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Huang J, Lin Y, Ding X, Lin S, Li X, Yan W, Chen M. Alteration of the gut microbiome in patients with heart failure: A systematic review and meta-analysis. Microb Pathog 2024; 192:106647. [PMID: 38788811 DOI: 10.1016/j.micpath.2024.106647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/02/2024] [Accepted: 04/13/2024] [Indexed: 05/26/2024]
Abstract
Recent research has revealed that alterations of the gut microbiome (GM) play a comprehensive role in the pathophysiology of HF. However, findings in this field remain controversial. In this study, we focus on differences in GM diversity and abundance between HF patients and non-HF people, based on previous 16 S ribosomal RNA (16rRNA) gene sequencing. Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, we conducted a comprehensive search of PubMed, Web of Science, Embase, Cochrane Library, and Ovid databases using the keyword "Heart failure" and "Gastrointestinal Microbiome". A significant decrease in alpha diversity was observed in the HF patients (Chao1, I2 = 87.5 %, p < 0.001; Shannon index, I2 = 62.8 %, p = 0.021). At the phylum level, the HF group exhibited higher abundances of Proteobacteria (I2 = 92.0 %, p = 0.004) and Actinobacteria (I2 = 82.5 %, p = 0.010), while Bacteroidetes (I2 = 45.1 %, p = 0.017) and F/B ratio (I2 = 0.0 %, p<0.001) were lower. The Firmicutes showed a decreasing trend but did not reach statistical significance (I2 = 82.3 %, p = 0.127). At the genus level, the relative abundances of Streptococcus, Bacteroides, Alistipes, Bifidobacterium, Escherichia-Shigella, Enterococcus and Klebsiella were increased in the HF group, whereas Ruminococcus, Faecalibacterium, Dorea and Megamona exhibited decreased relative abundances. Dialister, Blautia and Prevotella showed decreasing trends but without statistical significance. This observational meta-analysis suggests that GM changes are associated with HF, manifesting as alterations in GM abundance, disruptions in the production of short-chain fatty acids (SCFAs) bacteria, and an increase in trimethylamine N-oxide (TMAO) producing bacteria.
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Affiliation(s)
- Jiayi Huang
- Department of Cardiology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, 225300, China
| | - Yongping Lin
- Department of Cardiology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, 225300, China
| | - Xiangwei Ding
- Department of Cardiology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, 225300, China
| | - Song Lin
- Department of Cardiology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, 225300, China
| | - Xin Li
- Department of Cardiology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, 225300, China
| | - Wei Yan
- Department of Cardiology, Nanjing Pukou People's Hospital, Nanjing, 211800, China
| | - Minglong Chen
- Department of Cardiology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, 225300, China; Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China.
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2
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Li W, Huang Y, Tong S, Wan C, Wang Z. The characteristics of the gut microbiota in patients with pulmonary tuberculosis: A systematic review. Diagn Microbiol Infect Dis 2024; 109:116291. [PMID: 38581928 DOI: 10.1016/j.diagmicrobio.2024.116291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 03/08/2024] [Accepted: 03/26/2024] [Indexed: 04/08/2024]
Abstract
Increasing evidence has indicated dysbiosis of the gut microbiota in patients with pulmonary tuberculosis (PTB). However, the change in the intestinal microbiota varies between different studies. This systematic review was conducted to investigate the characteristics of the gut microbiota in PTB patients. The MBASE, MEDLINE, Web of Science, and Cochrane Library electronic databases were systematically searched, and the quality of the retrieved studies was evaluated using the Newcastle-Ottawa scale. A total of 12 studies were finally included in the systematic review. Compared with healthy controls, the index reflecting α-diversity including the richness and/or diversity index decreased in 6 studies, while β-diversity presented significant differences in PTB patients in 10 studies. Although the specific gut microbiota alterations were inconsistent, short-chain fatty acid-producing bacteria (including Lachnospiraceae, Ruminococcus, Blautia, Dorea, and Faecalibacterium), bacteria associated with an inflammatory state (e.g., Prevotellaceae and Prevotella), and beneficial bacteria (e.g., Bifidobacteriaceae and Bifidobacterium) were commonly noted. Our systematic review identifies key evidence for gut microbiota alterations in PTB patients, in comparison with healthy controls; however, no consistent conclusion could be drawn, due to the inconsistent results and heterogeneous methodologies of the enrolled studies. Therefore, more well-designed research with standard methodologies and large sample sizes is required.
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Affiliation(s)
- Weiran Li
- Department of Pediatrics, West China Second Hospital, Sichuan University, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, NHC Key Laboratory of Chronobiology (Sichuan University), China
| | - Yunfei Huang
- Department of Reproductive Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China
| | - Shuai Tong
- Department of Pediatrics, West China Second Hospital, Sichuan University, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, NHC Key Laboratory of Chronobiology (Sichuan University), China
| | - Chaomin Wan
- Department of Pediatrics, West China Second Hospital, Sichuan University, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, NHC Key Laboratory of Chronobiology (Sichuan University), China
| | - Zhiling Wang
- Department of Pediatrics, West China Second Hospital, Sichuan University, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, NHC Key Laboratory of Chronobiology (Sichuan University), China.
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Bellomo AR, Rotondi G, Rago P, Bloise S, Di Ruzza L, Zingoni A, Di Valerio S, Valzano E, Di Pierro F, Cazzaniga M, Bertuccioli A, Guasti L, Zerbinati N, Lubrano R. Effect of Bifidobacterium bifidum Supplementation in Newborns Born from Cesarean Section on Atopy, Respiratory Tract Infections, and Dyspeptic Syndromes: A Multicenter, Randomized, and Controlled Clinical Trial. Microorganisms 2024; 12:1093. [PMID: 38930475 PMCID: PMC11205812 DOI: 10.3390/microorganisms12061093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 05/24/2024] [Accepted: 05/26/2024] [Indexed: 06/28/2024] Open
Abstract
Cesarean section is considered a possible trigger of atopy and gut dysbiosis in newborns. Bifidobacteria, and specifically B. bifidum, are thought to play a central role in reducing the risk of atopy and in favoring gut eubiosis in children. Nonetheless, no trial has ever prospectively investigated the role played by this single bacterial species in preventing atopic manifestations in children born by cesarean section, and all the results published so far refer to mixtures of probiotics. We have therefore evaluated the impact of 6 months of supplementation with B. bifidum PRL2010 on the incidence, in the first year of life, of atopy, respiratory tract infections, and dyspeptic syndromes in 164 children born by cesarean (versus 249 untreated controls). The results of our multicenter, randomized, and controlled trial have shown that the probiotic supplementation significantly reduced the incidence of atopic dermatitis, upper and lower respiratory tract infections, and signs and symptoms of dyspeptic syndromes. Concerning the gut microbiota, B. bifidum supplementation significantly increased α-biodiversity and the relative values of the phyla Bacteroidota and Actinomycetota, of the genus Bacteroides, Bifidobacterium and of the species B. bifidum and reduced the relative content of Escherichia/Shigella and Haemophilus. A 6-month supplementation with B. bifidum in children born by cesarean section reduces the risk of gut dysbiosis and has a positive clinical impact that remains observable in the following 6 months of follow-up.
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Affiliation(s)
- Anna Rita Bellomo
- Dipartimento Materno Infantile e di Scienze Urologiche, Sapienza Università di Roma, UOC di Pediatria e Neonatologia-Polo Pontino, 04100 Latina, Italy; (A.R.B.); (P.R.)
| | - Giulia Rotondi
- Pediatric Surgery Unit, Gaslini Children Hospital and Research Institute, 16147 Genoa, Italy
| | - Prudenza Rago
- Dipartimento Materno Infantile e di Scienze Urologiche, Sapienza Università di Roma, UOC di Pediatria e Neonatologia-Polo Pontino, 04100 Latina, Italy; (A.R.B.); (P.R.)
| | - Silvia Bloise
- Dipartimento Materno Infantile e di Scienze Urologiche, Sapienza Università di Roma, UOC di Pediatria e Neonatologia-Polo Pontino, 04100 Latina, Italy; (A.R.B.); (P.R.)
| | - Luigi Di Ruzza
- UOC Pediatria e Nido, Ospedale S.S. Trinità, 03039 Sora, Italy
| | - Annamaria Zingoni
- UOC Pediatria e Neonatologia, Ospedale G.B. Grassi, 00122 Ostia, Italy
| | - Susanna Di Valerio
- UOC Neonatologia e Terapia Intensiva Neonatale, Ospedale S. Spirito, 65124 Pescara, Italy
| | - Eliana Valzano
- UOC Neonatologia e Terapia Intensiva Neonatale, Ospedale S. Spirito, 65124 Pescara, Italy
| | - Francesco Di Pierro
- Scientific & Research Department, Velleja Research, 20125 Milan, Italy
- Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy
| | | | - Alexander Bertuccioli
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy;
| | - Luigina Guasti
- Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy
| | - Nicola Zerbinati
- Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy
| | - Riccardo Lubrano
- Dipartimento Materno Infantile e di Scienze Urologiche, Sapienza Università di Roma, UOC di Pediatria e Neonatologia-Polo Pontino, 04100 Latina, Italy; (A.R.B.); (P.R.)
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4
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Hazan S, Smith M, Lander S, Carlson A, Walters C. Bifidobacterium Against COVID-19: A Mother and Her Newborn's Gut Microbiome. Cureus 2024; 16:e60038. [PMID: 38854284 PMCID: PMC11162645 DOI: 10.7759/cureus.60038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2024] [Indexed: 06/11/2024] Open
Abstract
Several treatments and preventive measures for SARS-CoV-2 were studied during the pandemic, but few focused on the neonatal gut microbiome and its role in the setting of COVID-19. This case report is unique because it describes the gut microbiomes of a mother and her newborn, who both contracted COVID-19 shortly after the baby's birth. In this prospective study, on day 11 postpartum, both the newborn and mother (38 years old), of white race/ethnicity, were exposed to a COVID-19-positive person. After exposure, the mother received a 40,000 IU bolus of vitamin D orally and started a five-day course of high-dose vitamin C (10,000 mg daily), after which she continued her daily combination of vitamins C, D, and zinc pill with probiotic skyr yogurt and manuka honey. Stool specimens and DNA were extracted, quantitated, and normalized from the mother and the newborn for downstream library fabrication utilizing shotgun methodology. Baseline Bifidobacteria level for the mother was 1.5% which increased to 19% on day 15 postpartum after testing positive for COVID-19 and taking vitamin C. Neonatal Bifidobacteriasteadily increased regardless of COVID-19 infection. We propose that the disease course was altered by maternal supplementation of vitamins C and D and zinc, which may have increased Bifidobacterium levels and led to improved outcomes for both patients.
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Affiliation(s)
| | - Megan Smith
- Biomedical Sciences, California University of Science and Medicine, Colton, USA
| | - Skye Lander
- Biomedical Sciences, California University of Science and Medicine, Colton, USA
| | - Abby Carlson
- Research and Development, ProgenaBiome, Ventura, USA
| | - Camila Walters
- Anesthesiology, Vanderbilt University Medical Center, Nashville, USA
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5
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Sibanda T, Marole TA, Thomashoff UL, Thantsha MS, Buys EM. Bifidobacterium species viability in dairy-based probiotic foods: challenges and innovative approaches for accurate viability determination and monitoring of probiotic functionality. Front Microbiol 2024; 15:1327010. [PMID: 38371928 PMCID: PMC10869629 DOI: 10.3389/fmicb.2024.1327010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 01/15/2024] [Indexed: 02/20/2024] Open
Abstract
Bifidobacterium species are essential members of a healthy human gut microbiota. Their presence in the gut is associated with numerous health outcomes such as protection against gastrointestinal tract infections, inflammation, and metabolic diseases. Regular intake of Bifidobacterium in foods is a sustainable way of maintaining the health benefits associated with its use as a probiotic. Owing to their global acceptance, fermented dairy products (particularly yogurt) are considered the ideal probiotic carrier foods. As envisioned in the definition of probiotics as "live organisms," the therapeutic functionalities of Bifidobacterium spp. depend on maintaining their viability in the foods up to the point of consumption. However, sustaining Bifidobacterium spp. viability during the manufacture and shelf-life of fermented dairy products remains challenging. Hence, this paper discusses the significance of viability as a prerequisite for Bifidobacterium spp. probiotic functionality. The paper focuses on the stress factors that influence Bifidobacterium spp. viability during the manufacture and shelf life of yogurt as an archetypical fermented dairy product that is widely accepted as a delivery vehicle for probiotics. It further expounds the Bifidobacterium spp. physiological and genetic stress response mechanisms as well as the methods for viability retention in yogurt, such as microencapsulation, use of oxygen scavenging lactic acid bacterial strains, and stress-protective agents. The report also explores the topic of viability determination as a critical factor in probiotic quality assurance, wherein, the limitations of culture-based enumeration methods, the challenges of species and strain resolution in the presence of lactic acid bacterial starter and probiotic species are discussed. Finally, new developments and potential applications of next-generation viability determination methods such as flow cytometry, propidium monoazide-quantitative polymerase chain reaction (PMA-qPCR), next-generation sequencing, and single-cell Raman spectroscopy (SCRS) methods are examined.
