but not Bl 372, reduced clinical symptoms and preserved expression of tight junction proteins. Importantly, Bl 7952 improved intestinal barrier function as demonstrated by reduced FITC-dextran levels in serum. CONCLUSIONS We have shown that Bl 7952, but not Bl 372, protected mice from the development of experimental colitis. Our data suggest that although some immunomodulatory properties might be widespread among the genus Bifidobacterium, others may be rare and characteristic only for a specific strain. Therefore, careful selection might be crucial in providing beneficial outcome in clinical trials with probiotics in IBD.
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Affiliation(s)
- Dagmar Srutkova
- Laboratory of Gnotobiology, Institute of Microbiology of the Czech Academy of Sciences, v.v.i., Novy Hradek, Czech Republic
| | - Martin Schwarzer
- Laboratory of Gnotobiology, Institute of Microbiology of the Czech Academy of Sciences, v.v.i., Novy Hradek, Czech Republic
| | - Tomas Hudcovic
- Laboratory of Gnotobiology, Institute of Microbiology of the Czech Academy of Sciences, v.v.i., Novy Hradek, Czech Republic
| | - Zuzana Zakostelska
- Laboratory of Cellular and Molecular Immunology, Institute of Microbiology of the Czech Academy of Sciences, v.v.i., Prague, Czech Republic
| | - Vladimir Drab
- Dairy Research Institute Ltd., Prague, Czech Republic
| | - Alena Spanova
- Brno University of Technology, Faculty of Chemistry, Brno, Czech Republic
| | - Bohuslav Rittich
- Brno University of Technology, Faculty of Chemistry, Brno, Czech Republic
| | - Hana Kozakova
- Laboratory of Gnotobiology, Institute of Microbiology of the Czech Academy of Sciences, v.v.i., Novy Hradek, Czech Republic
- * E-mail:
| | - Irma Schabussova
- Institute of Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
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Michelini S, Modesto M, Oki K, Stenico V, Stefanini I, Biavati B, Watanabe K, Ferrara A, Mattarelli P. Isolation and identification of cultivable Bifidobacterium spp. from the faeces of 5 baby common marmosets (Callithrix jacchus L.). Anaerobe 2015; 33:101-4. [PMID: 25746741 DOI: 10.1016/j.anaerobe.2015.03.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 03/03/2015] [Accepted: 03/04/2015] [Indexed: 12/16/2022]
Abstract
Ninety-two bifidobacterial strains were obtained from the faeces of 5 baby common marmosets, three known species Bifidobacterium aesculapii, Bifidobacterium callithricos and Bifidobacterium reuteri and 4 novel putative bifidobacterial species were retrieved. The occurrence of bifidobacteria in non-human primate babies is described for the first time.
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Affiliation(s)
- Samanta Michelini
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 42, Bologna 40127, Italy
| | - Monica Modesto
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 42, Bologna 40127, Italy
| | - Kaihei Oki
- Yakult Central Institute, 5-11 Izumi, Kunitachi, Tokyo 186-8650, Japan
| | - Verena Stenico
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 42, Bologna 40127, Italy
| | - Ilaria Stefanini
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 42, Bologna 40127, Italy
| | - Bruno Biavati
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 42, Bologna 40127, Italy
| | - Koichi Watanabe
- Yakult Central Institute, 5-11 Izumi, Kunitachi, Tokyo 186-8650, Japan
| | | | - Paola Mattarelli
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 42, Bologna 40127, Italy.
