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da Silva TF, Glória RDA, Americo MF, Freitas ADS, de Jesus LCL, Barroso FAL, Laguna JG, Coelho-Rocha ND, Tavares LM, le Loir Y, Jan G, Guédon É, Azevedo VADC. Unlocking the Potential of Probiotics: A Comprehensive Review on Research, Production, and Regulation of Probiotics. Probiotics Antimicrob Proteins 2024; 16:1687-1723. [PMID: 38539008 DOI: 10.1007/s12602-024-10247-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2024] [Indexed: 10/02/2024]
Abstract
This review provides a comprehensive overview of the current state of probiotic research, covering a wide range of topics, including strain identification, functional characterization, preclinical and clinical evaluations, mechanisms of action, therapeutic applications, manufacturing considerations, and future directions. The screening process for potential probiotics involves phenotypic and genomic analysis to identify strains with health-promoting properties while excluding those with any factor that could be harmful to the host. In vitro assays for evaluating probiotic traits such as acid tolerance, bile metabolism, adhesion properties, and antimicrobial effects are described. The review highlights promising findings from in vivo studies on probiotic mitigation of inflammatory bowel diseases, chemotherapy-induced mucositis, dysbiosis, obesity, diabetes, and bone health, primarily through immunomodulation and modulation of the local microbiota in human and animal models. Clinical studies demonstrating beneficial modulation of metabolic diseases and human central nervous system function are also presented. Manufacturing processes significantly impact the growth, viability, and properties of probiotics, and the composition of the product matrix and supplementation with prebiotics or other strains can modify their effects. The lack of regulatory oversight raises concerns about the quality, safety, and labeling accuracy of commercial probiotics, particularly for vulnerable populations. Advancements in multi-omics approaches, especially probiogenomics, will provide a deeper understanding of the mechanisms behind probiotic functionality, allowing for personalized and targeted probiotic therapies. However, it is crucial to simultaneously focus on improving manufacturing practices, implementing quality control standards, and establishing regulatory oversight to ensure the safety and efficacy of probiotic products in the face of increasing therapeutic applications.
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Affiliation(s)
- Tales Fernando da Silva
- Institute of Biological Sciences, Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, Brazil
- UMR1253, INRAE, L'Institut Agro Rennes Angers, STLO, Rennes, France
| | - Rafael de Assis Glória
- Institute of Biological Sciences, Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Monique Ferrary Americo
- Institute of Biological Sciences, Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Andria Dos Santos Freitas
- Institute of Biological Sciences, Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Luis Claudio Lima de Jesus
- Institute of Biological Sciences, Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Fernanda Alvarenga Lima Barroso
- Institute of Biological Sciences, Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Juliana Guimarães Laguna
- Institute of Biological Sciences, Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Nina Dias Coelho-Rocha
- Institute of Biological Sciences, Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Laisa Macedo Tavares
- Institute of Biological Sciences, Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Yves le Loir
- UMR1253, INRAE, L'Institut Agro Rennes Angers, STLO, Rennes, France
| | - Gwénaël Jan
- UMR1253, INRAE, L'Institut Agro Rennes Angers, STLO, Rennes, France
| | - Éric Guédon
- UMR1253, INRAE, L'Institut Agro Rennes Angers, STLO, Rennes, France
| | - Vasco Ariston de Carvalho Azevedo
- Institute of Biological Sciences, Department of Genetics, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, Brazil.
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Shi Z, Long X, Zhang C, Chen Z, Usman M, Zhang Y, Zhang S, Luo G. Viral and Bacterial Community Dynamics in Food Waste and Digestate from Full-Scale Biogas Plants. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:13010-13022. [PMID: 38989650 DOI: 10.1021/acs.est.4c04109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
Anaerobic digestion (AD) is commonly used in food waste treatment. Prokaryotic microbial communities in AD of food waste have been comprehensively studied. The role of viruses, known to affect microbial dynamics and metabolism, remains largely unexplored. This study employed metagenomic analysis and recovered 967 high-quality viral bins within food waste and digestate derived from 8 full-scale biogas plants. The diversity of viral communities was higher in digestate. In silico predictions linked 20.8% of viruses to microbial host populations, highlighting possible virus predators of key functional microbes. Lineage-specific virus-host ratio varied, indicating that viral infection dynamics might differentially affect microbial responses to the varying process parameters. Evidence for virus-mediated gene transfer was identified, emphasizing the potential role of viruses in controlling the microbiome. AD altered the specific process parameters, potentially promoting a shift in viral lifestyle from lysogenic to lytic. Viruses encoding auxiliary metabolic genes (AMGs) were involved in microbial carbon and nutrient cycling, and most AMGs were transcriptionally expressed in digestate, meaning that viruses with active functional states were likely actively involved in AD. These findings provided a comprehensive profile of viral and bacterial communities and expanded knowledge of the interactions between viruses and hosts in food waste and digestate.
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Affiliation(s)
- Zhijian Shi
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China
| | - Xinyi Long
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China
| | - Chao Zhang
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China
| | - Zheng Chen
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China
| | - Muhammad Usman
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Yalei Zhang
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Shicheng Zhang
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
- Shanghai Technical Service Platform for Pollution Control and Resource Utilization of Organic Wastes, Shanghai 200438, China
| | - Gang Luo
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
- Shanghai Technical Service Platform for Pollution Control and Resource Utilization of Organic Wastes, Shanghai 200438, China
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Daniel M, Szymanik-Grzelak H, Sierdziński J, Pańczyk-Tomaszewska M. Lactobacillus rhamnosus PL1 and Lactobacillus plantarum PM1 versus Placebo as Prophylaxis for Recurrence of Urinary Tract Infections in Children. Microorganisms 2024; 12:1037. [PMID: 38930419 PMCID: PMC11205481 DOI: 10.3390/microorganisms12061037] [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: 04/10/2024] [Revised: 05/03/2024] [Accepted: 05/17/2024] [Indexed: 06/28/2024] Open
Abstract
Urinary tract infections (UTIs) rank among the most prevalent bacterial infections in children. Probiotics appear to reduce the risk of recurrence of UTIs. This study aimed to evaluate whether probiotics containing Lactobacillus rhamnosus PL1 and Lactobacillus plantarum PM1 therapy prevent UTIs in the pediatric population compared to a placebo. A superiority, double-blind, randomized, controlled trial was conducted. In total, 54 children aged 3-18 years with recurrent UTIs or ≥one acute pyelonephritis and ≥one risk factor of recurrence of UTIs were randomly assigned (27 patients in each arm) to a 90-day probiotic or placebo arm. The age, sex, diagnosis, renal function, risk factors, and etiology of UTIs did not vary between the groups. During the intervention, 26% of children taking the probiotic had episodes of UTI, and it was not significantly less than in the placebo group. The number of UTI episodes during the intervention and the follow-up period decreased significantly in both groups, but the difference between them was insignificant. We observed a decrease in UTIs during the study of almost 50% in the probiotic group compared to the placebo group. Probiotics can be used as natural, safe prophylaxis for children with risk factors for UTIs in whom antibiotic prevention is not indicated.
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Affiliation(s)
- Maria Daniel
- Department of Pediatrics and Nephrology, Medical University of Warsaw, 02-091 Warsaw, Poland; (M.D.); (M.P.-T.)
| | - Hanna Szymanik-Grzelak
- Department of Pediatrics and Nephrology, Medical University of Warsaw, 02-091 Warsaw, Poland; (M.D.); (M.P.-T.)
| | - Janusz Sierdziński
- Department of Medical Informatics and Telemedicine, Medical University of Warsaw, 02-091 Warsaw, Poland;
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Wang K, Wang Y, Gu L, Yu J, Liu Q, Zhang R, Liang G, Chen H, Gu F, Liu H, Jiao X, Zhang Y. Characterization of Probiotic Properties and Whole-Genome Analysis of Lactobacillus johnsonii N5 and N7 Isolated from Swine. Microorganisms 2024; 12:672. [PMID: 38674616 PMCID: PMC11052194 DOI: 10.3390/microorganisms12040672] [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: 02/21/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
In our previous microbiome profiling analysis, Lactobacillus (L.) johnsonii was suggested to contribute to resistance against chronic heat stress-induced diarrhea in weaned piglets. Forty-nine L. johnsonii strains were isolated from these heat stress-resistant piglets, and their probiotic properties were assessed. Strains N5 and N7 exhibited a high survival rate in acidic and bile environments, along with an antagonistic effect against Salmonella. To identify genes potentially involved in these observed probiotic properties, the complete genome sequences of N5 and N7 were determined using a combination of Illumina and nanopore sequencing. The genomes of strains N5 and N7 were found to be highly conserved, with two N5-specific and four N7-specific genes identified. Multiple genes involved in gastrointestinal environment adaptation and probiotic properties, including acidic and bile stress tolerance, anti-inflammation, CAZymes, and utilization and biosynthesis of carbohydrate compounds, were identified in both genomes. Comparative genome analysis of the two genomes and 17 available complete L. johnsonii genomes revealed 101 genes specifically harbored by strains N5 and N7, several of which were implicated in potential probiotic properties. Overall, this study provides novel insights into the genetic basis of niche adaptation and probiotic properties, as well as the genome diversity of L. johnsonii.