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Affiliation(s)
- Thulani Sibanda
- Department of Consumer and Food Sciences, University of Pretoria, Pretoria, South Africa
- Department of Applied Biology and Biochemistry, National University of Science and Technology, Bulawayo, Zimbabwe
- Department of Biology, National of University of Lesotho, Maseru, Lesotho
| | - Tlaleo Azael Marole
- Department of Consumer and Food Sciences, University of Pretoria, Pretoria, South Africa
| | | | - Mapitsi S. Thantsha
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Elna M. Buys
- Department of Consumer and Food Sciences, University of Pretoria, Pretoria, South Africa
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6
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Liu M, Xu X, Sun C, Zheng X, Zhou Q, Song C, Xu P, Gao Q, Liu B. Tea Tree Oil Improves Energy Metabolism, Non-Specific Immunity, and Microbiota Diversity via the Intestine-Hepatopancreas Axis in Macrobrachium rosenbergii under Low Fish Meal Diet Administration. Antioxidants (Basel) 2023; 12:1879. [PMID: 37891958 PMCID: PMC10604904 DOI: 10.3390/antiox12101879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 10/07/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Tea tree oil (TTO) is an essential plant oil with diverse antibacterial and antioxidant properties; however, whether the role played by TTO in low fish meal (LF) diets induced the observed effects in the farmed crustaceans remains unclear. Therefore, this study used Macrobrachium rosenbergii as the model crustacean, and an 8-week feeding experiment with NF (normal fish meal), LF (soybean meal replacing 40% fish meal), and LFT (LF with 200 mg/kg TTO) diets was conducted to evaluate the positive effects of TTO under the LF diet. Compared to the NF diet, the LF diet reduced hemolymph antioxidant capacity and non-specific immunity, and induced hepatopancreas apoptosis and damage. However, in comparison with LF, LTF significantly ameliorated morphological impairment in the hepatopancreas, improved hepatopancreas energy metabolism by upregulating the Bcl-2/Bax and Akt/mTOR pathways, and enhanced antioxidant and non-specific immune capacity by activating the NF-κB/NO pathway. In addition, LFT repaired intestinal barrier injury and the imbalance of intestinal microbiota induced by the LF diet. Moreover, the Pearson correlation revealed the variations of the above indicators, which were related to the abundance changes of Klebsiella, Clostridium sensu stricto 12, Thermobifida, Bifidobacterium, and Alistipes, indicating that these microbes might serve as prospective targets for the intestine-hepatopancreas axis to affect hepatopancreas apoptosis, metabolism, and non-specific immunity. In summary, 200 mg/kg TTO supplementation mediated gut microbiota and positively improved energy metabolism and non-specific immunity, thereby alleviating hepatopancreas dysplasia and damage induced by the LF diet in M. rosenbergii.
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Affiliation(s)
- Mingyang Liu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; (M.L.); (X.X.); (C.S.); (Q.Z.)
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (X.Z.); (C.S.)
| | - Xiaodi Xu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; (M.L.); (X.X.); (C.S.); (Q.Z.)
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (X.Z.); (C.S.)
| | - Cunxin Sun
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; (M.L.); (X.X.); (C.S.); (Q.Z.)
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (X.Z.); (C.S.)
| | - Xiaochuan Zheng
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (X.Z.); (C.S.)
| | - Qunlan Zhou
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; (M.L.); (X.X.); (C.S.); (Q.Z.)
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (X.Z.); (C.S.)
| | - Changyou Song
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (X.Z.); (C.S.)
| | - Pao Xu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; (M.L.); (X.X.); (C.S.); (Q.Z.)
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (X.Z.); (C.S.)
| | - Qiang Gao
- Key Laboratory of Healthy Freshwater Aquaculture, Ministry of Agriculture and Rural Affairs, Key Laboratory of Fish Health and Nutrition of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou 313001, China
| | - Bo Liu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China; (M.L.); (X.X.); (C.S.); (Q.Z.)
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China; (X.Z.); (C.S.)
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7
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Chen M, Yao H, Tan H, Huang W, Wu Q, Nie S. Impact of Bifidobacterium longum NSP001 on DSS-induced colitis in conventional and humanised mice. FOOD SCIENCE AND HUMAN WELLNESS 2023. [DOI: 10.1016/j.fshw.2022.10.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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8
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Alessandri G, Fontana F, Tarracchini C, Rizzo SM, Bianchi MG, Taurino G, Chiu M, Lugli GA, Mancabelli L, Argentini C, Longhi G, Anzalone R, Viappiani A, Milani C, Turroni F, Bussolati O, van Sinderen D, Ventura M. Identification of a prototype human gut Bifidobacterium longum subsp. longum strain based on comparative and functional genomic approaches. Front Microbiol 2023; 14:1130592. [PMID: 36846784 PMCID: PMC9945282 DOI: 10.3389/fmicb.2023.1130592] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 01/17/2023] [Indexed: 02/10/2023] Open
Abstract
Bifidobacteria are extensively exploited for the formulation of probiotic food supplements due to their claimed ability to exert health-beneficial effects upon their host. However, most commercialized probiotics are tested and selected for their safety features rather than for their effective abilities to interact with the host and/or other intestinal microbial players. In this study, we applied an ecological and phylogenomic-driven selection to identify novel B. longum subsp. longum strains with a presumed high fitness in the human gut. Such analyses allowed the identification of a prototype microorganism to investigate the genetic traits encompassed by the autochthonous bifidobacterial human gut communities. B. longum subsp. longum PRL2022 was selected due to its close genomic relationship with the calculated model representative of the adult human-gut associated B. longum subsp. longum taxon. The interactomic features of PRL2022 with the human host as well as with key representative intestinal microbial members were assayed using in vitro models, revealing how this bifidobacterial gut strain is able to establish extensive cross-talk with both the host and other microbial residents of the human intestine.
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Affiliation(s)
- Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Federico Fontana
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy,GenProbio srl, Parma, Italy
| | - Chiara Tarracchini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Sonia Mirjam Rizzo
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Massimiliano G. Bianchi
- Department of Medicine and Surgery, University of Parma, Parma, Italy,Microbiome Research Hub, University of Parma, Parma, Italy
| | - Giuseppe Taurino
- Department of Medicine and Surgery, University of Parma, Parma, Italy,Microbiome Research Hub, University of Parma, Parma, Italy
| | - Martina Chiu
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Department of Medicine and Surgery, University of Parma, Parma, Italy,Microbiome Research Hub, University of Parma, Parma, Italy
| | - Chiara Argentini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Giulia Longhi
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy,GenProbio srl, Parma, Italy
| | | | | | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy,Microbiome Research Hub, University of Parma, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy,Microbiome Research Hub, University of Parma, Parma, Italy
| | - Ovidio Bussolati
- Department of Medicine and Surgery, University of Parma, Parma, Italy,Microbiome Research Hub, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy,Microbiome Research Hub, University of Parma, Parma, Italy,*Correspondence: Marco Ventura, ✉
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9
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Qu D, Yu L, Tian F, Zhang H, Chen W, Gu Z, Zhai Q. Bifidobacterium bifidum FJSWX19M5 alleviated 2,4,6-trinitrobenzene sulfonic acid (TNBS)-induced chronic colitis by mitigating gut barrier injury and increasing regulatory T cells. Food Funct 2023; 14:181-194. [PMID: 36477762 DOI: 10.1039/d2fo02659g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Probiotics have been evaluated as alternative approaches for preventing the relapse of Crohn's disease (CD). Previously, we observed strain-specific anti-inflammatory properties of Bifidobacterium bifidum in 2,4,6-trinitrobenzene sulfonic acid (TNBS) acute colitis models. In this study, we further assessed the effects of several B. bifidum strains on colonic damage, fibrosis, inflammatory factors, intestinal microbial and metabolic profiles, and peripheral regulatory T cells (Tregs) in the context of TNBS chronic colitis in mice. These results indicated that B. bifidum FJSWX19M5, but not FXJWS17M4, ameliorated body weight loss, reduced colonic shortening and injury, decreased markers of gut inflammation, and rebalanced colonic metabolism in TNBS-treated mice. FJSWX19M5 supplementation also promoted Treg cell differentiation and intestinal barrier restoration compared to other strains. All living B. bifidum strains (FJSWX19M5, FXJWS17M4 and FHENJZ3M6) seemed to restore the disruption of the gut microbiota caused by TNBS. The co-culture of B. bifidum strains and mesenteric lymph node cells from TNBS-treated mice showed that those strains with anti-colitis could induce higher IL-10 levels and a lower ratio of IL-22/IL-10 and IL-17/IL-10 when compared to those strains that were not protective. Furthermore, heat-killed FJSWX19M5 exhibited a relief effect on colitis-related symptoms (including body weight loss, colonic shortening and injury). These data imply that specific B. bifidum strains or their lysates may be the current therapeutic alternatives for CD.
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Affiliation(s)
- Dingwu Qu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China. .,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Leilei Yu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China. .,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Fengwei Tian
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China. .,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China. .,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China.,Wuxi Translational Medicine Research Center and Jiangsu Translational, Medicine Research Institute, Wuxi Branch, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China. .,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zhennan Gu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China. .,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China. .,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
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10
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Qu D, Feng S, Li M, Yu L, Tian F, Zhang H, Chen W, Zhai Q. Effects of Bifidobacteria bifidum strains on 2,4,6-trinitrobenzene sulfonic acid (TNBS)-induced acute colitis and its potential mechanism. FOOD BIOSCI 2023. [DOI: 10.1016/j.fbio.2023.102387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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11
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Yao BN, Liao FY, Yang JY, Liu A, Wang J, Zhu BG, Feng G, Yang SL. Effect of sea buckthorn extract on production performance, serum biochemical indexes, egg quality, and cholesterol deposition of laying ducks. Front Vet Sci 2023; 10:1127117. [PMID: 36923054 PMCID: PMC10008885 DOI: 10.3389/fvets.2023.1127117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/06/2023] [Indexed: 03/01/2023] Open
Abstract
The purpose of this experiment was to study the effect of sea buckthorn extract (SBE) supplementation on the production performance, serum biochemical indexes, egg quality, and cholesterol deposition of laying ducks. A total of 240 23-week-old laying ducks (female ducks) with similar body weight were randomly divided into four treatment groups with 6 replicates of 10 each. The experimental groups were fed diets supplemented with 0, 0.5, 1.0, and 1.5 g/kg of SBE, respectively. The results showed that the addition of 1.0 g/kg SBE to the diet had significant increase (P < 0.05) in average egg weight and feed conversion ratio. The inclusion of SBE showed the significant improvement (P < 0.05) in yolk weight, shell strength, egg white height and haugh unit. Ducks fed with 1.0 and 1.5 g/kg SBE displayed a significant decrease (P < 0.05) in yolk cholesterol. The significant improvements were observed in the contents of total amino acid essential amino acids, non-essential amino acids, umami amino acids, monounsaturated fatty acids, and docosahexenoic acids of eggs (P < 0.05) when supplemented with SBE. However, the contents of total saturated fatty acids, polyunsaturated fatty acids, n-3 polyunsaturated fatty acids and n-6 polyunsaturated fatty acids in eggs showed decrease when ducks fed with SBE diets (P < 0.05). SBE diets may reduce (P < 0.05) the levels of serum total cholesterol, triglyceride, and low-density lipoprotein cholesterol, while increased (P < 0.05) the levels of serum superoxide dismutase, total antioxidant capacity, and glutathione catalase compared to the control. The levels of serum immunoglobulin G, immunoglobulin A and immunoglobulin M were improved in SBE diets (P < 0.05) in comparation to the control. The addition of SBE to diets can improve feed nutrient utilization, increase egg weight, optimaze egg quality and amino acid content in eggs, reduce blood lipids, improve fatty acid profile and yolk cholesterol in eggs, and increase antioxidant capacity and immunity in laying ducks.