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Bukharin OV, Stepanova TF, Peruhova NB, Ivanova EV, Andryuschenko SV, Kataeva LV. [Protein profile strain specificity of Bifidobacterium genus members]. Zh Mikrobiol Epidemiol Immunobiol 2015:3-9. [PMID: 26016337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
AIM Analysis of differences in protein spectra of various bifidobacteria strains of intestine microsymbiocenosis using identification results from MALDI-TOF mass-spectrometer. MATERIALS AND METHODS Results of mass-spectrometry ("Bruker Daltonics", Germany) for 57 intestine isolates' of Bifidobacterium spp. are provided. 500,laser impulses were used for obtaining every mass-spectrum; parameters of mass-spectrometer were optimized for the 1000-18000 m/z (mass to charge) range. RESULTS Comparative analysis of mass-spectrometry biomarkers for Bifidobacterium genus members has detected variations in the quantity of peaks (4 to 56) among both various species and within bifidobacteria species, that reflects uniqueness of the protein profile of separate strains. Along with biomarkers, specific for most cultures, significant differences of the examined peaks were detected; including among microorganisms, that belong to the same species. As such, for B. bifidum species strains--only in 67 ± 7.5% of cultures the presence of common peaks in'the 9282-9901 m/z was detected, whereas protein spectra in other ranges differed by both quantity and molecular mass. CONCLUSION Differences in protein profile of Bifidobacterium genus microorganisms reflect uniqueness of protein spectra (proteome) of every separate strain; determining their functional activity, features of interaction, with associative microsymbionts and host organism in human associative symbiosis.
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Zhang LL, Miao JJ, Li M, Yu Q, Yao JR, Huang CY, He F. [Colonization and development of intestinal bifidobacteria in early infancy]. Zhongguo Dang Dai Er Ke Za Zhi 2015; 17:207-212. [PMID: 25815485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
OBJECTIVE To study the characteristics of the colonization of 8 species of bifidobacteria by systematically profiling fecal bifidobacterial community in the early life of infants. METHODS Fresh fecal samples including meconium samples were collected for culture and isolation of fecal bifidobacteria from 16 cases of full-term newborn infants born between March and April 2013 at their life of 2, 4, 7, 10, 14, 28, and 90 days. The isolated fecal bifidobacteria were taxonomically identified to genus and 8 species with PCR analysis. RESULTS One hundred and fifty-two predominant bifidobacteria strains were detected in the fecal samples, the detection rate of B. breve (22.4%) were the highest. Bifidobacteria were found in the feces of 8% infants 4 days after birth. The colonization rates increased to 54% and 60% at 28 days and 3 months respectively, significantly exceeding the colonization rate at 4 days after birth (P<0.05). Adult-type bifidobacteria B. catenulatum were found in the infants 10 days after birth, and infant-type bifidobacteria B. infantis were found at 14 days after birth, but infant-type bifidobacteria B. infantis were detected at a high level until 3 months after birth. The most tested infants had 2 species or less of bifidobacteria. CONCLUSIONS Intestinal bifidobacteria in infants might have less diversity in early infancy. Infant-type bifidobacteria appear late, while adult-type bifidobacteria colonize earlier.
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Affiliation(s)
- Ling-Lin Zhang
- Department of Public Health Laboratory Sciences, West China School of Public Health, Sichuan University, Chengdu 610041, China.
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41
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Beliaeva EA, Chervinetz YV, Chervinetz VM, Troshin AV, Mironov AY, Nezametdinova VZ, Averina OV, Danilenko VN. [The characteristics of probiotic properties of strains of genus of bifidobacterium separated from gastrointestinal tract of residents of the central region of Russia]. Klin Lab Diagn 2015; 60:53-58. [PMID: 26027262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The 156 samples of feces separated from healthy residents of the Central region of Russia were used to compose collection of 87 strains of Bifidobacterium out of which 5 strains with wide antagonistic activity related to pathogenic and opportunistic microorganisms were selected. The selected strains are characterized by high probiotic potentials. They have adhesive properties and sensitivity to antibiotics and preparations corresponding to main requirements of common pharmacopoeia articles to strains of microorganisms used in production of probiotics for medicinal application. The given strains of Bifidobacterium can be recommended for development of effective probiotic pharmaceuticals directed to residents of the Central region of Russia.