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Affiliation(s)
- Kun Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; (K.W.); (Y.W.); (L.G.); (J.Y.); (Q.L.); (R.Z.); (G.L.); (H.C.)
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; (F.G.); (H.L.)
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
| | - Yu Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; (K.W.); (Y.W.); (L.G.); (J.Y.); (Q.L.); (R.Z.); (G.L.); (H.C.)
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; (F.G.); (H.L.)
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
| | - Lifang Gu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; (K.W.); (Y.W.); (L.G.); (J.Y.); (Q.L.); (R.Z.); (G.L.); (H.C.)
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; (F.G.); (H.L.)
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
| | - Jinyan Yu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; (K.W.); (Y.W.); (L.G.); (J.Y.); (Q.L.); (R.Z.); (G.L.); (H.C.)
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; (F.G.); (H.L.)
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
| | - Qianwen Liu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; (K.W.); (Y.W.); (L.G.); (J.Y.); (Q.L.); (R.Z.); (G.L.); (H.C.)
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; (F.G.); (H.L.)
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
| | - Ruiqi Zhang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; (K.W.); (Y.W.); (L.G.); (J.Y.); (Q.L.); (R.Z.); (G.L.); (H.C.)
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; (F.G.); (H.L.)
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
| | - Guixin Liang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; (K.W.); (Y.W.); (L.G.); (J.Y.); (Q.L.); (R.Z.); (G.L.); (H.C.)
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; (F.G.); (H.L.)
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
| | - Huan Chen
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; (K.W.); (Y.W.); (L.G.); (J.Y.); (Q.L.); (R.Z.); (G.L.); (H.C.)
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; (F.G.); (H.L.)
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
| | - Fang Gu
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; (F.G.); (H.L.)
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Haoyu Liu
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; (F.G.); (H.L.)
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Xin’an Jiao
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; (K.W.); (Y.W.); (L.G.); (J.Y.); (Q.L.); (R.Z.); (G.L.); (H.C.)
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; (F.G.); (H.L.)
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
| | - Yunzeng Zhang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; (K.W.); (Y.W.); (L.G.); (J.Y.); (Q.L.); (R.Z.); (G.L.); (H.C.)
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; (F.G.); (H.L.)
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
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Bai L, Paek J, Kim H, Kim SH, Shin JH, Kook JK, Chang YH. Limosilactobacillus kribbianus sp. nov., isolated from pig faeces. Int J Syst Evol Microbiol 2023; 73. [PMID: 37486340 DOI: 10.1099/ijsem.0.005988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023] Open
Abstract
A rod-shaped, aerotolerant, Gram-stain-positive bacterium isolated from pig faeces was designated as strain YH-lim2214T. Analysis of the 16S rRNA gene sequence revealed that the isolate was most closely related to Limosilactobacillus pontis KCTC 25258T with 98.0 % similarity. The average nucleotide identity and average amino acid identity values between YH-lim2214T and the most closely related strain Lm. pontis KCTC 25258T were 81.4 and 81.3 %, respectively. The major fatty acids were C18 : 1 ω9c, summed feature 7 and C16 : 0. The cell-wall peptidoglycan type was A4α l-Lys-d-Asp. The genomic DNA G+C content was 51.1 mol%. The chemotaxonomic, phenotypic and phylogenetic properties of YH-lim2214T (=KCTC 25572T=JCM 35701T) suggest that it represents a novel taxon, for which the name Limosilactobacillus kribbianus sp. nov. is proposed.
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Affiliation(s)
- Lu Bai
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Jayoung Paek
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hongik Kim
- Vitabio, Inc., Daejeon, 305-500, Republic of Korea
| | - Si Hyun Kim
- Department of Clinical Laboratory Science, Semyung University, Jecheon, Republic of Korea
| | - Jeong Hwan Shin
- Department of Laboratory Medicine, Inje University College of Medicine, Busan 614-735, Republic of Korea
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, 501-759, Republic of Korea
| | - Young Hyo Chang
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
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Kwoji ID, Aiyegoro OA, Okpeku M, Adeleke MA. 'Multi-omics' data integration: applications in probiotics studies. NPJ Sci Food 2023; 7:25. [PMID: 37277356 DOI: 10.1038/s41538-023-00199-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 05/22/2023] [Indexed: 06/07/2023] Open
Abstract
The concept of probiotics is witnessing increasing attention due to its benefits in influencing the host microbiome and the modulation of host immunity through the strengthening of the gut barrier and stimulation of antibodies. These benefits, combined with the need for improved nutraceuticals, have resulted in the extensive characterization of probiotics leading to an outburst of data generated using several 'omics' technologies. The recent development in system biology approaches to microbial science is paving the way for integrating data generated from different omics techniques for understanding the flow of molecular information from one 'omics' level to the other with clear information on regulatory features and phenotypes. The limitations and tendencies of a 'single omics' application to ignore the influence of other molecular processes justify the need for 'multi-omics' application in probiotics selections and understanding its action on the host. Different omics techniques, including genomics, transcriptomics, proteomics, metabolomics and lipidomics, used for studying probiotics and their influence on the host and the microbiome are discussed in this review. Furthermore, the rationale for 'multi-omics' and multi-omics data integration platforms supporting probiotics and microbiome analyses was also elucidated. This review showed that multi-omics application is useful in selecting probiotics and understanding their functions on the host microbiome. Hence, recommend a multi-omics approach for holistically understanding probiotics and the microbiome.
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Affiliation(s)
- Iliya Dauda Kwoji
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, 4090, Durban, South Africa
| | - Olayinka Ayobami Aiyegoro
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, Northwest, South Africa
| | - Moses Okpeku
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, 4090, Durban, South Africa
| | - Matthew Adekunle Adeleke
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, 4090, Durban, South Africa.
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Aziz T, Naveed M, Jabeen K, Shabbir MA, Sarwar A, Zhennai Y, Alharbi M, Alshammari A, Alasmari AF. Integrated genome based evaluation of safety and probiotic characteristics of Lactiplantibacillus plantarum YW11 isolated from Tibetan kefir. Front Microbiol 2023; 14:1157615. [PMID: 37152722 PMCID: PMC10158936 DOI: 10.3389/fmicb.2023.1157615] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 03/22/2023] [Indexed: 05/09/2023] Open
Abstract
The comparative genomic analysis of Lactiplantibacillus plantarum YW11 (L. plantarum YW11) isolated from Tibetan kefir involves comparison of the complete genome sequences of the isolated strain with other closely related L. plantarum strains. This type of analysis can be used to identify the genetic diversity among strains and to explore the genetic characteristics of the YW11 strain. The genome of L. plantarum YW11 was found to be composed of a circular single chromosome of 4,597,470 bp with a G + C content of 43.2%. A total of 4,278 open reading frames (ORFs) were identified in the genome and the coding density was found to be 87.8%. A comparative genomic analysis was conducted using two other L. plantarum strains, L. plantarum C11 and L. plantarum LMG21703. Genomic comparison revealed that L. plantarum YW11 shared 72.7 and 75.2% of gene content with L. plantarum C11 and L. plantarum LMG21703, respectively. Most of the genes shared between the three L. plantarum strains were involved in carbohydrate metabolism, energy production and conversion, amino acid metabolism, and transcription. In this analysis, 10 previously sequenced entire genomes of the species were compared using an in-silico technique to discover genomic divergence in genes linked with carbohydrate intake and their potential adaptations to distinct human intestinal environments. The subspecies pan-genome was open, which correlated with its extraordinary capacity to colonize several environments. Phylogenetic analysis revealed that the novel genomes were homogenously grouped among subspecies of l Lactiplantibacillus. L. plantarum was resistant to cefoxitin, erythromycin, and metronidazole, inhibited pathogens including Listeria monocytogenes, Clostridium difficile, Vibrio cholera, and others, and had excellent aerotolerance, which is useful for industrial operations. The comparative genomic analysis of L. plantarum YW11 isolated from Tibetan kefir can provide insights into the genetic characteristics of the strain, which can be used to further understand its role in the production of kefir.