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Affiliation(s)
- Bing-Nong Yao
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang, China.,College of Animal Science, Guizhou University, Guiyang, China
| | - Fu-You Liao
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang, China.,College of Animal Science, Guizhou University, Guiyang, China
| | - Jiao-Yi Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang, China.,College of Animal Science, Guizhou University, Guiyang, China
| | - Ai Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang, China.,College of Animal Science, Guizhou University, Guiyang, China
| | - Jiao Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang, China.,College of Animal Science, Guizhou University, Guiyang, China
| | - Bao-Guo Zhu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang, China.,College of Animal Science, Guizhou University, Guiyang, China
| | - Gang Feng
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang, China.,College of Animal Science, Guizhou University, Guiyang, China
| | - Sheng-Lin Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang, China.,College of Animal Science, Guizhou University, Guiyang, China
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12
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Fontana F, Alessandri G, Tarracchini C, Bianchi MG, Rizzo SM, Mancabelli L, Lugli GA, Argentini C, Vergna LM, Anzalone R, Longhi G, Viappiani A, Taurino G, Chiu M, Turroni F, Bussolati O, van Sinderen D, Milani C, Ventura M. Designation of optimal reference strains representing the infant gut bifidobacterial species through a comprehensive multi-omics approach. Environ Microbiol 2022; 24:5825-5839. [PMID: 36123315 PMCID: PMC10092070 DOI: 10.1111/1462-2920.16205] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/10/2022] [Indexed: 01/12/2023]
Abstract
The genomic era has resulted in the generation of a massive amount of genetic data concerning the genomic diversity of bacterial taxa. As a result, the microbiological community is increasingly looking for ways to define reference bacterial strains to perform experiments that are representative of the entire bacterial species. Despite this, there is currently no established approach allowing a reliable identification of reference strains based on a comprehensive genomic, ecological, and functional context. In the current study, we developed a comprehensive multi-omics approach that will allow the identification of the optimal reference strains using the Bifidobacterium genus as test case. Strain tracking analysis based on 1664 shotgun metagenomics datasets of healthy infant faecal samples were employed to identify bifidobacterial strains suitable for in silico and in vitro analyses. Subsequently, an ad hoc bioinformatic tool was developed to screen local strain collections for the most suitable species-representative strain alternative. The here presented approach was validated using in vitro trials followed by metagenomics and metatranscriptomics analyses. Altogether, these results demonstrated the validity of the proposed model for reference strain selection, thus allowing improved in silico and in vitro investigations both in terms of cross-laboratory reproducibility and relevance of research findings.
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Affiliation(s)
- Federico Fontana
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.,GenProbio srl, Parma, Italy
| | - Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Chiara Tarracchini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Sonia Mirjam Rizzo
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Chiara Argentini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Laura Maria Vergna
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Giulia Longhi
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.,GenProbio srl, Parma, Italy
| | | | - Giuseppe Taurino
- Laboratory of General Pathology, Department of Medicine and Surgery, University of Parma, Parma, Italy.,Microbiome Research Hub, University of Parma, Parma, Italy
| | - Martina Chiu
- Laboratory of General Pathology, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.,Microbiome Research Hub, University of Parma, Parma, Italy
| | - Ovidio Bussolati
- Laboratory of General Pathology, Department of Medicine and Surgery, University of Parma, Parma, Italy.,Microbiome Research Hub, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.,Microbiome Research Hub, University of Parma, Parma, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.,Microbiome Research Hub, University of Parma, Parma, Italy
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13
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Javanshir N, Hosseini GNG, Sadeghi M, Esmaeili R, Satarikia F, Ahmadian G, Allahyari N. Evaluation of the Function of Probiotics, Emphasizing the Role of their Binding to the Intestinal Epithelium in the Stability and their Effects on the Immune System. Biol Proced Online 2021; 23:23. [PMID: 34847891 PMCID: PMC8903605 DOI: 10.1186/s12575-021-00160-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 11/04/2021] [Indexed: 12/11/2022] Open
Abstract
Due to the importance of using cost-effective methods for therapeutic purposes, the function of probiotics as safe microorganisms and the study of their relevant functional mechanisms have recently been in the spotlight. Finding the mechanisms of attachment and stability and their beneficial effects on the immune system can be useful in identifying and increasing the therapeutic effects of probiotics. In this review, the functional mechanisms of probiotics were comprehensively investigated. Relevant articles were searched in scientific sources, documents, and databases, including PubMed, NCBI, Bactibace, OptiBac, and Bagel4. The most important functional mechanisms of probiotics and their effects on strengthening the epithelial barrier, competitive inhibition of pathogenic microorganisms, production of antimicrobials, binding and interaction with the host, and regulatory effects on the immune system were discussed. In this regard, the attachment of probiotics to the epithelium is very important because the prerequisite for their proper functioning is to establish a proper connection to the epithelium. Therefore, more attention should be paid to the binding effect of probiotics, including sortase A, a significant factor involved in the expression of sortase-dependent proteins (SDP), on their surface as mediators of intestinal epithelial cell binding. In general, by investigating the functional mechanisms of probiotics, it was concluded that the mechanism by which probiotics regulate the immune system and adhesion capacity can directly and indirectly have preventive and therapeutic effects on a wide range of diseases. However, further study of these mechanisms requires extensive research on various aspects.
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Affiliation(s)
- Nahid Javanshir
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology. (NIGEB), P.O. Box: 14155-6343, Tehran, Iran
| | | | - Mahdieh Sadeghi
- Department of Science, Islamic Azad University - Parand Branch, Parand, Iran
| | | | - Fateme Satarikia
- Department of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Gholamreza Ahmadian
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology. (NIGEB), P.O. Box: 14155-6343, Tehran, Iran.
| | - Najaf Allahyari
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology. (NIGEB), P.O. Box: 14155-6343, Tehran, Iran.
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14
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Zeyneb H, Pei H, Cao X, Wang Y, Win Y, Gong L. In vitro study of the effect of quinoa and quinoa polysaccharides on human gut microbiota. Food Sci Nutr 2021; 9:5735-5745. [PMID: 34646541 PMCID: PMC8498072 DOI: 10.1002/fsn3.2540] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 08/04/2021] [Accepted: 08/09/2021] [Indexed: 12/24/2022] Open
Abstract
It has been shown that whole grains and dietary fiber are important for their fermentation characteristics in the large intestine, drawing more and more attention to quinoa and quinoa polysaccharides. In this study, we evaluated the prebiotic effect of quinoa seeds and quinoa polysaccharides after human simulated digestion. The modulatory effect of the quinoa and quinoa polysaccharides (QPs) on the gut microbiota was evaluated by the in vitro fermentation using human fecal microbiota. The yield of polysaccharides extraction was 15.45%. The digestibility of the cooked and uncooked quinoa after simulation of human digestion was 69.04% and 64.09%, respectively. The effect on the microbiota composition and their metabolic products was determined by the assessment of pH, short-chain fatty acids (SCFAs), and changes in the bacterial population. After 24 hr anaerobic incubation, the total SCFAs of cooked, uncooked quinoa, and quinoa polysaccharides were 82.99, 77.11, and 82.73 mM, respectively with a pH decrease. At the phylum, genus, and class level, it has been found that the quinoa substrates enhance the growth of certain beneficial bacteria such as Prevotella and Bacteroides. Quinoa polysaccharides can be considered prebiotic due to their ability to increase Bifidobacterium and Collinsella. Principal component analysis (PCA) showed that there was a distinct modulating effect on the fecal microbiota which represents different distribution. Our research suggests that quinoa and quinoa polysaccharides have a prebiotic potential due to their association with the positive shifts in microbiota composition and short-chain fatty acids production, which highlights the importance of further studies around this topic.
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Affiliation(s)
- Hitache Zeyneb
- Beijing Advanced Innovation Center for Food Nutrition and Human HealthBeijing Technology & Business UniversityBeijingChina
| | - Hairun Pei
- Beijing Advanced Innovation Center for Food Nutrition and Human HealthBeijing Technology & Business UniversityBeijingChina
| | - Xueli Cao
- Beijing Advanced Innovation Center for Food Nutrition and Human HealthBeijing Technology & Business UniversityBeijingChina
| | - Yuxin Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human HealthBeijing Technology & Business UniversityBeijingChina
| | - Yumon Win
- Beijing Advanced Innovation Center for Food Nutrition and Human HealthBeijing Technology & Business UniversityBeijingChina
| | - Lingxiao Gong
- Beijing Advanced Innovation Center for Food Nutrition and Human HealthBeijing Technology & Business UniversityBeijingChina
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15
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Wang Y, Sun M, Jin H, Yang J, Kang S, Liu Y, Yang S, Ma S, Ni J. Effects of Lycium barbarum Polysaccharides on Immunity and the Gut Microbiota in Cyclophosphamide-Induced Immunosuppressed Mice. Front Microbiol 2021; 12:701566. [PMID: 34421857 PMCID: PMC8377584 DOI: 10.3389/fmicb.2021.701566] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/14/2021] [Indexed: 11/13/2022] Open
Abstract
The mechanism of immunoregulation by Lycium barbarum polysaccharides (LBPs) was assessed by studying the effect of LBP on the immunity and the gut microbiota. LBP isolated and purified in this study was composed of nine monosaccharides, with an Mw 1,207 kDa. LBP showed immunomodulatory activity in cyclophosphamide (Cy)-treated mice by restoring the damaged immune organs and adjusting the T lymphocyte subsets. We also found that LBP increased the diversity of the gut microbiota and the relative abundances of bacteria, such as Rickenellaceae, Prevotellaceae, Bifidobacteriaceae, and so on, which were positively associated with immune traits. In addition, Caco2 cells model was used to explore the intestinal absorption of LBP. Results showed that LBP was hardly absorbed in the intestine, which suggesting that most LBP may interact with gut microbiota. These findings suggest that the immune response induced by LBP is associated with the regulation of the gut microbiota.
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Affiliation(s)
- Ying Wang
- Institute for Control of Chinese Traditional Medicine and Ethnic Medicine, National Institutes for Food and Drug Control, Beijing, China
| | - Mingyi Sun
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Hongyu Jin
- Institute for Control of Chinese Traditional Medicine and Ethnic Medicine, National Institutes for Food and Drug Control, Beijing, China
| | - Jianbo Yang
- Institute for Control of Chinese Traditional Medicine and Ethnic Medicine, National Institutes for Food and Drug Control, Beijing, China
| | - Shuai Kang
- Institute for Control of Chinese Traditional Medicine and Ethnic Medicine, National Institutes for Food and Drug Control, Beijing, China
| | - Yue Liu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Shuang Yang
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Shuangcheng Ma
- Institute for Control of Chinese Traditional Medicine and Ethnic Medicine, National Institutes for Food and Drug Control, Beijing, China
| | - Jian Ni
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
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16
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Kiousi DE, Rathosi M, Tsifintaris M, Chondrou P, Galanis A. Pro-biomics: Omics Technologies To Unravel the Role of Probiotics in Health and Disease. Adv Nutr 2021; 12:1802-1820. [PMID: 33626128 PMCID: PMC8483974 DOI: 10.1093/advances/nmab014] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/29/2020] [Accepted: 01/26/2021] [Indexed: 12/11/2022] Open
Abstract
The comprehensive characterization of probiotic action has flourished during the past few decades, alongside the evolution of high-throughput, multiomics platforms. The integration of these platforms into probiotic animal and human studies has provided valuable insights into the holistic effects of probiotic supplementation on intestinal and extraintestinal diseases. Indeed, these methodologies have informed about global molecular changes induced in the host and residing commensals at multiple levels, providing a bulk of metagenomic, transcriptomic, proteomic, and metabolomic data. The meaningful interpretation of generated data remains a challenge; however, the maturation of the field of systems biology and artificial intelligence has supported analysis of results. In this review article, we present current literature on the use of multiomics approaches in probiotic studies, we discuss current trends in probiotic research, and examine the possibility of tailor-made probiotic supplementation. Lastly, we delve deeper into newer technologies that have been developed in the last few years, such as single-cell multiomics analyses, and provide future directions for the maximization of probiotic efficacy.
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Affiliation(s)
- Despoina Eugenia Kiousi
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - Marina Rathosi
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - Margaritis Tsifintaris
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - Pelagia Chondrou
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
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17
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Bai X, Shen L, Gao X, Yu Z, Sakandar HA, Kwok LY, Sun Z. Differential structures and enterotype-like clusters of Bifidobacterium responses to probiotic fermented milk consumption across subjects using a Bifidobacterium-target procedure. Food Res Int 2020; 140:109839. [PMID: 33648165 DOI: 10.1016/j.foodres.2020.109839] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/13/2020] [Accepted: 10/18/2020] [Indexed: 02/07/2023]
Abstract
The health-promoting attributes of bifidobacteria have piqued interest of researchers worldwide. However, scant published studies are available pertinent to bifidobacteria in microbiota/metagenomics datasets due to its intrinsic low abundance and limitations of detection methods. In this work, we designed a procedure to optimize the detection of the bifidobacterial population in complex biological samples with single-molecule real-time sequencing (SMRT) technology, including one primer pair designated as Bif-6 and a Bifidobacterium-specific database. The optimized procedure detected 14 bifidobacterial species/subspecies in ten human stool samples (2024 sequences per sample) and eight breast milk samples (3473 sequences per sample), respectively. Furthermore, by using the optimized procedure of SMRT, we investigated the effect of a 4-week-intervention of probiotic fermented milk (PFM; 200 g/day) on the gut bifidobacteria population of adults. The results showed that consuming PFM changed the structure and enterotype-like clusters of Bifidobacterium. After the consumption of PFM, the level of gut Bifidobacterium animalis increased significantly, replacing several originally dominating taxa in some subjects, including B. catenulatum, B. breve, and B. bifidum. On the other hand, B. adolescentis was, unaffectedly, the representative species in subjects having an original enterotype-like cluster of B. adolescentis. In conclusion, our work designed a procedure for detecting the bifidobacterial population in complex samples. By applying the currently designed procedure, we found that the PFM intervention changed the bifidobacterial enterotype-like cluster of some subjects, and such change was dependent on the basal bifidobacterial population.