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Vazquez-Gutierrez P, Lacroix C, Jaeggi T, Zeder C, Zimmerman MB, Chassard C. Bifidobacteria strains isolated from stools of iron deficient infants can efficiently sequester iron. BMC Microbiol 2015; 15:3. [PMID: 25591860 PMCID: PMC4320568 DOI: 10.1186/s12866-014-0334-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 12/18/2014] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Bifidobacteria is one of the major gut commensal groups found in infants. Their colonization is commonly associated with beneficial effects to the host through mechanisms like niche occupation and nutrient competition against pathogenic bacteria. Iron is an essential element necessary for most microorganisms, including bifidobacteria and efficient competition for this micronutrient is linked to proliferation and persistence. For this research we hypothesized that bifidobacteria in the gut of iron deficient infants can efficiently sequester iron. The aim of the present study was to isolate bifidobacteria in fecal samples of iron deficient Kenyan infants and to characterize siderophore production and iron internalization capacity. RESULTS Fifty-six bifidobacterial strains were isolated by streaking twenty-eight stool samples from Kenyan infants, in enrichment media. To target strains with high iron sequestration mechanisms, a strong iron chelator 2,2-dipyridyl was supplemented to the agar media. Bifidobacterial isolates were first identified to species level by 16S rRNA sequencing, yielding B. bifidum (19 isolates), B. longum (15), B. breve (11), B. kashiwanohense (7), B. pseudolongum (3) and B. pseudocatenulatum (1). While most isolated bifidobacterial species are commonly encountered in the infantile gut, B. kashiwanohense was not frequently reported in infant feces. Thirty strains from culture collections and 56 isolates were characterized for their siderophore production, tested by the CAS assay. Siderophore activity ranged from 3 to 89% siderophore units, with 35 strains (41%) exhibiting high siderophore activity, and 31 (36%) and 20 (23%) showing intermediate or low activity. The amount of internalized iron of 60 bifidobacteria strains selected for their siderophore activity, was in a broad range from 8 to118 μM Fe. Four strains, B. pseudolongum PV8-2, B. kashiwanohense PV20-2, B. bifidum PV28-2a and B. longum PV5-1 isolated from infant stool samples were selected for both high siderophore activity and iron internalization. CONCLUSIONS A broad diversity of bifidobacteria were isolated in infant stools using iron limited conditions, with some strains exhibiting high iron sequestration properties. The ability of bifidobacteria to efficiently utilize iron sequestration mechanism such as siderophore production and iron internalization may confer an ecological advantage and be the basis for enhanced competition against enteropathogens.
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Affiliation(s)
- Pamela Vazquez-Gutierrez
- Laboratory of Food Biotechnology, ETH Zurich, Institute of Food, Nutrition and Health, Schmelzbergstrasse 7, Zurich, Switzerland.
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, ETH Zurich, Institute of Food, Nutrition and Health, Schmelzbergstrasse 7, Zurich, Switzerland.
| | - Tanja Jaeggi
- Laboratory of Human Nutrition, ETH Zurich, Institute of Food, Nutrition and Health, Schmelzbergstrasse 7, Zurich, Switzerland.
| | - Christophe Zeder
- Laboratory of Human Nutrition, ETH Zurich, Institute of Food, Nutrition and Health, Schmelzbergstrasse 7, Zurich, Switzerland.
| | - Michael Bruce Zimmerman
- Laboratory of Human Nutrition, ETH Zurich, Institute of Food, Nutrition and Health, Schmelzbergstrasse 7, Zurich, Switzerland.
| | - Christophe Chassard
- Laboratory of Food Biotechnology, ETH Zurich, Institute of Food, Nutrition and Health, Schmelzbergstrasse 7, Zurich, Switzerland.
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Zuo L, Yuan KT, Yu L, Meng QH, Chung PCK, Yang DH. Bifidobacterium infantis attenuates colitis by regulating T cell subset responses. World J Gastroenterol 2014; 20:18316-18329. [PMID: 25561798 PMCID: PMC4277968 DOI: 10.3748/wjg.v20.i48.18316] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 06/17/2014] [Accepted: 07/22/2014] [Indexed: 02/06/2023] Open
Abstract
AIM: to investigate the effect of Bifidobacterium infantis (B. infantis) on the T cell subsets and in attenuating the severity of experimental colitis in mice.