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Affiliation(s)
- Tariq Aziz
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing, China
- Department of Agriculture, University of Ioannina, Ioannina, Greece
| | - Muhammad Naveed
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Khizra Jabeen
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Muhammad Aqib Shabbir
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Abid Sarwar
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing, China
| | - Yang Zhennai
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing, China
- *Correspondence: Yang Zhennai,
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah F. Alasmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
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Prebiotic potential of apple pomace and pectins from different apple varieties: Modulatory effects on key target commensal microbial populations. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2022.107958] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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9
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Liu J, Wang S, Yi R, Long X, Zhao X. Effect of Lactobacillus fermentum ZS40 on the NF-κB signaling pathway in an azomethane-dextran sulfate sodium-induced colon cancer mouse model. Front Microbiol 2022; 13:953905. [PMID: 36225358 PMCID: PMC9549056 DOI: 10.3389/fmicb.2022.953905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
The occurrence of intestinal diseases such as colon cancer is closely related to the intestinal flora. Lactobacillus fermentum is a gut probiotic that plays an important role in chronic intestinal inflammation and colon cancer. In the current study, we investigated the effect of Lactobacillus fermentum ZS40 on NF-κB signaling pathway of azomethane-dextran sulfate sodium (AOM-DSS) -induced colon cancer in mice. Animals were divided into control group (NC), AOM-DSS-induced model group (CRC), AOM-DSS plus high-dose Lactobacillus fermentum ZS40 (ZS40-H), AOM-DSS plus low-dose Lactobacillus fermentum ZS40 (ZS40-L), AOM-DSS plus Lactobacillus bulgaricus (BLA), and AOM-DSS plus sulfasalazine (SD)-treated group. Observation of animal physiological activity (body weight and defecation), biochemical measurements, histopathological examination of colon tissue, qPCR to evaluate the expression of inflammation-related genes, immunohistochemical analysis of CD34 and CD117, and Western blot analysis of NF-κB signaling pathway were performed. Compared with the CRC group, the ZS40-H, ZS40-L, BLA, and SD groups had decreased levels of colon cancer marker proteins CD34 and CD117, and the number of abnormal colonic lesions observed by colon histology decreased, while the ZS40-H group showed excellent results. In addition, all probiotic interventions showed weight loss effects. The expression of inflammatory stimulators TNF-α and IL-1β in the probiotic treatment group decreased; the expression of key proteins IκBα and p65 in the NF-κB signaling pathway also decreased, resulting in a decrease in the expression of the target protein Cox-2. Therefore, administration of Lactobacillus fermentum ZS40 as a probiotic can alleviate intestinal inflammation and prevent colon cancer in mice.
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Affiliation(s)
- Jia Liu
- Collaborative Innovation Center for Child Nutrition and Health Development, Chongqing Engineering Research Center of Functional Food, Chongqing Engineering Laboratory for Research and Development of Functional Food, Chongqing University of Education, Chongqing, China
| | - Shuaiqi Wang
- Gastrointestinal Tumor Center, Chongqing University Cancer Hospital, Chongqing, China
| | - Ruokun Yi
- Collaborative Innovation Center for Child Nutrition and Health Development, Chongqing Engineering Research Center of Functional Food, Chongqing Engineering Laboratory for Research and Development of Functional Food, Chongqing University of Education, Chongqing, China
| | - Xingyao Long
- Collaborative Innovation Center for Child Nutrition and Health Development, Chongqing Engineering Research Center of Functional Food, Chongqing Engineering Laboratory for Research and Development of Functional Food, Chongqing University of Education, Chongqing, China
| | - Xin Zhao
- Collaborative Innovation Center for Child Nutrition and Health Development, Chongqing Engineering Research Center of Functional Food, Chongqing Engineering Laboratory for Research and Development of Functional Food, Chongqing University of Education, Chongqing, China
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Kiousi DE, Efstathiou C, Tegopoulos K, Mantzourani I, Alexopoulos A, Plessas S, Kolovos P, Koffa M, Galanis A. Genomic Insight Into Lacticaseibacillus paracasei SP5, Reveals Genes and Gene Clusters of Probiotic Interest and Biotechnological Potential. Front Microbiol 2022; 13:922689. [PMID: 35783439 PMCID: PMC9244547 DOI: 10.3389/fmicb.2022.922689] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 05/16/2022] [Indexed: 12/22/2022] Open
Abstract
The Lacticaseibacillus paracasei species is comprised by nomadic bacteria inhabiting a wide variety of ecological niches, from fermented foodstuffs to host-associated microenvironments. Lc. paracasei SP5 is a novel strain, originally isolated from kefir grains that presents desirable probiotic and biotechnological attributes. In this study, we applied genomic tools to further characterize the probiotic and biotechnological potential of the strain. Firstly, whole genome sequencing and assembly, were performed to construct the chromosome map of the strain and determine its genomic stability. Lc. paracasei SP5 carriers several insertion sequences, however, no plasmids or mobile elements were detected. Furthermore, phylogenomic and comparative genomic analyses were utilized to study the nomadic attributes of the strain, and more specifically, its metabolic capacity and ability to withstand environmental stresses imposed during food processing and passage through the gastrointestinal (GI) tract. More specifically, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Carbohydrate-active enzyme (CAZymes) analyses provided evidence for the ability of the stain to utilize an array of carbohydrates as growth substrates. Consequently, genes for heat, cold, osmotic shock, acidic pH, and bile salt tolerance were annotated. Importantly bioinformatic analysis showed that the novel strain does not harbor acquired antimicrobial resistance genes nor virulence factors, in agreement with previous experimental data. Putative bacteriocin biosynthesis clusters were identified using BAGEL4, suggesting its potential antimicrobial activity. Concerning microbe-host interactions, adhesins, moonlighting proteins, exopolysaccharide (EPS) biosynthesis genes and pilins mediating the adhesive phenotype were, also, pinpointed in the genome of Lc. paracasei SP5. Validation of this phenotype was performed by employing a microbiological method and confocal microscopy. Conclusively, Lc. paracasei SP5 harbors genes necessary for the manifestation of the probiotic character and application in the food industry. Upcoming studies will focus on the mechanisms of action of the novel strain at multiple levels.
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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
| | - Christos Efstathiou
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - Konstantinos Tegopoulos
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - Ioanna Mantzourani
- Department of Agricultural Development, Democritus University of Thrace, Orestiada, Greece
| | - Athanasios Alexopoulos
- Department of Agricultural Development, Democritus University of Thrace, Orestiada, Greece
| | - Stavros Plessas
- Department of Agricultural Development, Democritus University of Thrace, Orestiada, Greece
- *Correspondence: Stavros Plessas,
| | - Petros Kolovos
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - Maria Koffa
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
| | - Alex Galanis
- Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece
- Alex Galanis,
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Perez M, Ntemiri A, Tan H, Harris HMB, Roager HM, Ribière C, O’Toole PW. A synthetic consortium of 100 gut commensals modulates the composition and function in a colon model of the microbiome of elderly subjects. Gut Microbes 2021; 13:1-19. [PMID: 33993839 PMCID: PMC8128205 DOI: 10.1080/19490976.2021.1919464] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Administration of cultured gut isolates holds promise for modulating the altered composition and function of the microbiota in older subjects, and for promoting their health. From among 692 initial isolates, we selected 100 gut commensal strains (MCC100) based on emulating the gut microbiota of healthy subjects, and retaining strain diversity within selected species. MCC100 susceptibility to seven antibiotics was determined, and their genomes were screened for virulence factor, antimicrobial resistance and bacteriocin genes. Supplementation of healthy and frail elderly microbiota types with the MCC100 in an in vitro colon model increased alpha-diversity, raised relative abundance of taxa including Blautia luti, Bacteroides fragilis, and Sutterella wadsworthensis; and introduced taxa such as Bifidobacterium spp. Microbiota changes correlated with higher levels of branched chain amino acids, which are health-associated in elderly. The study establishes that the MCC100 consortium can modulate older subjects' microbiota composition and associated metabolome in vitro, paving the way for pre-clinical and human trials.