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Affiliation(s)
- Xiaoye Bai
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Lingling Shen
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Xu Gao
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Zhongjie Yu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Hafiz Arbab Sakandar
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Lai-Yu Kwok
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Zhihong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China.
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18
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Liu G, Wang Z, Li X, Liu R, Li B, Huang L, Chen Y, Zhang C, Zhang H, Li Y, Chen Y, Yin H, Fang W. Total glucosides of paeony (TGP) alleviates constipation and intestinal inflammation in mice induced by Sjögren's syndrome. JOURNAL OF ETHNOPHARMACOLOGY 2020; 260:113056. [PMID: 32525066 DOI: 10.1016/j.jep.2020.113056] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/15/2020] [Accepted: 05/30/2020] [Indexed: 06/11/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Sjögren's syndrome (SS) is an autoimmune disease and can cause gastrointestinal disorders such as constipation and intestinal inflammation. As a kind of medicinal material, Paeonia lactiflora Pall has a variety of pharmacological effects, and it is also an indispensable component in many pharmaceutical preparations, which has been widely concerned by the medical and pharmaceutical circles. Total glucosides of paeony (TGP) is a mixture of biologically active compounds extracted from the root of Paeonia lactiflora Pall and has therapeutic effects on a variety of autoimmune diseases. AIM OF THE STUDY To investigate the therapeutic effect of TGP on constipation and intestinal inflammation in mice modeled by SS, and to provide a basis for clinical research. MATERIALS AND METHODS The SS model was set up by submandibular gland (SMG) immune induction method and then treated with TGP for 24 weeks. The fecal characteristics were observed and the fecal number and moisture content were measured. Colonic pathology was observed by H&E staining. The levels of serum P substance (SP), vasoactive intestinal peptide (VIP), interleukin (IL)-1β, tumor necrosis factor (TNF)-α, nuclear factor (NF)-κB, nitric oxide (NO), and nitric oxide synthase (NOS) were determined by enzyme linked immunosorbent assay (ELISA) and microplate method, respectively. Reverse transcription polymerase chain reaction (RT-PCR) was employed to analyze the mRNA expression of c-kit and stem cell factor (SCF) in colon. RESULTS Compared with the model group, the dry and rough condition of the feces was improved, and the fecal gloss, number and moisture content significantly increased after the administration of TGP capsules. Meanwhile, TGP treatment improved colonic pathological damage, inhibited the serum concentrations of NO, NOS, IL-1β, TNF-α, NF-κB and SP, increased serum VIP concentration, and up-regulated mRNA expression of SCF and c-kit in colon. CONCLUSIONS TGP could obviously attenuate SS-mediated constipation and intestinal inflammation in mice by acting on some intestinal motility related factors and inflammatory factors.
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Affiliation(s)
- Ge Liu
- State Key Laboratory of Natural Medicines, School of Basic Medical Sciences and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China.
| | - Ziyu Wang
- State Key Laboratory of Natural Medicines, School of Basic Medical Sciences and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China.
| | - Xiang Li
- State Key Laboratory of Natural Medicines, School of Basic Medical Sciences and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China.
| | - Rui Liu
- State Key Laboratory of Natural Medicines, School of Basic Medical Sciences and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China.
| | - Binbin Li
- State Key Laboratory of Natural Medicines, School of Basic Medical Sciences and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China.
| | - Liangliang Huang
- State Key Laboratory of Natural Medicines, School of Basic Medical Sciences and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China.
| | - Yan Chen
- State Key Laboratory of Natural Medicines, School of Basic Medical Sciences and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China.
| | - Chongxi Zhang
- State Key Laboratory of Natural Medicines, School of Basic Medical Sciences and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China.
| | - Honghao Zhang
- State Key Laboratory of Natural Medicines, School of Basic Medical Sciences and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China.
| | - Yunman Li
- State Key Laboratory of Natural Medicines, School of Basic Medical Sciences and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China.
| | - Yongjian Chen
- Ningbo Liwah Pharmaceutical Co, Ningbo, 315174, PR China.
| | - Hong Yin
- Ningbo Liwah Pharmaceutical Co, Ningbo, 315174, PR China.
| | - Weirong Fang
- State Key Laboratory of Natural Medicines, School of Basic Medical Sciences and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, PR China.
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19
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Kiu R, Treveil A, Harnisch LC, Caim S, Leclaire C, van Sinderen D, Korcsmaros T, Hall LJ. Bifidobacterium breve UCC2003 Induces a Distinct Global Transcriptomic Program in Neonatal Murine Intestinal Epithelial Cells. iScience 2020; 23:101336. [PMID: 32683312 PMCID: PMC7371750 DOI: 10.1016/j.isci.2020.101336] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/05/2020] [Accepted: 06/30/2020] [Indexed: 12/19/2022] Open
Abstract
The underlying health-driving mechanisms of Bifidobacterium during early life are not well understood, particularly how this microbiota member may modulate the intestinal barrier via programming of intestinal epithelial cells (IECs). We investigated the impact of Bifidobacterium breve UCC2003 on the transcriptome of neonatal murine IECs. Small IECs from two-week-old neonatal mice administered B. breve UCC2003 or PBS (control) were subjected to global RNA sequencing, and differentially expressed genes, pathways, and affected cell types were determined. We observed extensive regulation of the IEC transcriptome with ∼4,000 genes significantly up-regulated, including key genes linked with epithelial barrier function. Enrichment of cell differentiation pathways was observed, along with an overrepresentation of stem cell marker genes, indicating an increase in the regenerative potential of the epithelial layer. In conclusion, B. breve UCC2003 plays a central role in driving intestinal epithelium homeostatic development during early life and suggests future avenues for next-stage clinical studies.
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Affiliation(s)
- Raymond Kiu
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Agatha Treveil
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Lukas C Harnisch
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Shabhonam Caim
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Charlotte Leclaire
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Douwe van Sinderen
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork T12YT20, Ireland
| | - Tamas Korcsmaros
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Lindsay J Hall
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; Chair of Intestinal Microbiome, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany; ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany.
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20
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Gupta P, Singh MP, Goyal K. Diversity of Vaginal Microbiome in Pregnancy: Deciphering the Obscurity. Front Public Health 2020; 8:326. [PMID: 32793540 PMCID: PMC7393601 DOI: 10.3389/fpubh.2020.00326] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 06/15/2020] [Indexed: 12/12/2022] Open
Abstract
Human microbiota plays an indispensable role in physiology, nutrition and most significantly, in imparting immunity. The role of microbiota has remained cryptic for years, until recently meticulous studies revealed the interaction and dynamics of these microbial communities. This diversified state is governed by hormonal, behavioral and physio-chemical changes in the genital tract. Many inclusive studies have revealed "Lactobacillus" to be the most dominant member of vaginal flora in most of the healthy, reproductive age group and pregnant females. A total of five community state types have been described, out of which four are dominated by Lactobacillus while the fifth one by facultative or strict anaerobic species. A variation between species stability and gestational age has also been revealed. Studies have divulged a significant higher stability of vaginal microbiota in early stages of pregnancy and the same increased subsequently. Inter-species and racial variation has shown women belonging to White, Asian, and Caucasian race to harbor more of the anaerobic flora. The vaginal microbiome in pregnancy play a significant role in preterm and spontaneous labor. This Lactobacillus-rich microbiome falls tremendously, becoming more diverse in post-partum period. Apart from these known bacterial communities in human vagina, other microbial communities have also been traced. The major fragment is constituted by vaginal viral virome and very little information exists in relation to vaginal mycobiome. Studies have revealed the abundance of ds DNA viruses in vaginal microbiome, followed by ssDNA, and few unidentified viruses. The eukaryotic viruses detected were very few, with Herpesvirales, and Papillomaviridae being the only pathogenic ones. This flora is transmitted to infants either via maternal gut, vagina or breast milk. Recent studies have given an insight for vaginal microbiome, dissociating the old concept of "healthy" and "diseased." However, more extensive studies are required to study evolution of virome and mycobiome in relation to their association with bacterial communities; to establish and decode full array of vaginal virome under the influence of genotypic and environmental factors, using novel bioinformatic, multi-omic, statistical model, and CRISPR/Cas approaches.
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Flavonoid-Rich Orange Juice Intake and Altered Gut Microbiome in Young Adults with Depressive Symptom: A Randomized Controlled Study. Nutrients 2020; 12:nu12061815. [PMID: 32570775 PMCID: PMC7353347 DOI: 10.3390/nu12061815] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/11/2020] [Accepted: 06/16/2020] [Indexed: 12/26/2022] Open
Abstract
Depression is not just a general mental health problem but a serious medical illness that can worsen without treatment. The gut microbiome plays a major role in the two-way communication system between the intestines and brain. The current study examined the effects of flavonoids on depression by observing the changes in the gut microbiome and depressive symptoms of young participants consuming flavonoid-rich orange juice. The depressive symptom was assessed using the Center for Epidemiological Studies Depression Scale (CES-D), a psychiatric screening tool used to detect preexisting mental disorders. The study population was randomly divided into two groups: the flavonoid-rich orange juice (FR) and an equicaloric flavonoid-low orange cordial (FL) group. For 8 weeks, participants consumed FR (serving a daily 380 mL, 600 ± 5.4 mg flavonoids) or FL (serving a daily 380 mL, 108 ± 2.6 mg flavonoids). In total, 80 fecal samples from 40 participants (mean age, 21.83 years) were sequenced. Regarding depression, we observed positive correlations between brain-derived neurotrophic factor (BDNF) and the Lachnospiraceae family (Lachnospiraceae_uc and Murimonas) before flavonoid orange juice treatment. Most notably, the abundance of the Lachnospiraceae family (Lachnospiraceae_uc, Eubacterium_g4, Roseburia_uc, Coprococcus_g2_uc, Agathobacter_uc) increased after FR treatment compared to that after FL treatment. We also validated the presence of unclassified Lachnospiraceae through sensitive real-time quantitative polymerase chain reaction using stool samples from participants before and after flavonoid treatment. Our results provide novel interventional evidence that alteration in the microbiome due to flavonoid treatment is related to a potential improvement in depression in young adults.
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22
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Turroni F, Milani C, Duranti S, Lugli GA, Bernasconi S, Margolles A, Di Pierro F, van Sinderen D, Ventura M. The infant gut microbiome as a microbial organ influencing host well-being. Ital J Pediatr 2020; 46:16. [PMID: 32024556 PMCID: PMC7003403 DOI: 10.1186/s13052-020-0781-0] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 01/29/2020] [Indexed: 12/16/2022] Open
Abstract
Initial establishment of the human gut microbiota is generally believed to occur immediately following birth, involving key gut commensals such as bifidobacteria that are acquired from the mother. The subsequent development of this early gut microbiota is driven and modulated by specific dietary compounds present in human milk that support selective colonization. This represents a very intriguing example of host-microbe co-evolution, where both partners are believed to benefit. In recent years, various publications have focused on dissecting microbial infant gut communities and their interaction with their human host, being a determining factor in host physiology and metabolic activities. Such studies have highlighted a reduction of microbial diversity and/or an aberrant microbiota composition, sometimes referred to as dysbiosis, which may manifest itself during the early stage of life, i.e., in infants, or later stages of life. There are growing experimental data that may explain how the early human gut microbiota affects risk factors related to adult health conditions. This concept has fueled the development of various nutritional strategies, many of which are based on probiotics and/or prebiotics, to shape the infant microbiota. In this review, we will present the current state of the art regarding the infant gut microbiota and the role of key commensal microorganisms like bifidobacteria in the establishment of the first microbial communities in the human gut.
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Affiliation(s)
- Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | | | - Abelardo Margolles
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, IPLA - CSIC, Villaviciosa, Asturias, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias-ISPA, Oviedo, Spain
| | | | - Douwe van Sinderen
- School of Microbiology & APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy.
- Microbiome Research Hub, University of Parma, Parma, Italy.