METHODS: Normal BALB/c mice were fed different doses of B. infantis for 3 wk, and T cell subsets and related cytokine profiles in mesenteric lymph nodes (MLNs) were detected by flow cytometry and real-time RT-PCR. Colitis was induced by administration of trinitrobenzene sulfonic acid (TNBS) in mice. Before colitis induction, mice were fed high dose B. infantis for 3 wk. Cytokine profiles in MLNs and histological changes of colonic tissue were examined 6 d after colitis induction.
RESULTS: No significant change in cytokine profiles was observed in normal mice fed low dose B. infantis. However, Th1-related cytokines (IL-2, IFN-γ, IL-12p40), Th17-related transcription factor and cytokines (RORγt, IL-21, IL-23), regulatory T cell (Treg)-related transcription factor and cytokines (Foxp3, IL-10) were increased in normal mice fed high dose B. infantis. Furthermore, flow cytometry assay showed B. infantis increased the numbers of CD4+Foxp3+ Tregs and Th17 cells in MLNs. Colitis was successfully induced by TNBS in mice, characterized by colonic inflammation and aberrant Th1 and Th17 responses. Feeding high dose B. infantis for 3 wk before colitis induction decreased the inflammatory cell infiltration and goblet cell depletion and restored the intestinal epithelium. In addition, B. infantis feeding reduced Th1-related cytokines (T-bet, IL-2 and IFN-γ) and Th17-related cytokines (IL-12p40, RORγt, IL-17A, IL-21 and IL-23), and increased Treg-related molecules (Foxp3, IL-10 and TGF-β) in colitis mice.
CONCLUSION: B. infantis effectively attenuates TNBS-induced colitis by decreasing Th1 and Th17 responses and increasing Foxp3+ Treg response in the colonic mucosa.
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Andriushchenko SV, Perunova NB, Ivanova EV, Bukharin OV. [Application of multiplex-PCR for bifidobacteria and propionibacteria genus identification]. Zh Mikrobiol Epidemiol Immunobiol 2014:78-82. [PMID: 25536776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
AIM Creation of a PCR test-system for determination of Actinobacteria class bacteria belonging to 2 genera that are the most widely represented among obligate anaerobic microbiota of human intestine: Bifidobacterium and Propionibacterium. MATERIALS AND METHODS 8 strains of Bifidobacterium spp. and 6 strains of Propionibacterium genus were identified by morphologic, cultural and biochemical properties. Isolation of matrix DNA of the strains for PCR was carried out by "DNA-Express" kit (SPF "Lytech", Russia). Primers for determination of genus membership for obligate anaerobes were developed based on variability of 16S RNA gene by using "Lasergene 7.1" ("DNASTAR, Inc.", USA) program. PCR screening of the isolated DNA was carried out based on "Syntol" LLC primers and reagents. Amplicon detection was carried out by agarose gel electrophoresis. RESULTS Multiplexing of 2 different primer pairs in a single probe at.68 degrees C annealing temperature for 30 cycles showed the presence of non-specific amplicons that form in samples with bifidobacteria DNA-matrix. The increase of annealing temperature to 70 degrees C and reduction of the number of PCR cycles to 25 resulted in the exclusion of formation of non-specific amplicons. Because the annealing temperature reached the level of values optimal for Taq-polymerase, a 2-phase PCR algorithm could be implemented. This solution allowed reducing the overall time of reaction to 45 minutes. Further increase of annealing temperature to 72 degrees C and reduction of elongation phase up to 15 seconds at 30 PCR cycles did not result in a visible reduction of reaction effectiveness: CONCLUSION A rapid system for identification of Bifidobacterium and Pronionibacterium genera using a system of 2-phase multiple PCR was developed. The system is part of a screening system for identification of major genera and species of cultured obligate anaerobic bacteria isolated from human intestine biotopes.
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Bunesova V, Killer J, Vlkova E, Musilova S, Tomaska M, Rada V, Kmet V. Isolation and characterization of bifidobacteria from ovine cheese. Int J Food Microbiol 2014; 188:26-30. [PMID: 25086349 DOI: 10.1016/j.ijfoodmicro.2014.07.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Revised: 06/21/2014] [Accepted: 07/01/2014] [Indexed: 11/18/2022]
Abstract
Animal products are one of the niches of bifidobacteria, a fact probably attributable to secondary contamination. In this study, 2 species of the genus Bifidobacterium were isolated by culture-dependent methods from ovine cheeses that were made from unpasteurized milk without addition of starter cultures. The isolates were identified as Bifidobacterium crudilactis and Bifidobacterium animalis subsp. lactis using matrix-assisted laser desorption/ionization time-of-flight analysis and sequencing of phylogenetic markers (16S rRNA, hsp60, and fusA).