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Affiliation(s)
- Marta Perez
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Alexandra Ntemiri
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Huizi Tan
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Hugh M. B. Harris
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Henrik M. Roager
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark
| | - Céline Ribière
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Paul W. O’Toole
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland,CONTACT Paul W. O’Toole School of Microbiology & APC Microbiome Ireland, Food Science Building, University College Cork, CorkT12 YN60, Ireland
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12
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Nader-Macías MEF, De Gregorio PR, Silva JA. Probiotic lactobacilli in formulas and hygiene products for the health of the urogenital tract. Pharmacol Res Perspect 2021; 9:e00787. [PMID: 34609059 PMCID: PMC8491456 DOI: 10.1002/prp2.787] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 03/04/2021] [Accepted: 04/02/2021] [Indexed: 12/13/2022] Open
Abstract
Lactobacilli are the predominant microorganisms of the healthy human vagina. A novel alternative for the prevention and treatment of female urogenital tract infections (UGTI) is the inclusion of these microorganisms as active pharmaceutical ingredients in probiotic formulas, and more recently in female hygienic products. Probiotics are defined as “live microorganisms that, when administered in adequate amounts, confer a health benefit on the host.” A list of requirements must be considered during the development of probiotic product/formula for the female urogenital tract (UGT). This review aims to resume the requirements, probiotic characteristics, and clinical trial applied to determine the effect of probiotic and potentially probiotic strains on different woman’s physiological and pathological conditions, and in preterm birth prevention. A revision of female hygienic products available in the world market is included, together with novel studies applying nanotechnology for Lactobacillus incorporation in hygienic products. Further studies and well‐designed clinical trials are urgently required to complement the current knowledge and applications of probiotics in the female UGT. The use of probiotic formulas and products will improve and restore the ecological equilibrium of the UGT microbiome to prevent and treat UGTI in women under different conditions.
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Affiliation(s)
- María Elena Fátima Nader-Macías
- Centro de Referencia para Lactobacilos-Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina (CERELA-CONICET), San Miguel de Tucumán, Argentina
| | - Priscilla Romina De Gregorio
- Centro de Referencia para Lactobacilos-Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina (CERELA-CONICET), San Miguel de Tucumán, Argentina
| | - Jessica Alejandra Silva
- Centro de Referencia para Lactobacilos-Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina (CERELA-CONICET), San Miguel de Tucumán, Argentina
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Amin N, Schwarzkopf S, Kinoshita A, Tröscher-Mußotter J, Dänicke S, Camarinha-Silva A, Huber K, Frahm J, Seifert J. Evolution of rumen and oral microbiota in calves is influenced by age and time of weaning. Anim Microbiome 2021; 3:31. [PMID: 33883031 PMCID: PMC8059317 DOI: 10.1186/s42523-021-00095-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 04/04/2021] [Indexed: 01/04/2023] Open
Abstract
Background The rumen bacterial communities are changing dynamically throughout the first year of calf’s life including the weaning period as a critical event. Rumen microbiome analysis is often limited to invasive rumen sampling procedures but the oral cavity of ruminants is expected to harbour rumen microbes due to regurgitation activity. The present study used buccal swab samples to define the rumen core microbiome and characterize the shifts in rumen and oral microbial communities occurring as result of calf’s age as well as time of weaning. Results Buccal swab samples of 59 calves were collected along the first 140 days of life and compared to stomach tubing sample of the rumen at day 140. Animals were randomly divided into two weaning groups. Microbiota of saliva and rumen content was analysed by 16S rRNA gene amplicon sequencing. Our study showed that most rumen-specific bacterial taxa were equally observed in rumen samples as well as in the buccal swabs, though relative abundance varied. The occurrence of rumen-specific OTUs in buccal swab samples increased approximately 1.7 times from day 70 to day 140, indicating the gradual development of rumen as calf aged. The rumen-specific bacterial taxa diversity increased, and inter-animal variations decreased with age. Early weaning (7 weeks of age) rapidly increased the rumen microbial diversity from pre- to post-weaned state. Rumen microbiota of early-weaned calves seemed to have a suppressed growth of starch- and carbohydrate-utilizing bacteria and increased fibre degraders. Whereas, in late-weaned calves (17 weeks of age) no impact of dietary modifications on rumen microbiota composition was observed after weaning. Oral-specific bacterial community composition was significantly affected by calf’s age and time of weaning. Conclusions The present study showed the significant impact of calf’s age and weaning on the establishment of rumen- and oral-specific bacterial communities utilizing buccal swab samples. The results emphasize the possibility of using buccal swab samples as a replacement of complex stomach tube method for large-scale predictive studies on ruminants. For in-depth rumen microbiome studies, the time of sampling should be carefully considered using an active phase of regurgitation. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-021-00095-3.
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Affiliation(s)
- Nida Amin
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593, Stuttgart, Germany
| | - Sarah Schwarzkopf
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593, Stuttgart, Germany
| | - Asako Kinoshita
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593, Stuttgart, Germany.,Institute of Animal Nutrition, Friedrich-Loeffler-Institute, Federal Research Institute for Animal Health, Bundesallee 37, 38116, Braunschweig, Germany
| | - Johanna Tröscher-Mußotter
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593, Stuttgart, Germany
| | - Sven Dänicke
- Institute of Animal Nutrition, Friedrich-Loeffler-Institute, Federal Research Institute for Animal Health, Bundesallee 37, 38116, Braunschweig, Germany
| | - Amélia Camarinha-Silva
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593, Stuttgart, Germany
| | - Korinna Huber
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593, Stuttgart, Germany
| | - Jana Frahm
- Institute of Animal Nutrition, Friedrich-Loeffler-Institute, Federal Research Institute for Animal Health, Bundesallee 37, 38116, Braunschweig, Germany
| | - Jana Seifert
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593, Stuttgart, Germany.
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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: 15] [Impact Index Per Article: 5.0] [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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Rocchetti MT, Di Iorio BR, Vacca M, Cosola C, Marzocco S, di Bari I, Calabrese FM, Ciarcia R, De Angelis M, Gesualdo L. Ketoanalogs' Effects on Intestinal Microbiota Modulation and Uremic Toxins Serum Levels in Chronic Kidney Disease (Medika2 Study). J Clin Med 2021; 10:jcm10040840. [PMID: 33670711 PMCID: PMC7922022 DOI: 10.3390/jcm10040840] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 02/10/2021] [Accepted: 02/13/2021] [Indexed: 02/06/2023] Open
Abstract
Nutritional therapy (NT) is a therapeutic option in the conservative treatment of chronic kidney disease (CKD) patients to delay the start of dialysis. The aim of this study was to evaluate the specific effect of ketoanalogs (KA)-supplemented diets for gut microbiota modulation. In a previous study we observed that the Mediterranean diet (MD) and a KA-supplemented very-low-protein diet (VLPD) modulated beneficially gut microbiota, reducing indoxyl- and p-cresyl-sulfate (IS, PCS) serum levels, and ameliorating the intestinal permeability in CKD patients. In the current study, we added a third diet regimen consisting of KA-supplemented MD. Forty-three patients with CKD grades 3B–4 continuing the crossover clinical trial were assigned to six months of KA-supplemented MD (MD + KA). Compared to MD, KA-supplementation in MD + KA determined (i) a decrease of Clostridiaceae, Methanobacteriaceae, Prevotellaceae, and Lactobacillaceae while Bacteroidaceae and Lachnospiraceae increased; (ii) a reduction of total and free IS and PCS compared to a free diet (FD)—more than the MD, but not as effectively as the VLPD. These results further clarify the driving role of urea levels in regulating gut integrity status and demonstrating that the reduction of azotemia produced by KA-supplemented VLPD was more effective than KA-supplemented MD in gut microbiota modulation mainly due to the effect of the drastic reduction of protein intake rather than the effect of KA.