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Ali F, Lui K, Wang A, Day AS, Leach ST. The perinatal period, the developing intestinal microbiome and inflammatory bowel diseases: What links early life events with later life disease? J R Soc N Z 2020. [DOI: 10.1080/03036758.2019.1706586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Fathalla Ali
- School of Women’s and Children’s Health, University of New South Wales, Sydney, Australia
| | - Kei Lui
- School of Women’s and Children’s Health, University of New South Wales, Sydney, Australia
- Department of Newborn Care, Royal Hospital for Women, Sydney, Australia
| | - Alex Wang
- Faculty of Health, University of Technology Sydney, Sydney, Australia
| | - Andrew S. Day
- Department of Paediatrics, University of Otago, Christchurch, New Zealand
| | - Steven T. Leach
- School of Women’s and Children’s Health, University of New South Wales, Sydney, Australia
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Bojović K, Ignjatović ÐDI, Soković Bajić S, Vojnović Milutinović D, Tomić M, Golić N, Tolinački M. Gut Microbiota Dysbiosis Associated With Altered Production of Short Chain Fatty Acids in Children With Neurodevelopmental Disorders. Front Cell Infect Microbiol 2020; 10:223. [PMID: 32509596 PMCID: PMC7248180 DOI: 10.3389/fcimb.2020.00223] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 04/22/2020] [Indexed: 12/20/2022] Open
Abstract
While gut microbiota dysbiosis has been linked with autism, its role in the etiology of other neurodevelopmental disorders (NDD) is largely underexplored. To our knowledge this is the first study to evaluate gut microbiota diversity and composition in 36 children from the Republic of Serbia diagnosed with NDD and 28 healthy children. The results revealed an increased incidence of potentially harmful bacteria, closely related to Clostridium species, in the NDD patient group compared to the Control group: Desulfotomaculum guttoideum (P < 0.01), Intestinibacter bartlettii (P < 0.05), and Romboutsia ilealis (P < 0.001). On the other hand, significantly lower diversity of common commensal bacteria in the NDD group of patients was noticed. Enterococcus faecalis (P < 0.05), Enterococcus gallinarum (P < 0.01), Streptococcus pasteurianus (P < 0.05), Lactobacillus rhamnosus (P < 0.01) and Bifidobacteria sp. were detected in lower numbers of patients or were even absent in some NDD patients. In addition, butyrate-producing bacteria Faecalibacterium prausnitzii (P < 0.01), Butyricicoccus pullicaecorum (P < 0.05), and Eubacterium rectale (P = 0.07) were less frequent in the NDD patient group. In line with that, the levels of fecal short chain fatty acids (SCFAs) were determined. Although significant differences in SCFA levels were not detected between NDD patients and the Control group, a positive correlation was noted between number of rDNA amplicons obtained with universal primers and level of propionic acid, as well as a trend for levels of total SCFAs and butyric acid in the Control group. This correlation is lost in the NDD patient group, indicating that NDD patients' microbiota differs from the microbiota of healthy children in the presence or number of strong SCFA-producing bacteria. According to a range-weighted richness index it was observed that microbial diversity was significantly lower in the NDD patient group. Our study reveals that the intestinal microbiota from NDD patients differs from the microbiota of healthy children. It is hypothesized that early life microbiome might have an impact on GI disturbances and accompanied behavioral problems frequently observed in patients with a broad spectrum of NDD.
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Affiliation(s)
| | - Ður -d ica Ignjatović
- Department of Biochemistry, Institute for Biological Research “Siniša Stanković”, University of Belgrade, Belgrade, Serbia
- *Correspondence: Ðurđica Ignjatović
| | - Svetlana Soković Bajić
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Danijela Vojnović Milutinović
- Department of Biochemistry, Institute for Biological Research “Siniša Stanković”, University of Belgrade, Belgrade, Serbia
| | - Mirko Tomić
- Department of Biochemistry, Institute for Biological Research “Siniša Stanković”, University of Belgrade, Belgrade, Serbia
| | - Nataša Golić
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Maja Tolinački
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
- Maja Tolinački
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The Th17/Treg Cell Balance: A Gut Microbiota-Modulated Story. Microorganisms 2019; 7:microorganisms7120583. [PMID: 31756956 PMCID: PMC6956175 DOI: 10.3390/microorganisms7120583] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/14/2019] [Accepted: 11/18/2019] [Indexed: 12/17/2022] Open
Abstract
The intestinal tract of vertebrates is normally colonized with a remarkable number of commensal microorganisms that are collectively referred to as gut microbiota. Gut microbiota has been demonstrated to interact with immune cells and to modulate specific signaling pathways involving both innate and adaptive immune processes. Accumulated evidence suggests that the imbalance of Th17 and Treg cells is associated with the development of many diseases. Herein, we emphatically present recent findings to show how specific gut microbiota organisms and metabolites shape the balance of Th17 and Treg cells. We also discuss the therapeutic potential of fecal microbiota transplantation (FMT) in diseases caused by the imbalance of Th17 and Treg cells
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26
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Uncovering Bifidobacteria via Targeted Sequencing of the Mammalian Gut Microbiota. Microorganisms 2019; 7:microorganisms7110535. [PMID: 31698863 PMCID: PMC6920958 DOI: 10.3390/microorganisms7110535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/28/2019] [Accepted: 11/04/2019] [Indexed: 12/23/2022] Open
Abstract
Bifidobacteria are among the most prevalent gut commensals in mammals, playing crucial functional roles that start from their early colonization of the infant gastrointestinal tract and last throughout the life span of their host. Metagenomic approaches have been employed to unveil the genetic features of bifidobacteria in order to understand how they participate in the correct development of a healthy microbiome. Nevertheless, their low relative abundance in many environmental samples may represent a major limitation for metagenomics approaches. To overcome this restriction, we applied an enrichment method that allows amplification of bifidobacterial DNA obtained from human or animal fecal samples for up to 26,500-fold, resulting in the metagenomic reconstruction of genomes belonging to bifidobacterial strains, present at very low abundance in collected samples. Functional predictions of the genes from these reconstructed genomes allows us to identify unique signatures among members of the same bifidobacterial species, highlighting genes correlated with the uptake of nutrients and adhesion to the intestinal mucosa.
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Bifidobacterial Transfer from Mother to Child as Examined by an Animal Model. Microorganisms 2019; 7:microorganisms7090293. [PMID: 31461893 PMCID: PMC6780879 DOI: 10.3390/microorganisms7090293] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 08/21/2019] [Accepted: 08/22/2019] [Indexed: 01/12/2023] Open
Abstract
Bifidobacteria commonly constitute the most abundant group of microorganisms in the healthy infant gut. Their intestinal establishment is believed to be maternally driven, and their acquisition has even been postulated to occur during pregnancy. In the current study, we evaluated bifidobacterial mother-to infant transmission events in a rat model by means of quantitative PCR (qPCR), as well as by Internally Transcribed Spacer (ITS) bifidobacterial profiling. The occurrence of strains supplied by mothers during pregnancy to their corresponding newborns was observed and identified by analysis immediately following C-section delivery. These findings provide intriguing support for the existence of an unknown route to facilitate bifidobacterial transfer during the very early stages of life.
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28
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Sun Y, Cui X, Duan M, Ai C, Song S, Chen X. In vitro fermentation of κ-carrageenan oligosaccharides by human gut microbiota and its inflammatory effect on HT29 cells. J Funct Foods 2019. [DOI: 10.1016/j.jff.2019.05.036] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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29
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Singh RP. Glycan utilisation system in Bacteroides and Bifidobacteria and their roles in gut stability and health. Appl Microbiol Biotechnol 2019; 103:7287-7315. [PMID: 31332487 DOI: 10.1007/s00253-019-10012-z] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 07/02/2019] [Accepted: 07/03/2019] [Indexed: 02/07/2023]
Abstract
Gut residential hundred trillion microbial cells are indispensable for maintaining gut homeostasis and impact on host physiology, development and immune systems. Many of them have displayed excellence in utilising dietary- and host-derived complex glycans and are producing useful postbiotics including short-chain fatty acids to primarily fuel different organs of the host. Therefore, employing individual microbiota is nowadays becoming a propitious target in biomedical for improving gut dysbiosis conditions of the host. Among other gut microbial communities, Bacteroides and Bifidobacteria are coevolved to utilise diverse ranges of diet- and host-derived glycans through harmonising distinct glycan utilisation systems. These gut symbionts frequently share digested oligosaccharides, carbohydrate-active enzymes and fermentable intermediate molecules for sustaining gut microbial symbiosis and improving fitness of own or other communities. Genomics approaches have provided unprecedented insights into these functions, but their precise mechanisms of action have poorly known. Sympathetic glycan-utilising strategy of each gut commensal will provide overview of mechanistic dynamic nature of the gut environment and will then assist in applying aptly personalised nutritional therapy. Thus, the review critically summarises cutting edge understanding of major plant- and host-derived glycan-utilising systems of Bacteroides and Bifidobacteria. Their evolutionary adaptation to gut environment and roles of postbiotics in human health are also highlighted.
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Affiliation(s)
- Ravindra Pal Singh
- Food and Nutritional Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), SAS, Nagar, Punjab, 140306, India.
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30
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Progesterone Increases Bifidobacterium Relative Abundance during Late Pregnancy. Cell Rep 2019; 27:730-736.e3. [DOI: 10.1016/j.celrep.2019.03.075] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 02/12/2019] [Accepted: 03/20/2019] [Indexed: 12/14/2022] Open
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In vitro digestion under simulated saliva, gastric and small intestinal conditions and fermentation by human gut microbiota of polysaccharides from the fruits of Lycium barbarum. Int J Biol Macromol 2019; 125:751-760. [DOI: 10.1016/j.ijbiomac.2018.12.081] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/27/2018] [Accepted: 12/07/2018] [Indexed: 12/18/2022]
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32
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Xie X, He Y, Li H, Yu D, Na L, Sun T, Zhang D, Shi X, Xia Y, Jiang T, Rong S, Yang S, Ma X, Xu G. Effects of prebiotics on immunologic indicators and intestinal microbiota structure in perioperative colorectal cancer patients. Nutrition 2018; 61:132-142. [PMID: 30711862 DOI: 10.1016/j.nut.2018.10.038] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 10/24/2018] [Accepted: 10/29/2018] [Indexed: 01/23/2023]
Abstract
OBJECTIVE The aim of the present study was to investigate the effects of prebiotics (containing fructooligosaccharides, xylooligosaccharides, polydextrose, and resistant dextrin) intake on immune function and intestinal microbiota structure in perioperative patients with colorectal cancer (CRC). METHODS A randomized, double-blind, no-treatment parallel control clinical trial involving 140 perioperative patients (90 men and 50 women, aged 40-75 y) with CRC was performed. Patients were randomly divided into two groups: an intervention group (prebiotic group, n = 70) that received prebiotic supplementation of 30 g/d for 7 d, and a control group (non-prebiotic group, n = 70) that received no prebiotic supplementation. The nutritional and immunologic indices were evaluated for both groups before and after operation and analyzed against baseline values. Moreover, fecal samples were collected from 40 patients randomly chosen from the two groups to study intestinal microbiota, which was analyzed by sequencing the V3-V4 region of 16S ribosomal DNA using the Illumina (San Diego, CA) MiSeq (PE 2 × 300 bp) platform. RESULTS Oral intake of prebiotics produced significant effects on immunologic indices in both the preoperative and postoperative periods, but the patterns of effects were different. In the preoperative period, prebiotics increased serum levels of immunoglobulin G (IgG; P = 0.02), IgM (P = 0.00), and transferrin (P = 0.027; all P < 0.05). In the postoperative period, enhanced levels of IgG (P = 0.003), IgA (P = 0.007), suppressor/cytotoxic T cells (CD3+CD8+; P = 0.043), and total B lymphocytes (CD19+; P = 0.012) were identified in the prebiotic group (all P < 0.05). The differences in the intestinal microbiota at the phylum level were not statistically significant between the intervention and control groups (P > 0.05). At the genus level, prebiotics increased the abundance of Bifidobacterium (P = 0.017) and Enterococcus (P = 0.02; both P < 0.05) but decreased the abundance of Bacteroides (P = 0.04) in the preoperative period (all P < 0.05). In the postoperative period, the abundance of Bacteroides (P = 0.04) was decreased, but the abundance of Enterococcus (P = 0.00), Bacillus (P = 0.01), Lactococcus (P = 0.00), and Streptococcus (P = 0.037) increased in the non-prebiotic group (all P < 0.05); however, no significant change was identified in the abundance of Enterococcus (P = 0.56), Lactococcus (P = 0.07), and Streptococcus (P = 0.56) as a result of prebiotic intervention in this period (all P > 0.05). The abundance of Escherichia-Shigella was increased after prebiotic intake in the postoperative period (P = 0.014, P < 0.05). There was a notable trend of decline in the abundance of intestinal microbiota from preoperative to postoperative in the non-prebiotic group. CONCLUSIONS Prebiotic intake is recommended to improve serum immunologic indicators in patients with CRC 7 d before operation. Prebiotics improved the abundance of four commensal microbiota containing opportunistic pathogens in patients with CRC. Surgical stress decreased the abundance of most intestinal microbiota in the intestinal tract but increased the abundance of some opportunistic pathogens and commensal microbiota. Bacteroides is a relevant bacterial species for further research on the mechanism of prebiotics.