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Affiliation(s)
- Vera Bunesova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, Prague 6-Suchdol 165 21, Czech Republic.
| | - Jiri Killer
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, Prague 6-Suchdol 165 21, Czech Republic; Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 4-Krč 14 200, Czech Republic
| | - Eva Vlkova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, Prague 6-Suchdol 165 21, Czech Republic
| | - Sarka Musilova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, Prague 6-Suchdol 165 21, Czech Republic
| | - Martin Tomaska
- Dairy Research Institute, Dlhá 95, 010 01 Žilina, Slovakia
| | - Vojtech Rada
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, Prague 6-Suchdol 165 21, Czech Republic
| | - Vladimir Kmet
- Institute of Animal Physiology of Slovak Academy of Sciences, Soltesovej 4, 040 01 Kosice, Slovakia
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Huo D, Zhang J, Bai N, Huang W, Zhang H. [Selective medium to isolate human Bifidobacterium]. Wei Sheng Wu Xue Bao 2014; 54:433-441. [PMID: 25007656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
OBJECTIVE To compare five selective media to isolate human Bifidobacterium. METHODS Feces from six healthy human volunteers were diluted and cultivated on five Bifidobacterium selective media. After anaerobic cultivation, bacterial colonies were counted, selected and identified. Meanwhile, bacterial genomic DNA was extracted from the feces samples, and the Denaturing Gradient Gel Electrophoresis (DGGE) and Quantitative Polymerase Chain Reaction (q-PCR) were applied to reveal the diversity of Bifidobacterium. RESULTS The amount of Bifidobacterium grown on BSM and BLM media was similar to the result detected by q-PCR and was significantly higher than that on three other media. Bifidobacterium isolated from BLM medium was similar to the identified result of DGGE profile. CONCLUSION BLM medium is the best selective medium for Bifidobacterium isolation from human gastrointestinal tract.
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Torrazza RM, Ukhanova M, Wang X, Sharma R, Hudak ML, Neu J, Mai V. Intestinal microbial ecology and environmental factors affecting necrotizing enterocolitis. PLoS One 2013; 8:e83304. [PMID: 24386174 PMCID: PMC3875440 DOI: 10.1371/journal.pone.0083304] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 11/02/2013] [Indexed: 12/12/2022] Open
Abstract
Necrotizing enterocolitis (NEC) is the most devastating intestinal disease affecting preterm infants. In addition to being associated with short term mortality and morbidity, survivors are left with significant long term sequelae. The cost of caring for these infants is high. Epidemiologic evidence suggests that use of antibiotics and type of feeding may cause an intestinal dysbiosis important in the pathogenesis of NEC, but the contribution of specific infectious agents is poorly understood. Fecal samples from preterm infants ≤32 weeks gestation were analyzed using 16S rRNA based methods at 2, 1, and 0 weeks, prior to diagnosis of NEC in 18 NEC cases and 35 controls. Environmental factors such as antibiotic usage, feeding type (human milk versus formula) and location of neonatal intensive care unit (NICU) were also evaluated. Microbiota composition differed between the three neonatal units where we observed differences in antibiotic usage. In NEC cases we observed a higher proportion of Proteobacteria (61%) two weeks and of Actinobacteria (3%) 1 week before diagnosis of NEC compared to controls (19% and 0.4%, respectively) and lower numbers of Bifidobacteria counts and Bacteroidetes proportions in the weeks before NEC diagnosis. In the first fecal samples obtained during week one of life we detected a novel signature sequence, distinct from but matching closest to Klebsiella pneumoniae, that was strongly associated with NEC development later in life. Infants who develop NEC exhibit a different pattern of microbial colonization compared to controls. Antibiotic usage correlated with these differences and combined with type of feeding likely plays a critical role in the development of NEC.