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Affiliation(s)
- Maria Teresa Rocchetti
- Department of Emergency and Organ Transplantation, Nephrology, Dialysis and Transplantation Unit, “AldoMoro” University, 70124 Bari, Italy; (C.C.); (I.d.B.); (L.G.)
- Correspondence:
| | | | - Mirco Vacca
- Department of Soil, Plant and Food Science, “Aldo Moro” University, Bari, Via G. Amendola 165/a, 70126 Bari, Italy; (M.V.); (F.M.C.); (M.D.A.)
| | - Carmela Cosola
- Department of Emergency and Organ Transplantation, Nephrology, Dialysis and Transplantation Unit, “AldoMoro” University, 70124 Bari, Italy; (C.C.); (I.d.B.); (L.G.)
| | - Stefania Marzocco
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy;
| | - Ighli di Bari
- Department of Emergency and Organ Transplantation, Nephrology, Dialysis and Transplantation Unit, “AldoMoro” University, 70124 Bari, Italy; (C.C.); (I.d.B.); (L.G.)
| | - Francesco Maria Calabrese
- Department of Soil, Plant and Food Science, “Aldo Moro” University, Bari, Via G. Amendola 165/a, 70126 Bari, Italy; (M.V.); (F.M.C.); (M.D.A.)
| | - Roberto Ciarcia
- Department of Veterinary Medicine and Animal Productions, Faculty of Veterinary, University of Naples, 80138 Naples, Italy;
| | - Maria De Angelis
- Department of Soil, Plant and Food Science, “Aldo Moro” University, Bari, Via G. Amendola 165/a, 70126 Bari, Italy; (M.V.); (F.M.C.); (M.D.A.)
| | - Loreto Gesualdo
- Department of Emergency and Organ Transplantation, Nephrology, Dialysis and Transplantation Unit, “AldoMoro” University, 70124 Bari, Italy; (C.C.); (I.d.B.); (L.G.)
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Role of Lactic Acid Bacteria Phospho-β-Glucosidases during the Fermentation of Cereal by-Products. Foods 2021; 10:foods10010097. [PMID: 33466465 PMCID: PMC7830935 DOI: 10.3390/foods10010097] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 12/22/2020] [Accepted: 12/29/2020] [Indexed: 02/07/2023] Open
Abstract
Bioprocessing using lactic acid bacteria (LAB) is a powerful means to exploit plant-derived by-products as a food ingredient. LAB have the capability to metabolize a large variety of carbohydrates, but such metabolism only relies on few metabolic routes, conferring on them a high fermentation potential. One example of these pathways is that involving phospho-β-glucosidase genes, which are present in high redundancy within LAB genomes. This enzymatic activity undertakes an ambivalent role during fermentation of plant-based foods related to the release of a wide range of phenolic compounds, from their β-D-glycosylated precursors and the degradation of β-glucopyranosyl derived carbohydrates. We proposed a novel phenomic approach to characterize the metabolism drift of Lactiplantibacillus plantarum and Leuconostoc pseudomesenteroides caused by a lignocellulosic by-product, such as the brewers’ spent grain (BSG), in contrast to Rich De Man, Rogosa and Sharpe (MRS) broth. We observed an increased metabolic activity for gentiobiose, cellobiose and β-glucoside conjugates of phenolic compounds during BSG fermentation. Gene expression analysis confirmed the importance of cellobiose metabolism while a release of lignin-derived aglycones was found during BSG fermentation. We provided a comprehensive view of the important role exerted by LAB 6-phospho-β-glucosidases as well the major metabolic routes undertaken during plant-based fermentations. Further challenges will consider a controlled characterization of pbg gene expression correlated to the metabolism of β-glucosides with different aglycone moieties.
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Verma A, Zhu P, Xu K, Du T, Liao S, Liang Z, Raizada MK, Li Q. Angiotensin-(1-7) Expressed From Lactobacillus Bacteria Protect Diabetic Retina in Mice. Transl Vis Sci Technol 2020; 9:20. [PMID: 33344064 PMCID: PMC7735952 DOI: 10.1167/tvst.9.13.20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 11/03/2020] [Indexed: 01/04/2023] Open
Abstract
Purpose A multitude of animal studies substantiates the beneficial effects of Ang-(1-7), a peptide hormone in the protective axis of the renin angiotensin system, in diabetes and its associated complications including diabetic retinopathy (DR). However, the clinical application of Ang-(1-7) is limited due to unfavorable pharmacological properties. As emerging evidence implicates gut dysbiosis in pathogenesis of diabetes and supports beneficial effects of probiotics, we sought to develop probiotics-based expression and delivery system to enhance Ang-(1-7) and evaluate the efficacy of engineered probiotics expressing Ang-(1-7) in attenuation of DR in animal models. Methods Ang-(1-7) was expressed in the Lactobacillus species as a secreted fusion protein with a trans-epithelial carrier to allow uptake into circulation. To evaluate the effects of Ang-(1-7) expressed from Lactobacillus paracasei (LP), adult diabetic eNOS-/- and Akita mice were orally gavaged with either 1 × 109 CFU of LP secreting Ang-(1-7) (LP-A), LP alone or vehicle, 3 times/week, for 8 and 12 weeks, respectively. Results Ang-(1-7) is efficiently expressed from different Lactobacillus species and secreted into circulation in mice fed with LP-A. Oral administration of LP-A significantly reduced diabetes-induced loss of retinal vascular capillaries. LP-A treatment also prevented loss of retinal ganglion cells, and significantly decreased retinal inflammatory cytokine expression in both diabetic eNOS-/- and Akita mice. Conclusions These results provide proof-of-concept for feasibility and efficacy of using engineered probiotic species as live vector for delivery of Ang-(1-7) with enhanced bioavailability. Translational Relevance Probiotics-based delivery of Ang-(1-7) may hold important therapeutic potential for the treatment of DR and other diabetic complications.
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Affiliation(s)
- Amrisha Verma
- Department of Ophthalmology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Ping Zhu
- Department of Ophthalmology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Kang Xu
- Department of Ophthalmology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Tao Du
- Department of Ophthalmology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Shengquan Liao
- Department of Ophthalmology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Zhibing Liang
- Department of Ophthalmology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Mohan K. Raizada
- Physiology & Functional Genomics, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Qiuhong Li
- Department of Ophthalmology, College of Medicine, University of Florida, Gainesville, Florida, USA
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Daniel M, Szymanik-Grzelak H, Turczyn A, Pańczyk-Tomaszewska M. Lactobacillus rhamnosus PL1 and Lactobacillus plantarum PM1 versus placebo as a prophylaxis for recurrence urinary tract infections in children: a study protocol for a randomised controlled trial. BMC Urol 2020; 20:168. [PMID: 33097017 PMCID: PMC7583233 DOI: 10.1186/s12894-020-00723-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 09/17/2020] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Urinary tract infections (UTIs) are one of the most common bacterial infections in children. In children < 7 years of age, the prevalence of one episode of symptomatic UTI has been estimated at 3-7% in girls and 1-2% in boys, whereas 8-30% of them will have one or more episodes of UTI. The use of some probiotics appears to reduce the risk of recurrence of UTIs. Since the effects of probiotics are strain-specific, the efficacy and safety of each strain has to be assessed. The main aim of this study is to determine whether probiotics (containing Lactobacillus rhamnosus PL1 and Lactobacillus plantarum PM1) therapy are effective in preventing UTI in children compared to placebo. METHOD A superiority, double-blind, randomised, controlled trial is being conducted. One hundred and six patients aged 3 to 18 years with recurrent UTIs in last year (defined as: ≥ 2 episodes of UTI with acute pyelonephritis/upper UTI; or 1 episode of UTI with acute pyelonephritis and ≥ 1 episodes of UTI with cystitis/lower UTI; or ≥ 3 episodes of UTI with cystitis/lower UTI) or children with ≥ 1 infection in the upper urinary tract and ≥ 1 of recurrent UTIs risk factors (congenital anomalies of the kidney and urinary tract, constipation, bladder dysfunction, myelomeningocele, sexual activity in girls) will be randomly assigned to receive a 90-day prophylaxis arm (probiotic containing L. rhamnosus PL1 and L. plantarum PM1) or a 90-day placebo arm. The primary outcome measure will be the frequency of recurrence of UTI during the intervention and in the period 9 months after the intervention. DISCUSSION The findings of this randomised controlled trial (RCT), whether positive or negative, will contribute to the formulation of further recommendations on prevention of recurrent UTIs in children. TRIAL REGISTRATION NUMBER NCT03462160, date of trial registration 12th March 2018.