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Affiliation(s)
- Xiaoliang Xie
- Department of Colorectal Surgery, General Hospital of Ningxia Medical University, Yinchuan, China; College of Clinical Medicine, Ningxia Medical University, Yinchuan, China
| | - Yaqin He
- Surgical Department, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Hai Li
- Department of Colorectal Surgery, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Dong Yu
- Department of Colorectal Surgery, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Li Na
- Biobank of the General Hospital of Ningxia Medical University, Yinchuan, China
| | - Ting Sun
- Biobank of the General Hospital of Ningxia Medical University, Yinchuan, China
| | - Dong Zhang
- Department of Colorectal Surgery, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Xinrong Shi
- Department of Colorectal Surgery, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Yuhan Xia
- Nutrition Department, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Tao Jiang
- Department of Colorectal Surgery, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Shikuo Rong
- College of Clinical Medicine, Ningxia Medical University, Yinchuan, China
| | - Shaoqi Yang
- Department of Gastroenterology, General Hospital of Ningxia Medical University, Yinchuan, China.
| | - Xiaoqiang Ma
- Department of Colorectal Surgery, General Hospital of Ningxia Medical University, Yinchuan, China.
| | - Guangxian Xu
- Ningxia Key Laboratory of Clinical and Pathogenic Microbiology, General Hospital of Ningxia Medical University, Yinchuan, China.
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Duranti S, Vivo V, Zini I, Milani C, Mangifesta M, Anzalone R, Mancabelli L, Viappiani A, Cantoni AM, Barocelli E, van Sinderen D, Bertoni S, Turroni F. Bifidobacterium bifidum PRL2010 alleviates intestinal ischemia/reperfusion injury. PLoS One 2018; 13:e0202670. [PMID: 30161157 PMCID: PMC6116995 DOI: 10.1371/journal.pone.0202670] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 08/07/2018] [Indexed: 02/01/2023] Open
Abstract
Mesenteric ischemia/reperfusion is a clinical emergency with high morbidity and mortality due to the transient reduction of blood supply to the bowel. In recent years, the critical contribution of gut microbiome to human health and proper gastrointestinal functions has gradually emerged. In the current study, we investigated the protective effects of five days supplementation with Bifidobacterium bifidum PRL2010 in a murine model of gut ischemia/reperfusion. Our findings indicate that animals pretreated with B. bifidum PRL2010 showed lower neutrophil recruitment in the lungs, remarkably reduced bacterial translocation and decreased transcription levels of TNFalpha and IL-10 both in liver and kidneys, at the same time increasing those of IL-12 in kidneys. Inhibiting the adhesion of pathogenic bacteria and boosting host innate immunity responses are among the possible protective mechanisms enacted by the probiotic. These results demonstrate that short-period treatment with B. bifidum PRL2010 is a potential strategy to dampen remote organ injury due to mesenteric ischemia/reperfusion.
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Affiliation(s)
- Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemical Sciences, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Valentina Vivo
- Food and Drug Department, University of Parma, Parma, Italy
| | - Irene Zini
- Food and Drug Department, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemical Sciences, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Rosaria Anzalone
- Laboratory of Probiogenomics, Department of Chemical Sciences, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemical Sciences, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Alice Viappiani
- Laboratory of Probiogenomics, Department of Chemical Sciences, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Elisabetta Barocelli
- Laboratory of Probiogenomics, Department of Chemical Sciences, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Simona Bertoni
- Food and Drug Department, University of Parma, Parma, Italy
- * E-mail:
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemical Sciences, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
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Lugli GA, Mangifesta M, Duranti S, Anzalone R, Milani C, Mancabelli L, Alessandri G, Turroni F, Ossiprandi MC, van Sinderen D, Ventura M. Phylogenetic classification of six novel species belonging to the genus Bifidobacterium comprising Bifidobacterium anseris sp. nov., Bifidobacterium criceti sp. nov., Bifidobacterium imperatoris sp. nov., Bifidobacterium italicum sp. nov., Bifidobacterium margollesii sp. nov. and Bifidobacterium parmae sp. nov. Syst Appl Microbiol 2018; 41:173-183. [PMID: 29395537 DOI: 10.1016/j.syapm.2018.01.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 12/22/2017] [Accepted: 01/08/2018] [Indexed: 10/18/2022]
Abstract
Six Bifidobacterium strains, i.e., Goo31D, Ham19E, Rab10A, Tam1G, Uis4E and Uis1B, were isolated from domestic goose (Anser domesticus), European hamster (Cricetus cricetus), European rabbit (Oryctolagus cuniculus), emperor tamarin (Saguinus imperator) and pygmy marmoset (Callithrix pygmaea). Cells are Gram-positive, non-motile, non-sporulating, facultative anaerobic and fructose 6-phosphate phosphoketolase-positive. Phylogenetic analyses based on 16S rRNA, ITS-, multilocus- sequences and the core genome revealed that bifidobacterial strains Goo31D, Ham19E, Rab10A, Tam1G, Uis4E and Uis1B exhibit close phylogenetic relatedness with Bifidobacterium choerinum LMG 10510, Bifidobacterium hapali DSM 100202, Bifidobacterium saguini DSM 23967 and Bifidobacterium stellenboschense DSM 23968. Genotyping based on the genome sequence of the isolated strains combined with phenotypic analyses, clearly show that these strains are distinct from each of the type strains of the so far recognized Bifidobacterium species. Thus, Bifidobacterium anseris sp. nov. (Goo31D=LMG 30189T=CCUG 70960T), Bifidobacterium criceti sp. nov. (Ham19E=LMG 30188T=CCUG 70962T), Bifidobacterium imperatoris sp. nov. (Tam1G=LMG 30297T=CCUG 70961T), Bifidobacterium italicum sp. nov. (Rab10A=LMG 30187T=CCUG 70963T), Bifidobacterium margollesii sp. nov. (Uis1B=LMG 30296T=CCUG 70959T) and Bifidobacterium parmae sp. nov. (Uis4E=LMG 30295T=CCUG 70964T) are proposed as novel Bifidobacterium species.
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Affiliation(s)
- Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Rosaria Anzalone
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.
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Duranti S, Lugli GA, Mancabelli L, Armanini F, Turroni F, James K, Ferretti P, Gorfer V, Ferrario C, Milani C, Mangifesta M, Anzalone R, Zolfo M, Viappiani A, Pasolli E, Bariletti I, Canto R, Clementi R, Cologna M, Crifò T, Cusumano G, Fedi S, Gottardi S, Innamorati C, Masè C, Postai D, Savoi D, Soffiati M, Tateo S, Pedrotti A, Segata N, van Sinderen D, Ventura M. Maternal inheritance of bifidobacterial communities and bifidophages in infants through vertical transmission. MICROBIOME 2017; 5:66. [PMID: 28651630 PMCID: PMC5485682 DOI: 10.1186/s40168-017-0282-6] [Citation(s) in RCA: 203] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/05/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND The correct establishment of the human gut microbiota represents a crucial development that commences at birth. Different hypotheses propose that the infant gut microbiota is derived from, among other sources, the mother's fecal/vaginal microbiota and human milk. RESULTS The composition of bifidobacterial communities of 25 mother-infant pairs was investigated based on an internal transcribed spacer (ITS) approach, combined with cultivation-mediated and genomic analyses. We identified bifidobacterial strains/communities that are shared between mothers and their corresponding newborns. Notably, genomic analyses together with growth profiling assays revealed that bifidobacterial strains that had been isolated from human milk are genetically adapted to utilize human milk glycans. In addition, we identified particular bacteriophages specific of bifidobacterial species that are common in the viromes of mother and corresponding child. CONCLUSIONS This study highlights the transmission of bifidobacterial communities from the mother to her child and implies human milk as a potential vehicle to facilitate this acquisition. Furthermore, these data represent the first example of maternal inheritance of bifidobacterial phages, also known as bifidophages in infants following a vertical transmission route.
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Affiliation(s)
- Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | | | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Kieran James
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Pamela Ferretti
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | | | - Chiara Ferrario
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | | | - Rosaria Anzalone
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy
| | - Moreno Zolfo
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | | | - Edoardo Pasolli
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | | | - Rosarita Canto
- Azienda Provinciale per i Servizi Sanitari, Trento, Italy
| | | | - Marina Cologna
- Azienda Provinciale per i Servizi Sanitari, Trento, Italy
| | - Tiziana Crifò
- Azienda Provinciale per i Servizi Sanitari, Trento, Italy
| | | | - Sabina Fedi
- Azienda Provinciale per i Servizi Sanitari, Trento, Italy
| | | | | | - Caterina Masè
- Azienda Provinciale per i Servizi Sanitari, Trento, Italy
| | - Daniela Postai
- Azienda Provinciale per i Servizi Sanitari, Trento, Italy
| | - Daniela Savoi
- Azienda Provinciale per i Servizi Sanitari, Trento, Italy
| | | | - Saverio Tateo
- Azienda Provinciale per i Servizi Sanitari, Trento, Italy
| | - Anna Pedrotti
- Azienda Provinciale per i Servizi Sanitari, Trento, Italy
| | - Nicola Segata
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124, Parma, Italy.
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Hu L, Wang L, Lu W, Zhao J, Zhang H, Chen W. Selection, Characterization and Interaction Studies of a DNA Aptamer for the Detection of Bifidobacterium bifidum. Int J Mol Sci 2017; 18:ijms18050883. [PMID: 28441340 PMCID: PMC5454810 DOI: 10.3390/ijms18050883] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 04/14/2017] [Accepted: 04/18/2017] [Indexed: 01/10/2023] Open
Abstract
A whole-bacterium-based SELEX (Systematic Evolution of Ligands by Exponential Enrichment) procedure was adopted in this study for the selection of an ssDNA aptamer that binds to Bifidobacterium bifidum. After 12 rounds of selection targeted against B. bifidum, 30 sequences were obtained and divided into seven families according to primary sequence homology and similarity of secondary structure. Four FAM (fluorescein amidite) labeled aptamer sequences from different families were selected for further characterization by flow cytometric analysis. The results reveal that the aptamer sequence CCFM641-5 demonstrated high-affinity and specificity for B. bifidum compared with the other sequences tested, and the estimated Kd value was 10.69 ± 0.89 nM. Additionally, sequence truncation experiments of the aptamer CCFM641-5 led to the conclusion that the 5'-primer and 3'-primer binding sites were essential for aptamer-target binding. In addition, the possible component of the target B. bifidum, bound by the aptamer CCFM641-5, was identified as a membrane protein by treatment with proteinase. Furthermore, to prove the potential application of the aptamer CCFM641-5, a colorimetric bioassay of the sandwich-type structure was used to detect B. bifidum. The assay had a linear range of 10⁴ to 10⁷ cfu/mL (R² = 0.9834). Therefore, the colorimetric bioassay appears to be a promising method for the detection of B. bifidum based on the aptamer CCFM641-5.
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Affiliation(s)
- Lujun Hu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
| | - Linlin Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
| | - Wenwei Lu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
- International Joint Research Center for Probiotics & Gut Health, Jiangnan University, Wuxi 214122, China.
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
- International Joint Research Center for Probiotics & Gut Health, Jiangnan University, Wuxi 214122, China.
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
- International Joint Research Center for Probiotics & Gut Health, Jiangnan University, Wuxi 214122, China.
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
- International Joint Research Center for Probiotics & Gut Health, Jiangnan University, Wuxi 214122, China.
- Beijing Innovation Centre of Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China.
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Smolinska S, Groeger D, O'Mahony L. Biology of the Microbiome 1: Interactions with the Host Immune Response. Gastroenterol Clin North Am 2017; 46:19-35. [PMID: 28164850 DOI: 10.1016/j.gtc.2016.09.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The intestinal immune system is intimately connected with the vast diversity of microbes present within the gut and the diversity of food components that are consumed daily. The discovery of novel molecular mechanisms, which mediate host-microbe-nutrient communication, have highlighted the important roles played by microbes and dietary factors in influencing mucosal immune responses. Dendritic cells, epithelial cells, innate lymphoid cells, T regulatory cells, effector lymphocytes, natural killer T cells, and B cells can all be influenced by the microbiome. Many of the mechanisms being described are bacterial strain or metabolite specific.