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MESH Headings
- Anti-Bacterial Agents/pharmacology
- Anti-Bacterial Agents/therapeutic use
- Bifidobacterium/classification
- Bifidobacterium/genetics
- Biodiversity
- Case-Control Studies
- Cluster Analysis
- Enterocolitis, Necrotizing/drug therapy
- Enterocolitis, Necrotizing/etiology
- Enterocolitis, Necrotizing/microbiology
- Environment
- Female
- Humans
- Infant, Newborn
- Infant, Premature
- Infant, Premature, Diseases/drug therapy
- Infant, Premature, Diseases/etiology
- Infant, Premature, Diseases/microbiology
- Intestines/drug effects
- Intestines/microbiology
- Intestines/pathology
- Male
- Metagenome
- Microbiota
- RNA, Ribosomal, 16S
- Risk Factors
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Affiliation(s)
- Roberto Murgas Torrazza
- Department of Pediatrics, College of Medicine University of Florida, Gainesville, Florida, United States of America
| | - Maria Ukhanova
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine and Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
| | - Xiaoyu Wang
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine and Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
| | - Renu Sharma
- Department of Pediatrics University of Florida College of Medicine, Jacksonville, Florida, United States of America
| | - Mark Lawrence Hudak
- Department of Pediatrics University of Florida College of Medicine, Jacksonville, Florida, United States of America
| | - Josef Neu
- Department of Pediatrics, College of Medicine University of Florida, Gainesville, Florida, United States of America
| | - Volker Mai
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine and Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
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48
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Peacock KS, Ruhaak LR, Tsui MK, Mills DA, Lebrilla CB. Isomer-specific consumption of galactooligosaccharides by bifidobacterial species. J Agric Food Chem 2013; 61:12612-12619. [PMID: 24313277 PMCID: PMC3912189 DOI: 10.1021/jf403789r] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Prebiotics are nondigestible substrates that stimulate the growth of beneficial microbes in the human intestine. Galactooligosaccharides (GOS) are food ingredients that possess prebiotic properties, in particular, promoting the growth of bifidobacteria in situ. However, precise mechanistic details of GOS consumption by bifidobacteria remain poorly understood. Because GOS are mixtures of polymers of different lengths and linkages, there is interest in determining which specific structures provide prebiotic effects to potentially create better supplements. This paper presents a method comprising porous graphitic carbon separation, isotopic labeling, and mass spectrometry analysis for the structure-specific analysis of GOS isomers and their bacterial consumption rate. Using this strategy, the differential bacterial consumption of GOS by the bifidobacteria species Bifidobacterium longum subsp. infantis, Bifidobacterium animalis subsp. lactis, and Bifidobacterium adolescentis was determined, indicating that the use of specific GOS isomers in infant formula may provide enrichment of distinct species.
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Affiliation(s)
- Kyle S. Peacock
- Department of Chemistry, University of California Davis. One Shields Avenue, Davis, CA, USA
| | - L. Renee Ruhaak
- Department of Chemistry, University of California Davis. One Shields Avenue, Davis, CA, USA
| | - Man Ki Tsui
- Department of Viticulture and Enology, University of California Davis, One Shields Avenue, Davis, CA, USA
- Foods for Health Institute, University of California Davis, One Shields Avenue, Davis, CA, USA
| | - David A. Mills
- Department of Viticulture and Enology, University of California Davis, One Shields Avenue, Davis, CA, USA
- Foods for Health Institute, University of California Davis, One Shields Avenue, Davis, CA, USA
- Department of Food Science and Technology, University of California Davis, One Shields Avenue, Davis, CA, USA
| | - Carlito B. Lebrilla
- Department of Chemistry, University of California Davis. One Shields Avenue, Davis, CA, USA
- Foods for Health Institute, University of California Davis, One Shields Avenue, Davis, CA, USA
- To whom correspondence should be addressed: University of California, Davis Department of Chemistry One Shields Avenue Davis, CA, 95616 USA Phone: 1-530-752-0504 FAX: 1-530-754-8995
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49