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Affiliation(s)
- Maria Daniel
- Department of Paediatric Nephrology, Medical University of Warsaw, Żwirki i Wigury 63A, 02-091, Warsaw, Poland
| | - Hanna Szymanik-Grzelak
- Department of Paediatric Nephrology, Medical University of Warsaw, Żwirki i Wigury 63A, 02-091, Warsaw, Poland.
| | - Agnieszka Turczyn
- Department of Paediatric Nephrology, Medical University of Warsaw, Żwirki i Wigury 63A, 02-091, Warsaw, Poland
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19
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Lapirattanakul J, Nomura R, Okawa R, Morimoto S, Tantivitayakul P, Maudcheingka T, Nakano K, Matsumoto-Nakano M. Oral Lactobacilli Related to Caries Status of Children with Primary Dentition. Caries Res 2020; 54:194-204. [DOI: 10.1159/000506468] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 02/12/2020] [Indexed: 11/19/2022] Open
Abstract
Oral lactobacilli are members of a group of bacteria implicated in caries progression, although information regarding their transmission, colonization, and caries-associated species is not well established. This study isolated oral lactobacilli from a group of children with primary dentition for determination of Lactobacillus prevalence, detection of Streptococcus mutans, a major pathogen of caries initiation, and dental caries status of the children. Species of Lactobacillus isolates were determined from examination of 16S rDNA sequences. Subsequently, the most prevalent species was evaluated for involvement in caries status, and binding ability to type I collagen of all Lactobacillus isolates was determined in association with caries status. Multilocus sequence typing (MLST) of eleven loci was carried out to study strains of the predominant Lactobacillus sp. The detection of oral lactobacilli together with S. mutans was significantly associated with the highest dental caries indices, but there was no involvement of collagen-binding properties of Lactobacillus isolates in caries status. Lactobacillus fermentum was the most prevalent, and its presence was related to high scores of caries indices. MLST analysis of L. fermentum population could not specify a particular clone associated with caries status, but revealed sharing of identical L. fermentum strains among children in the same classrooms. Taken together, the data contributed useful information on the role of oral lactobacilli, in particular L. fermentum in dental caries.
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20
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Rocha J, Botelho J, Ksiezarek M, Perovic SU, Machado M, Carriço JA, Pimentel LL, Salsinha S, Rodríguez-Alcalá LM, Pintado M, Ribeiro TG, Peixe L. Lactobacillus mulieris sp. nov., a new species of Lactobacillus delbrueckii group. Int J Syst Evol Microbiol 2020; 70:1522-1527. [DOI: 10.1099/ijsem.0.003901] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
One Gram-stain-positive, non-motile, non-spore-forming, catalase-negative, and coccobacilli-shaped strain, designated c10Ua161MT, was isolated from a urine sample from a reproductive-age healthy woman. Comparative 16S rRNA gene sequence analysis indicated that strain c10Ua161MT belonged to the genus
Lactobacillus
. Phylogenetic analysis based on pheS and rpoA gene sequences strongly supported a clade encompassing strains c10Ua161MT and eight other strains from public databases, distinct from currently recognized species of the genus Lactobacillus. In silico Average Nucleotide Identity (ANI) and Genome-to-Genome Distance Calculator (GGDC), showed 87.9 and 34.3 % identity to the closest relative
Lactobacillus jensenii
, respectively. The major fatty acids of strain c10Ua161MT were C18 : 1ω9c (65.0%), C16 : 0 (17.8%), and summed feature 8 (10.2 %; comprising C18 : 1ω7c, and/or C18 : 1ω6c). The DNA G+C content of the strains is 34.2 mol%. On the basis of data presented here, strain c10Ua161MT represents a novel species of the genus
Lactobacillus
, for which the name Lactobacillus mulieris sp. nov. is proposed. The type strain is c10Ua161MT (=CECT 9755T=DSM 108704T).
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Affiliation(s)
- Joana Rocha
- UCIBIO-REQUIMTE. Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - João Botelho
- UCIBIO-REQUIMTE. Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Magdalena Ksiezarek
- UCIBIO-REQUIMTE. Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Svetlana Ugarcina Perovic
- UCIBIO-REQUIMTE. Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Miguel Machado
- Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - João André Carriço
- Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Lígia L. Pimentel
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Porto, Portugal
| | - Sofia Salsinha
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Porto, Portugal
| | - Luís M. Rodríguez-Alcalá
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Porto, Portugal
| | - Manuela Pintado
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Porto, Portugal
| | - Teresa G. Ribeiro
- UCIBIO-REQUIMTE. Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Luísa Peixe
- UCIBIO-REQUIMTE. Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
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21
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Smiljanec K, Lennon SL. Sodium, hypertension, and the gut: does the gut microbiota go salty? Am J Physiol Heart Circ Physiol 2019; 317:H1173-H1182. [PMID: 31585045 DOI: 10.1152/ajpheart.00312.2019] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Recent evidence suggests that the gut microbiota contributes to the pathogenesis of hypertension (HTN). The gut microbiota is a highly dynamic organ mediating numerous physiological functions, which can be influenced by external factors such as diet. In particular, a major modifiable risk factor for HTN is dietary sodium intake. Sodium consumption in the United States is significantly greater than that recommended by the federal government and organizations such as the American Heart Association. Because of the emerging connection between the gut microbiota and HTN, the interaction between dietary sodium and gut microbiota has sparked interest. High-sodium diets promote local and systemic tissue inflammation and impair intestinal anatomy compared with low sodium intake in both human and animal studies. It is biologically plausible that the gut microbiota mediates the inflammatory response, as it is in constant interaction with the immune system and is necessary for proper maturation of immune cells. Recent rodent data demonstrate that dietary sodium disrupts gut microbial homeostasis as gut microbiota composition shifts with dietary sodium manipulation. In this review, we will focus on gut microbiota activity in HTN and the influence of high dietary sodium intake with an emphasis on the immune system, bacterial metabolites, and the circadian clock.
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Affiliation(s)
- Katarina Smiljanec
- Department of Kinesiology and Applied Physiology, University of Delaware, Newark, Delaware
| | - Shannon L Lennon
- Department of Kinesiology and Applied Physiology, University of Delaware, Newark, Delaware
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22
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Shiferaw Terefe N, Augustin MA. Fermentation for tailoring the technological and health related functionality of food products. Crit Rev Food Sci Nutr 2019; 60:2887-2913. [PMID: 31583891 DOI: 10.1080/10408398.2019.1666250] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Fermented foods are experiencing a resurgence due to the consumers' growing interest in foods that are natural and health promoting. Microbial fermentation is a biotechnological process which transforms food raw materials into palatable, nutritious and healthy food products. Fermentation imparts unique aroma, flavor and texture to food, improves digestibility, degrades anti-nutritional factors, toxins and allergens, converts phytochemicals such as polyphenols into more bioactive and bioavailable forms, and enriches the nutritional quality of food. Fermentation also modifies the physical functional properties of food materials, rendering them differentiated ingredients for use in formulated foods. The science of fermentation and the technological and health functionality of fermented foods is reviewed considering the growing interest worldwide in fermented foods and beverages and the huge potential of the technology for reducing food loss and improving nutritional food security.