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Affiliation(s)
- Sylwia Smolinska
- Department of Clinical Immunology, Wroclaw Medical University, Chalubinskiego 5, Wroclaw 50-368, Poland
| | - David Groeger
- Alimentary Health Pharma Davos, Obere Strasse 22, Davos Platz 7270, Switzerland
| | - Liam O'Mahony
- Molecular Immunology, Swiss Institute of Allergy and Asthma Research, University of Zurich, Obere Strasse 22, Davos Platz 7270, Switzerland.
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Taibi A, Singh N, Chen J, Arioli S, Guglielmetti S, Comelli EM. Time- and strain-specific downregulation of intestinal EPAS1
via miR-148a by Bifidobacterium bifidum. Mol Nutr Food Res 2017; 61. [DOI: 10.1002/mnfr.201600596] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 10/07/2016] [Accepted: 11/18/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Amel Taibi
- Department of Nutritional Sciences; University of Toronto; ON Canada
| | - Natasha Singh
- Department of Nutritional Sciences; University of Toronto; ON Canada
| | - Jianmin Chen
- Department of Nutritional Sciences; University of Toronto; ON Canada
| | - Stefania Arioli
- Department of Nutritional Sciences; University of Toronto; ON Canada
- Department of Food; Environmental and Nutritional Sciences (DeFENS); University of Milan; Milan Italy
| | - Simone Guglielmetti
- Department of Food; Environmental and Nutritional Sciences (DeFENS); University of Milan; Milan Italy
| | - Elena M. Comelli
- Department of Nutritional Sciences; University of Toronto; ON Canada
- Centre for Child Nutrition and Health; Faculty of Medicine; University of Toronto; ON Canada
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Gosiewski T, Ludwig-Galezowska AH, Huminska K, Sroka-Oleksiak A, Radkowski P, Salamon D, Wojciechowicz J, Kus-Slowinska M, Bulanda M, Wolkow PP. Comprehensive detection and identification of bacterial DNA in the blood of patients with sepsis and healthy volunteers using next-generation sequencing method - the observation of DNAemia. Eur J Clin Microbiol Infect Dis 2016; 36:329-336. [PMID: 27771780 PMCID: PMC5253159 DOI: 10.1007/s10096-016-2805-7] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 09/26/2016] [Indexed: 12/17/2022]
Abstract
Blood is considered to be a sterile microenvironment, in which bacteria appear only periodically. Previously used methods allowed only for the detection of either viable bacteria with low sensitivity or selected species of bacteria. The Next-Generation Sequencing method (NGS) enables the identification of all bacteria in the sample with their taxonomic classification. We used NGS for the analysis of blood samples from healthy volunteers (n = 23) and patients with sepsis (n = 62) to check whether any bacterial DNA exists in the blood of healthy people and to identify bacterial taxonomic profile in the blood of septic patients. The presence of bacterial DNA was found both in septic and healthy subjects; however, bacterial diversity was significantly different (P = 0.002) between the studied groups. Among healthy volunteers, a significant predominance of anaerobic bacteria (76.2 %), of which most were bacteria of the order Bifidobacteriales (73.0 %), was observed. In sepsis, the majority of detected taxa belonged to aerobic or microaerophilic microorganisms (75.1 %). The most striking difference was seen in the case of Actinobacteria phyla, the abundance of which was decreased in sepsis (P < 0.001) and Proteobacteria phyla which was decreased in the healthy volunteers (P < 0.001). Our research shows that bacterial DNA can be detected in the blood of healthy people and that its taxonomic composition is different from the one seen in septic patients. Detection of bacterial DNA in the blood of healthy people may suggest that bacteria continuously translocate into the blood, but not always cause sepsis; this observation can be called DNAemia.
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Affiliation(s)
- T Gosiewski
- Department of Microbiology, Jagiellonian University Medical College, Krakow, Poland
| | - A H Ludwig-Galezowska
- Center for Medical Genomics OMICRON, Jagiellonian University Medical College, 7C Kopernika Str., 31-034, Krakow, Poland
| | - K Huminska
- Genomic Laboratory, DNA Research Center, Poznan, Poland.,Laboratory of High Throughput Technologies, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - A Sroka-Oleksiak
- Department of Microbiology, Jagiellonian University Medical College, Krakow, Poland
| | - P Radkowski
- Center for Medical Genomics OMICRON, Jagiellonian University Medical College, 7C Kopernika Str., 31-034, Krakow, Poland
| | - D Salamon
- Department of Microbiology, Jagiellonian University Medical College, Krakow, Poland
| | | | | | - M Bulanda
- Department of Microbiology, Jagiellonian University Medical College, Krakow, Poland
| | - P P Wolkow
- Center for Medical Genomics OMICRON, Jagiellonian University Medical College, 7C Kopernika Str., 31-034, Krakow, Poland.
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Duranti S, Gaiani F, Mancabelli L, Milani C, Grandi A, Bolchi A, Santoni A, Lugli GA, Ferrario C, Mangifesta M, Viappiani A, Bertoni S, Vivo V, Serafini F, Barbaro MR, Fugazza A, Barbara G, Gioiosa L, Palanza P, Cantoni AM, de'Angelis GL, Barocelli E, de'Angelis N, van Sinderen D, Ventura M, Turroni F. Elucidating the gut microbiome of ulcerative colitis: bifidobacteria as novel microbial biomarkers. FEMS Microbiol Ecol 2016; 92:fiw191. [PMID: 27604252 DOI: 10.1093/femsec/fiw191] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2016] [Indexed: 12/21/2022] Open
Abstract
Ulcerative colitis (UC) is associated with a substantial alteration of specific gut commensals, some of which may be involved in microbiota-mediated protection. In this study, microbiota cataloging of UC patients by 16S rRNA microbial profiling revealed a marked reduction of bifidobacteria, in particular the Bifidobacterium bifidum species, thus suggesting that this taxon plays a biological role in the aetiology of UC. We investigated this further through an in vivo trial by testing the effects of oral treatment with B. bifidum PRL2010 in a wild-type murine colitis model. TNBS-treated mice receiving 10(9) cells of B. bifidum PRL2010 showed a marked reduction of all colitis-associated histological indices as well as maintenance of mucosal integrity as it was shown by the increase in the expression of many tight junction-encoding genes. The protective role of B. bifidum PRL2010, as well as its sortase-dependent pili, appears to be established through the induction of an innate immune response of the host. These results highlight the importance of B. bifidum as a microbial biomarker for UC, revealing its role in protection against experimentally induced colitis.
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Affiliation(s)
- Sabrina Duranti
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11A, 43124 Parma, Italy
| | - Federica Gaiani
- Gastroenterology Unit, University Hospital of Parma, Via Gramsci 14, 43126 Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11A, 43124 Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11A, 43124 Parma, Italy
| | - Andrea Grandi
- Department of Pharmacy, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Angelo Bolchi
- Laboratory of Molecular Biology, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| | - Andrea Santoni
- Laboratory of Molecular Biology, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11A, 43124 Parma, Italy
| | - Chiara Ferrario
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11A, 43124 Parma, Italy
| | | | - Alice Viappiani
- GenProbio srl, Parco Area delle Scienze 11A, 43124 Parma, Italy
| | - Simona Bertoni
- Department of Pharmacy, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Valentina Vivo
- Department of Pharmacy, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Fausta Serafini
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11A, 43124 Parma, Italy
| | - Maria Raffaella Barbaro
- Department of Medical and Surgical Sciences and Center for Applied Biomedical Research (CRBA), University of Bologna, Via Massarenti 9, Bologna 40138, Italy
| | - Alessandro Fugazza
- Gastroenterology Unit, University Hospital of Parma, Via Gramsci 14, 43126 Parma, Italy
| | - Giovanni Barbara
- Department of Medical and Surgical Sciences and Center for Applied Biomedical Research (CRBA), University of Bologna, Via Massarenti 9, Bologna 40138, Italy
| | - Laura Gioiosa
- Department of Neurosciences, University of Parma, 43124 Parma, Italy
| | - Paola Palanza
- Department of Neurosciences, University of Parma, 43124 Parma, Italy
| | - Anna Maria Cantoni
- Department of Veterinary Science, University of Parma, Via del Taglio 10, 43126 Parma, Italy
| | - Gian Luigi de'Angelis
- Gastroenterology Unit, University Hospital of Parma, Via Gramsci 14, 43126 Parma, Italy
| | - Elisabetta Barocelli
- Department of Pharmacy, University of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Nicola de'Angelis
- Unit of Digestive, Hepato-Pancreato-Biliary Surgery and Liver Transplantation, Henri Mondor Hospital, 51 Avenue du Maréchal de Lattre de Tassigny, Créteil 94010, France
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11A, 43124 Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parco Area delle Scienze 11A, 43124 Parma, Italy
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Bifidobacteria-Insight into clinical outcomes and mechanisms of its probiotic action. Microbiol Res 2016; 192:159-171. [PMID: 27664734 DOI: 10.1016/j.micres.2016.07.001] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 06/12/2016] [Accepted: 07/07/2016] [Indexed: 02/07/2023]
Abstract
The invasion of pathogens causes a disruption of the gut homeostasis. Innate immune responses and those triggered by endogenous microbiota form the first line of defence in our body. Pathogens often successfully overcome the resistances offered, calling for therapeutic intervention. Conventional strategy involving antibiotics might eradicate pathogens, but often leave the gut uncolonised and susceptible to recurrences. Probiotic supplements are useful alternatives. Bifidobacterium is one of widely studied probiotic genus, effective in restoring gut homeostasis. Mechanisms of probiotic action of bifidobacteria are several, often with strain-specificity. Analysis of streamlined literature reports reveal that although most studies report the probiotic aspect of bifidobacteria, sporadic documented contradictory results exist, challenging its therapeutic application and prompting studies to unambiguously establish the strain-associated probiotic activity and negate adverse effects prior to its clinical administration. Multi-strain/combinatorial therapy possibly relies on a combination of underlying operating mechanisms, each contributing towards enhanced probiotic efficacy, understanding which could help in developing customised formulations against targeted pathogens. Bifidogenic activity is also mediated by surface-associated structural components such as exopolysaccharides, lipoteichoic acids along with metabolites and bifidocins. This highlights scope for developing advanced structural therapeutic strategy which might be pivotal in replacing intact cell probiotics therapy.
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Whisner CM, Martin BR, Nakatsu CH, Story JA, MacDonald-Clarke CJ, McCabe LD, McCabe GP, Weaver CM. Soluble Corn Fiber Increases Calcium Absorption Associated with Shifts in the Gut Microbiome: A Randomized Dose-Response Trial in Free-Living Pubertal Females. J Nutr 2016; 146:1298-306. [PMID: 27281813 DOI: 10.3945/jn.115.227256] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 04/29/2016] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Soluble corn fiber (SCF; 12 g fiber/d) is shown to increase calcium absorption efficiency, associated with shifts in the gut microbiota in adolescent males and females who participated in a controlled feeding study. OBJECTIVE We evaluated the dose response of 0, 10, and 20 g fiber/d delivered by PROMITOR SCF 85 (85% fiber) on calcium absorption, biochemical bone properties, and the fecal microbiome in free-living adolescents. METHODS Healthy adolescent females (n = 28; aged 11-14 y) randomly assigned into a 3-phase, double-blind, crossover study consumed SCF for 4 wk at each dose (0, 10, and 20 g fiber/d from SCF) alongside their habitual diet and were followed by 3-d clinical visits and 3-wk washout periods. Stable isotope ((44)Ca and (43)Ca) enrichment in pooled urine was measured by inductively coupled plasma mass spectrometry. Fecal microbial community composition was assessed by high-throughput sequencing (Illumina) of polymerase chain reaction-amplified 16S rRNA genes. Mixed model ANOVA and Friedman analysis were used to determine effects of SCF on calcium absorption and to compare mean microbial proportions, respectively. RESULTS Calcium absorption increased significantly with 10 (13.3% ± 5.3%; P = 0.042) and 20 g fiber/d (12.9% ± 3.6%; P = 0.026) from SCF relative to control. Significant differences in fecal microbial community diversity were found after consuming SCF (operational taxonomic unit measures of 601.4 ± 83.5, 634.5 ± 83.8, and 649.6 ± 75.5 for 0, 10, and 20 g fiber/d, respectively; P < 0.05). Proportions of the genus Parabacteroides significantly increased with SCF dose (1.1% ± 0.8%, 2.1% ± 1.6%, and 3.0% ± 2.0% for 0, 10, and 20 g fiber/d from SCF, respectively; P < 0.05). Increases in calcium absorption positively correlated with increases in Clostridium (r = 0.44, P = 0.023) and unclassified Clostridiaceae (r = 0.40, P = 0.040). CONCLUSIONS SCF, a nondigestible carbohydrate, increased calcium absorption in free-living adolescent females. Two groups of bacteria may be involved, one directly fermenting SCF and the second fermenting SCF metabolites further, thereby promoting increased calcium absorption. This trial was registered at clinicaltrials.gov as NCT01660503.