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Guglielmetti S, Fracassetti D, Taverniti V, Del Bo' C, Vendrame S, Klimis-Zacas D, Arioli S, Riso P, Porrini M. Differential modulation of human intestinal bifidobacterium populations after consumption of a wild blueberry (Vaccinium angustifolium) drink. J Agric Food Chem 2013; 61:8134-8140. [PMID: 23883473 DOI: 10.1021/jf402495k] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Bifidobacteria are gaining increasing interest as health-promoting bacteria. Nonetheless, the genus comprises several species, which can exert different effects on human host. Previous studies showed that wild blueberry drink consumption could selectively increase intestinal bifidobacteria, suggesting an important role for the polyphenols and fiber present in wild blueberries. This study evaluated the modulation of the most common and abundant bifidobacterial taxonomic groups inhabiting the human gut in the same fecal samples. The analyses carried out showed that B. adolescentis, B. breve, B. catenulatum/pseudocatelulatum, and B. longum subsp. longum were always present in the group of subjects enrolled, whereas B. bifidum and B. longum subsp. infantis were not. Furthermore, it was found that the most predominant bifidobacterial species were B. longum subsp. longum and B. adolescentis. The results obtained revealed a high interindividual variability; however, a significant increase of B. longum subsp. infantis cell concentration was observed in the feces of volunteers after the wild blueberry drink treatment. This bifidobacterial group was shown to possess immunomodulatory abilities and to relieve symptoms and promote the regression of several gastrointestinal disorders. Thus, an increased cell concentration of B. longum subsp. infantis in the human gut could be considered of potential health benefit. In conclusion, wild blueberry consumption resulted in a specific bifidogenic effect that could positively affect certain populations of bifidobacteria with demonstrated health-promoting properties.
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Affiliation(s)
- Simone Guglielmetti
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Division of Food Microbiology and Bioprocessing, Università degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy.
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50
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Respondek F, Gerard P, Bossis M, Boschat L, Bruneau A, Rabot S, Wagner A, Martin JC. Short-chain fructo-oligosaccharides modulate intestinal microbiota and metabolic parameters of humanized gnotobiotic diet induced obesity mice. PLoS One 2013; 8:e71026. [PMID: 23951074 PMCID: PMC3741321 DOI: 10.1371/journal.pone.0071026] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 07/01/2013] [Indexed: 12/19/2022] Open
Abstract
Prebiotic fibres like short-chain fructo-oligosaccharides (scFOS) are known to selectively modulate the composition of the intestinal microbiota and especially to stimulate Bifidobacteria. In parallel, the involvement of intestinal microbiota in host metabolic regulation has been recently highlighted. The objective of the study was to evaluate the effect of scFOS on the composition of the faecal microbiota and on metabolic parameters in an animal model of diet-induced obesity harbouring a human-type microbiota. Forty eight axenic C57BL/6J mice were inoculated with a sample of faecal human microbiota and randomly assigned to one of 3 diets for 7 weeks: a control diet, a high fat diet (HF, 60% of energy derived from fat)) or an isocaloric HF diet containing 10% of scFOS (HF-scFOS). Mice fed with the two HF gained at least 21% more weight than mice from the control group. Addition of scFOS partially abolished the deposition of fat mass but significantly increased the weight of the caecum. The analysis of the taxonomic composition of the faecal microbiota by FISH technique revealed that the addition of scFOS induced a significant increase of faecal Bifidobacteria and the Clostridium coccoides group whereas it decreased the Clostridium leptum group. In addition to modifying the composition of the faecal microbiota, scFOS most prominently affected the faecal metabolome (e.g. bile acids derivatives, hydroxyl monoenoic fatty acids) as well as urine, plasma hydrophilic and plasma lipid metabolomes. The increase in C. coccoides and the decrease in C. leptum, were highly correlated to these metabolic changes, including insulinaemia, as well as to the weight of the caecum (empty and full) but not the increase in Bifidobacteria. In conclusion scFOS induce profound metabolic changes by modulating the composition and the activity of the intestinal microbiota, that may partly explain their effect on the reduction of insulinaemia.
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