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23
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Verma A, Xu K, Du T, Zhu P, Liang Z, Liao S, Zhang J, Raizada MK, Grant MB, Li Q. Expression of Human ACE2 in Lactobacillus and Beneficial Effects in Diabetic Retinopathy in Mice. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2019; 14:161-170. [PMID: 31380462 PMCID: PMC6661465 DOI: 10.1016/j.omtm.2019.06.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 06/25/2019] [Indexed: 02/06/2023]
Abstract
The angiotensin converting enzyme 2 (ACE2) catalyzes the degradation of Angiotensin II (Ang II) to generate Angiotensin-(1-7), which reduces inflammation and oxidative stress stimulated by Ang II. ACE2 has been shown to be protective in cardiovascular and metabolic diseases including diabetes and its complications. However, the challenge for its clinical application is large-scale production of high-quality ACE2 with sufficient target tissue bioavailability. We developed an expression and delivery system based on the use of probiotic species Lactobacillus paracasei (LP) to serve as a live vector for oral delivery of human ACE2. We show that codon-optimized ACE2 can be efficiently expressed in LP. Mice treated with the recombinant LP expressing the secreted ACE2 in fusion with the non-toxic subunit B of cholera toxin, which acts as a carrier to facilitate transmucosal transport, showed increased ACE2 activities in serum and tissues. ACE2-LP administration reduced the number of acellular capillaries, blocked retinal ganglion cell loss, and decreased retinal inflammatory cytokine expression in two mouse models of diabetic retinopathy. These results provide proof of concept for feasibility of using engineered probiotic species as live vector for delivery of human ACE2 with enhanced tissue bioavailability for treating diabetic retinopathy, as well as other diabetic complications.
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Affiliation(s)
- Amrisha Verma
- Department of Ophthalmology, College of Medicine, University of Florida, Gainesville, FL 32610-0284, USA
| | - Kang Xu
- Department of Ophthalmology, College of Medicine, University of Florida, Gainesville, FL 32610-0284, USA
| | - Tao Du
- Department of Ophthalmology, College of Medicine, University of Florida, Gainesville, FL 32610-0284, USA
| | - Ping Zhu
- Department of Ophthalmology, College of Medicine, University of Florida, Gainesville, FL 32610-0284, USA
| | - Zhibing Liang
- Department of Ophthalmology, College of Medicine, University of Florida, Gainesville, FL 32610-0284, USA
| | - Shengquan Liao
- Department of Ophthalmology, College of Medicine, University of Florida, Gainesville, FL 32610-0284, USA
| | - Juantao Zhang
- Department of Ophthalmology, College of Medicine, University of Florida, Gainesville, FL 32610-0284, USA
| | - Mohan K Raizada
- Department of Physiology & Functional Genomics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Maria B Grant
- Department of Ophthalmology & Visual Sciences, University of Alabama, Birmingham, AL 35294, USA
| | - Qiuhong Li
- Department of Ophthalmology, College of Medicine, University of Florida, Gainesville, FL 32610-0284, USA
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24
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Salvetti E, Harris HMB, Felis GE, O'Toole PW. Comparative Genomics of the Genus Lactobacillus Reveals Robust Phylogroups That Provide the Basis for Reclassification. Appl Environ Microbiol 2018; 84:e00993-18. [PMID: 29915113 PMCID: PMC6102987 DOI: 10.1128/aem.00993-18] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 06/12/2018] [Indexed: 12/12/2022] Open
Abstract
The genus Lactobacillus includes over 200 species that are widely used in fermented food preservation and biotechnology or that are explored for beneficial effects on health. Naming, classifying, and comparing lactobacilli have been challenging due to the high level of phenotypic and genotypic diversity that they display and because of the uncertain degree of relatedness between them and associated genera. The aim of this study was to investigate the feasibility of dividing the genus Lactobacillus into more homogeneous genera/clusters, exploiting genome-based data. The relatedness of 269 species belonging primarily to the families Lactobacillaceae and Leuconostocaceae was investigated through phylogenetic analysis (by the use of ribosomal proteins and housekeeping genes) and the assessment of the average amino acid identity (AAI) and the percentage of conserved proteins (POCP). For each subgeneric group that emerged, conserved signature genes were identified. Both distance-based and sequence-based metrics showed that the Lactobacillus genus was paraphyletic and revealed the presence of 10 methodologically consistent subclades, which were also characterized by a distinct distribution of conserved signature orthologues. We present two ways to reclassify lactobacilli: a conservative division into two subgeneric groups based on the presence/absence of a key carbohydrate utilization gene or a more radical subdivision into 10 groups that satisfy more stringent criteria for genomic relatedness.IMPORTANCE Lactobacilli have significant scientific and economic value, but their extraordinary diversity means that they are not robustly classified. The 10 homogeneous genera/subgeneric entities that we identify here are characterized by uniform patterns of the presence/absence of specific sets of genes which offer potential as discovery tools for understanding differential biological features. Reclassification/subdivision of the genus Lactobacillus into more uniform taxonomic nuclei will also provide accurate molecular markers that will be enabling for regulatory approval applications. Reclassification will facilitate scientific communication related to lactobacilli and prevent misidentification issues, which are still the major cause of mislabeling of probiotic and food products reported worldwide.
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Affiliation(s)
- Elisa Salvetti
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Hugh M B Harris
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Giovanna E Felis
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Paul W O'Toole
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
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25
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Milani C, Duranti S, Mangifesta M, Lugli GA, Turroni F, Mancabelli L, Viappiani A, Anzalone R, Alessandri G, Ossiprandi MC, van Sinderen D, Ventura M. Phylotype-Level Profiling of Lactobacilli in Highly Complex Environments by Means of an Internal Transcribed Spacer-Based Metagenomic Approach. Appl Environ Microbiol 2018; 84:e00706-18. [PMID: 29728382 PMCID: PMC6029092 DOI: 10.1128/aem.00706-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 04/27/2018] [Indexed: 12/12/2022] Open
Abstract
The genus Lactobacillus is a widespread taxon, members of which are highly relevant to functional and fermented foods, while they are also commonly present in host-associated gut and vaginal microbiota. Substantial efforts have been undertaken to disclose the genetic repertoire of all members of the genus Lactobacillus, and yet their species-level profiling in complex matrices is still undeveloped due to the poor phylotype resolution of profiling approaches based on the 16S rRNA gene. To overcome this limitation, an internal transcribed spacer (ITS)-based profiling method was developed to accurately profile lactobacilli at the species level. This approach encompasses a genus-specific primer pair combined with a database of ITS sequences retrieved from all available Lactobacillus genomes and a script for the QIIME software suite that performs all required steps to reconstruct a species-level profile. This methodology was applied to several environments, i.e., human gut and vagina and the ceca of free-range chickens, as well as whey and fresh cheese. Interestingly, the data collected confirmed a relevant role of lactobacilli present in functional and fermented foods in defining the population harbored by the human gut, while, unsurprisingly perhaps, the ceca of free-range chickens were observed to be dominated by lactobacilli characterized in birds living in natural environments. Moreover, vaginal swabs confirmed the existence of previously hypothesized community state types, while analysis of whey and fresh cheese revealed a dominant presence of single Lactobacillus species used as starters for cheese production. Furthermore, application of this ITS profiling method to a mock Lactobacillus community allowed a minimal resolution level of <0.006 ng/μl.IMPORTANCE The genus Lactobacillus is a large and ubiquitous taxon of high scientific and commercial relevance. Despite the fact that the genetic repertoire of Lactobacillus species has been extensively characterized, the ecology of this genus has been explored by metataxonomic techniques that are accurate down to the genus or phylogenetic group level only. Thus, the distribution of lactobacilli in environmental or processed food samples is relatively unexplored. The profiling protocol described here relies on the use of the internal transcribed spacer to perform an accurate classification in a target population of lactobacilli with a <0.006-ng/μl sensitivity. This approach was used to analyze five sample types collected from both human and animal host-associated microbiota, as well as from the cheese production chain. The availability of a tool for species-level profiling of lactobacilli may be highly useful for both academic research and a wide range of industrial applications.