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Affiliation(s)
- Corrie M Whisner
- School of Nutrition and Health Promotion, Arizona State University, Phoenix, AZ; and Departments of Nutrition Science
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Wang BG, Wu Y, Qiu L, Shah NP, Xu F, Wei H. Integration of genomic and proteomic data to identify candidate genes in HT-29 cells after incubation with Bifidobacterium bifidum ATCC 29521. J Dairy Sci 2016; 99:6874-6888. [PMID: 27372578 DOI: 10.3168/jds.2015-10577] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 01/31/2016] [Indexed: 11/19/2022]
Abstract
As the predominant group inhabiting the human gastrointestinal tract, bifidobacteria play a vital role in human nutrition, therapeutics, and health by shaping and maintaining the gut ecosystem, reducing blood cholesterol, and promoting the supply of nutrients. The interaction between bacterial cells and human intestinal epithelial cell lines has been studied for decades in an attempt to understand the mechanisms of action. These studies, however, have been limited by lack of genomic and proteomic database to aid in achieving comprehensive understanding of these mechanisms at molecular levels. Microarray data (GSE: 74119) coupled with isobaric tags for relative and absolute quantitation (iTRAQ) were performed to detect differentially expressed genes and proteins in HT-29 cells after incubation with Bifidobacterium bifidum. Real-time quantitative PCR, gene ontology, and Kyoto Encyclopedia of Genes and Genomes analyses were further conducted for mRNA validation, functional annotation, and pathway identification, respectively. According to the results of microarray, 1,717 differentially expressed genes, including 1,693 upregulated and 24 downregulated genes, were selected and classified by the gene ontology database. The iTRAQ analysis identified 43 differentially expressed proteins, where 29 proteins were upregulated and 14 proteins were downregulated. Eighty-two candidate genes showing consistent differences with microarray and iTRAQ were further validated in HT-29 and Caco-2 cells by real-time quantitative PCR. Nine of the top genes showing interesting results with high confidence were further investigated in vivo in mice intestine samples. Integration of genomic and proteomic data provides an approach to identify candidate genes that are more likely to function in ubiquitin-mediated proteolysis, positive regulation of apoptosis, membrane proteins, and transferase catalysis. These findings might contribute to our understanding of molecular mechanisms regulating the interaction between probiotics and intestinal epithelial cell lines.
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Affiliation(s)
- Bao-Gui Wang
- State Key Laboratory of Food Science and Engineering, Nanchang University, Nanchang, Jiangxi 330047, P. R. China
| | - Yaoping Wu
- State Key Laboratory of Food Science and Engineering, Nanchang University, Nanchang, Jiangxi 330047, P. R. China
| | - Liang Qiu
- State Key Laboratory of Food Science and Engineering, Nanchang University, Nanchang, Jiangxi 330047, P. R. China; Jiangxi University of Traditional Chinese Medicine, Nanchang, 330004, P.R. China
| | - Nagendra P Shah
- Food and Nutritional Science, School of Biological Sciences, The University of Hong Kong, Hong Kong
| | - Feng Xu
- State Key Laboratory of Food Science and Engineering, Nanchang University, Nanchang, Jiangxi 330047, P. R. China
| | - Hua Wei
- State Key Laboratory of Food Science and Engineering, Nanchang University, Nanchang, Jiangxi 330047, P. R. China.
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Deciphering bifidobacterial-mediated metabolic interactions and their impact on gut microbiota by a multi-omics approach. ISME JOURNAL 2016; 10:1656-68. [PMID: 26859770 DOI: 10.1038/ismej.2015.236] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 10/12/2015] [Accepted: 11/10/2015] [Indexed: 12/28/2022]
Abstract
The intricacies of cooperation and competition between microorganisms are poorly investigated for particular components of the gut microbiota. In order to obtain insights into the manner by which different bifidobacterial species coexist in the mammalian gut, we investigated possible interactions between four human gut commensals, Bifidobacterium bifidum PRL2010, Bifidobacterium adolescentis 22L, Bifidobacterium breve 12L and Bifidobacterium longum subsp. infantis ATCC15697, in the intestine of conventional mice. The generated information revealed various ecological/metabolic strategies, including glycan-harvesting, glycan-breakdown and cross-feeding behavior, adopted by bifidobacteria in the highly competitive environment of the mammalian intestine. Introduction of two or multiple bifidobacterial strains caused a clear shift in the microbiota composition of the murine cecum. Whole-genome transcription profiling coupled with metagenomic analyses of single, dual or multiple associations of bifidobacterial strains revealed an expansion of the murine gut glycobiome toward enzymatic degradation of plant-derived carbohydrates, such as xylan, arabinoxylan, starch and host-derived glycan substrates. Furthermore, these bifidobacterial communities evoked major changes in the metabolomic profile of the microbiota as observed by shifts in short chain fatty acid production and carbohydrate availability in the murine cecum. Overall, these data support an ecological role of bifidobacteria acting directly or through cross-feeding activities in shaping the gut murine microbiome to instigate an enrichment of saccharolytic microbiota.
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45
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In silico mining and characterization of bifidobacterial lipoprotein with CHAP domain secreted in an aggregated form. Int J Biol Macromol 2016; 82:653-62. [DOI: 10.1016/j.ijbiomac.2015.10.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 10/02/2015] [Accepted: 10/07/2015] [Indexed: 12/13/2022]
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46
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47
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Ferrario C, Duranti S, Milani C, Mancabelli L, Lugli GA, Turroni F, Mangifesta M, Viappiani A, Ossiprandi MC, van Sinderen D, Ventura M. Exploring Amino Acid Auxotrophy in Bifidobacterium bifidum PRL2010. Front Microbiol 2015; 6:1331. [PMID: 26635786 PMCID: PMC4656816 DOI: 10.3389/fmicb.2015.01331] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 11/12/2015] [Indexed: 01/01/2023] Open
Abstract
The acquisition and assimilation strategies followed by members of the infant gut microbiota to retrieve nitrogen from the gut lumen are still largely unknown. In particular, no information on these metabolic processes is available regarding bifidobacteria, which are among the first microbial colonizers of the human intestine. Here, evaluation of amino acid auxotrophy and prototrophy of Bifidobacterium bifidum, with particular emphasis on B. bifidum strain PRL2010 (LMG S-28692), revealed a putative auxotrophy for cysteine. In addition, we hypothesized that cysteine plays a role in the oxidative stress response in B. bifidum. The use of glutathione as an alternative reduced sulfur compound did not alleviate cysteine auxotrophy of this strain, though it was shown to stimulate expression of the genes involved in cysteine biosynthesis, reminiscent of oxidative stress response. When PRL2010 was grown on a medium containing complex substrates, such as whey proteins or casein hydrolysate, we noticed a distinct growth-promoting effect of these compounds. Transcriptional analysis involving B. bifidum PRL2010 cultivated on whey proteins or casein hydrolysate revealed that the biosynthetic pathways for cysteine and methionine are modulated by the presence of casein hydrolysate. Such findings support the notion that certain complex substrates may act as potential prebiotics for bifidobacteria in their ecological niche.
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Affiliation(s)
- Chiara Ferrario
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma Parma, Italy
| | - Gabriele A Lugli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma Parma, Italy
| | | | | | - Maria C Ossiprandi
- Department of Medical-Veterinary Science, University of Parma Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, University College Cork, National University of Ireland Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma Parma, Italy
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Grimm V, Radulovic K, Riedel CU. Colonization of C57BL/6 Mice by a Potential Probiotic Bifidobacterium bifidum Strain under Germ-Free and Specific Pathogen-Free Conditions and during Experimental Colitis. PLoS One 2015; 10:e0139935. [PMID: 26439388 PMCID: PMC4595203 DOI: 10.1371/journal.pone.0139935] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 09/18/2015] [Indexed: 12/18/2022] Open
Abstract
The effects of at least some probiotics are restricted to live, metabolically active bacteria at their site of action. Colonization of and persistence in the gastrointestinal tract is thus contributing to the beneficial effects of these strains. In the present study, colonization of an anti-inflammatory Bifidobacterium bifidum strain was studied in C57BL/6J mice under germ-free (GF) and specific pathogen-free (SPF) conditions as well as during dextran sulfate sodium (DSS)-induced colitis. B. bifidum S17/pMGC was unable to stably colonize C57BL/6J mice under SPF conditions. Mono-association of GF mice by three doses on consecutive days led to long-term, stable detection of up to 109 colony forming units (CFU) of B. bifidum S17/pMGC per g feces. This stable population was rapidly outcompeted upon transfer of mono-associated animals to SPF conditions. A B. animalis strain was isolated from the microbiota of these re-conventionalized mice. This B. animalis strain displayed significantly higher adhesion to murine CMT-93 intestinal epithelial cells (IECs) than to human Caco-2 IECs (p = 0.018). Conversely, B. bifidum S17/pMGC, i.e., a strain of human origin, adhered at significantly higher levels to human compared to murine IECs (p < 0.001). Disturbance of the gut ecology and induction of colitis by DSS-treatment did not promote colonization of the murine gastrointestinal tract (GIT) by B. bifidum S17/pMGC. Despite its poor colonization of the mouse GIT, B. bifidum S17/pMGC displayed a protective effect on DSS-induced colitis when administered as viable bacteria but not as UV-inactivated preparation. Collectively, these results suggest a selective disadvantage of B. bifidum S17/pMGC in the competition with the normal murine microbiota and an anti-inflammatory effect that requires live, metabolically active bacteria.
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Affiliation(s)
- Verena Grimm
- Institute of Microbiology and Biotechnology, University of Ulm, 89068, Ulm, Germany
| | - Katarina Radulovic
- Institute of Microbiology and Biotechnology, University of Ulm, 89068, Ulm, Germany
| | - Christian U. Riedel
- Institute of Microbiology and Biotechnology, University of Ulm, 89068, Ulm, Germany
- * E-mail:
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Chaplin AV, Efimov BA, Smeianov VV, Kafarskaia LI, Pikina AP, Shkoporov AN. Intraspecies Genomic Diversity and Long-Term Persistence of Bifidobacterium longum. PLoS One 2015; 10:e0135658. [PMID: 26275230 PMCID: PMC4537262 DOI: 10.1371/journal.pone.0135658] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Accepted: 07/23/2015] [Indexed: 12/28/2022] Open
Abstract
Members of genus Bifidobacterium are Gram-positive bacteria, representing a large part of the human infant microbiota and moderately common in adults. However, our knowledge about their diversity, intraspecific phylogeny and long-term persistence in humans is still limited. Bifidobacterium longum is generally considered to be the most common and prevalent species in the intestinal microbiota. In this work we studied whole genome sequences of 28 strains of B. longum, including 8 sequences described in this paper. Part of these strains were isolated from healthy children during a long observation period (up to 10 years between isolation from the same patient). The three known subspecies (longum, infantis and suis) could be clearly divided using sequence-based phylogenetic methods, gene content and the average nucleotide identity. The profiles of glycoside hydrolase genes reflected the different ecological specializations of these three subspecies. The high impact of horizontal gene transfer on genomic diversity was observed, which is possibly due to a large number of prophages and rapidly spreading plasmids. The pan-genome characteristics of the subspecies longum corresponded to the open pan-genome model. While the major part of the strain-specific genetic loci represented transposons and phage-derived regions, a large number of cell envelope synthesis genes were also observed within this category, representing high variability of cell surface molecules. We observed the cases of isolation of high genetically similar strains of B. longum from the same patients after long periods of time, however, we didn’t succeed in the isolation of genetically identical bacteria: a fact, reflecting the high plasticity of microbiota in children.
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Affiliation(s)
- Andrei V Chaplin
- Microbiology and Virology Department, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Boris A Efimov
- Microbiology and Virology Department, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Vladimir V Smeianov
- Department of Natural Sciences, Medical Institute, North Caucasus State Academy for Humanities and Technologies, Cherkessk, Russia
| | - Lyudmila I Kafarskaia
- Microbiology and Virology Department, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Alla P Pikina
- Microbiology and Virology Department, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Andrei N Shkoporov
- Microbiology and Virology Department, Pirogov Russian National Research Medical University, Moscow, Russia
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50
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Zanotti I, Turroni F, Piemontese A, Mancabelli L, Milani C, Viappiani A, Prevedini G, Sanchez B, Margolles A, Elviri L, Franco B, van Sinderen D, Ventura M. Evidence for cholesterol-lowering activity by Bifidobacterium bifidum PRL2010 through gut microbiota modulation. Appl Microbiol Biotechnol 2015; 99:6813-29. [DOI: 10.1007/s00253-015-6564-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 03/17/2015] [Accepted: 03/19/2015] [Indexed: 12/22/2022]
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