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Affiliation(s)
- Christian Milani
- 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
| | - Marta Mangifesta
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | | | - Rosaria Anzalone
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | - Giulia Alessandri
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
| | | | - Douwe van Sinderen
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
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26
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Martinic A, Barouei J, Bendiks Z, Mishchuk D, Heeney DD, Martin R, Marco ML, Slupsky CM. Supplementation of Lactobacillus plantarum Improves Markers of Metabolic Dysfunction Induced by a High Fat Diet. J Proteome Res 2018; 17:2790-2802. [PMID: 29931981 DOI: 10.1021/acs.jproteome.8b00282] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Obesity is a prevalent chronic condition in many developed and developing nations that raises the risk for developing heart disease, stroke, and diabetes. Previous studies have shown that consuming particular probiotic strains of Lactobacillus is associated with improvement in the obese and diabetic phenotype; however, the mechanisms of these beneficial effects are not well understood. In this study, C57BL/6J male mice were fed a lard-based high fat diet for 15 weeks with Lactobacillus plantarum supplementation NCIMB8826 (Lp) between weeks 10 and 15 ( n = 10 per group). Systemic metabolic effects of supplementation were analyzed by NMR metabolomics, protein expression assays, gene transcript quantification, and 16S rRNA marker gene sequencing. Body and organ weights were not significantly different with Lp supplementation, and no microbiota community structure changes were observed in the cecum; however, L. plantarum numbers were increased in the treatment group according to culture-based and 16S rRNA gene quantification. Significant differences in metabolite and protein concentrations (serum, liver, and colon), gene expression (ileum and adipose), and cytokines (colon) were observed between groups with increases in the gene expression of tight junction proteins in the ileum and cecum and improvement of some markers of glucose homeostasis in blood and tissue with Lp supplementation. These results indicate Lp supplementation impacts systemic metabolism and immune signaling before phenotypic changes and without large-scale changes to the microbiome. This study supports the notion that Lp is a beneficial probiotic, even in the context of a high fat diet.
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Affiliation(s)
| | | | | | | | | | - Roy Martin
- Western Human Nutrition Research Center , USDA , Davis , California 95616 , United States
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27
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Ringot-Destrez B, D'Alessandro Z, Lacroix JM, Mercier-Bonin M, Léonard R, Robbe-Masselot C. A Sensitive and Rapid Method to Determin the Adhesion Capacity of Probiotics and Pathogenic Microorganisms to Human Gastrointestinal Mucins. Microorganisms 2018; 6:E49. [PMID: 29844291 PMCID: PMC6027390 DOI: 10.3390/microorganisms6020049] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 05/22/2018] [Accepted: 05/28/2018] [Indexed: 12/25/2022] Open
Abstract
Mucus is the habitat for the microorganisms, bacteria and yeast that form the commensal flora. Mucins, the main macromolecules of mucus, and more specifically, the glycans that cover them, play essential roles in microbial gastrointestinal colonization. Probiotics and pathogens must also colonize mucus to have lasting positive or deleterious effects. The question of which mucin-harboured glycan motifs favour the adhesion of specific microorganisms remains very poorly studied. In the current study, a simple test based on the detection of fluorescent-labeled microorganisms raised against microgram amounts of mucins spotted on nitrocellulose was developed. The adhesion of various probiotic, commensal and pathogenic microorganisms was evaluated on a panel of human purified gastrointestinal mucins and compared with that of commercially available pig gastric mucins (PGM) and of mucins secreted by the colonic cancer cell line HT29-MTX. The latter two proved to be very poor indicators of adhesion capacity on intestinal mucins. Our results show that the nature of the sialylated cores of O-glycans, determined by MALDI MS-MS analysis, potentially enables sialic acid residues to modulate the adhesion of microorganisms either positively or negatively. Other identified factors affecting the adhesion propensity were O-glycan core types and the presence of blood group motifs. This test should help to select probiotics with enhanced adhesion capabilities as well as deciphering the role of specific mucin glycotopes on microbial adhesion.
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Affiliation(s)
- Bélinda Ringot-Destrez
- Univ.lille, CNRS, UMR8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, F59000 Lille, France.
| | - Zéa D'Alessandro
- Univ.lille, CNRS, UMR8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, F59000 Lille, France.
| | - Jean-Marie Lacroix
- Univ.lille, CNRS, UMR8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, F59000 Lille, France.
| | - Muriel Mercier-Bonin
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, 31000 Toulouse, France.
| | - Renaud Léonard
- Univ.lille, CNRS, UMR8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, F59000 Lille, France.
| | - Catherine Robbe-Masselot
- Univ.lille, CNRS, UMR8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, F59000 Lille, France.
- Unité de Glycobiologie Structurale et Fonctionnelle, Campus CNRS de la Haute Borne, 50 avenue de Halley, 59658 Villeneuve d'Ascq, France.
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29
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New insight and metrics to understand the ontogeny and succession of Lactobacillus plantarum subsp. plantarum and Lactobacillus plantarum subsp. argentoratensis. Sci Rep 2018; 8:6029. [PMID: 29662105 PMCID: PMC5902611 DOI: 10.1038/s41598-018-24541-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 04/05/2018] [Indexed: 12/16/2022] Open
Abstract
Lactobacillus plantarum is one of the most extensively studied Lactobacillus species because of its presence in a variety of environmental niches, versatility, and metabolic capabilities, resulting in the use of this organism in many industrial applications. However, although extensive effort has been invested in screening this species from a variety of habitats, a reliable and accurate method for studying the succession and ontogeny of this organism in complex ecosystems is still required to confirm the activity of L. plantarum at the subspecies level. Therefore, in this study, novel subspecies-specific genes for the quantitative detection of two L. plantarum subspecies were identified by comparative genomic analysis. The specificity of primer sets for selected genes specific to each targeted microbe was confirmed in kimchi samples. Interestingly, in all the kimchi samples at 4 °C, the presence of L. plantarum subsp. argentoratensis was not observed. Hence, we found that low temperatures markedly affected the ontogeny of L. plantarum subsp. argentoratensis during kimchi fermentation. Subsequently, this touchstone method will offer new insight and metrics to understand the ontogeny and succession of L. plantarum subsp. plantarum and L. plantarum subsp. argentoratensis in various niches.
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30
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Kashyap PC, Quigley EMM. Therapeutic implications of the gastrointestinal microbiome. Curr Opin Pharmacol 2018; 38:90-96. [DOI: 10.1016/j.coph.2018.01.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 10/23/2017] [Accepted: 01/23/2018] [Indexed: 12/27/2022]
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Schott AS, Behr J, Geißler AJ, Kuster B, Hahne H, Vogel RF. Quantitative Proteomics for the Comprehensive Analysis of Stress Responses of Lactobacillus paracasei subsp. paracasei F19. J Proteome Res 2017; 16:3816-3829. [PMID: 28862000 DOI: 10.1021/acs.jproteome.7b00474] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Lactic acid bacteria are broadly employed as starter cultures in the manufacture of foods. Upon technological preparation, they are confronted with drying stress that amalgamates numerous stress conditions resulting in losses of fitness and survival. To better understand and differentiate physiological stress responses, discover general and specific markers for the investigated stress conditions, and predict optimal preconditioning for starter cultures, we performed a comprehensive genomic and quantitative proteomic analysis of a commonly used model system, Lactobacillus paracasei subsp. paracasei TMW 1.1434 (isogenic with F19) under 11 typical stress conditions, including among others oxidative, osmotic, pH, and pressure stress. We identified and quantified >1900 proteins in triplicate analyses, representing 65% of all genes encoded in the genome. The identified genes were thoroughly annotated in terms of subcellular localization prediction and biological functions, suggesting unbiased and comprehensive proteome coverage. In total, 427 proteins were significantly differentially expressed in at least one condition. Most notably, our analysis suggests that optimal preconditioning toward drying was predicted to be alkaline and high-pressure stress preconditioning. Taken together, we believe the presented strategy may serve as a prototypic example for the analysis and utility of employing quantitative-mass-spectrometry-based proteomics to study bacterial physiology.
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Affiliation(s)
- Ann-Sophie Schott
- Chair of Technical Microbiology, Technische Universität München , Freising 85354, Germany
| | - Jürgen Behr
- Chair of Technical Microbiology, Technische Universität München , Freising 85354, Germany.,Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Freising 85354, Germany
| | - Andreas J Geißler
- Chair of Technical Microbiology, Technische Universität München , Freising 85354, Germany
| | - Bernhard Kuster
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Freising 85354, Germany.,Chair of Proteomics and Bioanalytics, Technische Universität München , Freising 85354, Germany.,Center for Integrated Protein Science Munich, Freising 85354, Germany
| | | | - Rudi F Vogel
- Chair of Technical Microbiology, Technische Universität München , Freising 85354, Germany
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