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Defaix R, Lokesh J, Frohn L, Le Bechec M, Pigot T, Véron V, Surget A, Biasutti S, Terrier F, Skiba-Cassy S, Roy J, Panserat S, Ricaud K. Exploring the effects of dietary inulin in rainbow trout fed a high-starch, 100% plant-based diet. J Anim Sci Biotechnol 2024; 15:6. [PMID: 38247008 PMCID: PMC10802069 DOI: 10.1186/s40104-023-00951-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 10/16/2023] [Indexed: 01/23/2024] Open
Abstract
BACKGROUND High dietary carbohydrates can spare protein in rainbow trout (Oncorhynchus mykiss) but may affect growth and health. Inulin, a prebiotic, could have nutritional and metabolic effects, along with anti-inflammatory properties in teleosts, improving growth and welfare. We tested this hypothesis in rainbow trout by feeding them a 100% plant-based diet, which is a viable alternative to fishmeal and fish oil in aquaculture feeds. In a two-factor design, we examined the impact of inulin (2%) as well as the variation in the carbohydrates (CHO)/plant protein ratio on rainbow trout. We assessed the influence of these factors on zootechnical parameters, plasma metabolites, gut microbiota, production of short-chain fatty acids and lactic acid, as well as the expression of free-fatty acid receptor genes in the mid-intestine, intermediary liver metabolism, and immune markers in a 12-week feeding trial. RESULTS The use of 2% inulin did not significantly change the fish intestinal microbiota, but interestingly, the high CHO/protein ratio group showed a change in intestinal microbiota and in particular the beta diversity, with 21 bacterial genera affected, including Ralstonia, Bacillus, and 11 lactic-acid producing bacteria. There were higher levels of butyric, and valeric acid in groups fed with high CHO/protein diet but not with inulin. The high CHO/protein group showed a decrease in the expression of pro-inflammatory cytokines (il1b, il8, and tnfa) in liver and a lower expression of the genes coding for tight-junction proteins in mid-intestine (tjp1a and tjp3). However, the 2% inulin did not modify the expression of plasma immune markers. Finally, inulin induced a negative effect on rainbow trout growth performance irrespective of the dietary carbohydrates. CONCLUSIONS With a 100% plant-based diet, inclusion of high levels of carbohydrates could be a promising way for fish nutrition in aquaculture through a protein sparing effect whereas the supplementation of 2% inulin does not appear to improve the use of CHO when combined with a 100% plant-based diet.
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Affiliation(s)
- Raphaël Defaix
- Université de Pau Et Des Pays de L'Adour, E2S UPPA, INRAE, NUMEA, Saint-Pée-Sur-Nivelle, France
| | - Jep Lokesh
- Université de Pau Et Des Pays de L'Adour, E2S UPPA, INRAE, NUMEA, Saint-Pée-Sur-Nivelle, France
| | - Laura Frohn
- Université de Pau Et Des Pays de L'Adour, E2S UPPA, INRAE, NUMEA, Saint-Pée-Sur-Nivelle, France
| | - Mickael Le Bechec
- Université de Pau Et Des Pays de L'Adour, E2S UPPA, CNRS, IMT Mines Ales, IPREM, Pau, France
| | - Thierry Pigot
- Université de Pau Et Des Pays de L'Adour, E2S UPPA, CNRS, IMT Mines Ales, IPREM, Pau, France
| | - Vincent Véron
- Université de Pau Et Des Pays de L'Adour, E2S UPPA, INRAE, NUMEA, Saint-Pée-Sur-Nivelle, France
| | - Anne Surget
- Université de Pau Et Des Pays de L'Adour, E2S UPPA, INRAE, NUMEA, Saint-Pée-Sur-Nivelle, France
| | - Sandra Biasutti
- Université de Pau Et Des Pays de L'Adour, E2S UPPA, IUT des Pays de l'Adour, Département Génie Biologique, Mont de Marsan, France
| | - Frédéric Terrier
- Université de Pau Et Des Pays de L'Adour, E2S UPPA, INRAE, NUMEA, Saint-Pée-Sur-Nivelle, France
| | - Sandrine Skiba-Cassy
- Université de Pau Et Des Pays de L'Adour, E2S UPPA, INRAE, NUMEA, Saint-Pée-Sur-Nivelle, France
| | - Jérôme Roy
- Université de Pau Et Des Pays de L'Adour, E2S UPPA, INRAE, NUMEA, Saint-Pée-Sur-Nivelle, France
| | - Stéphane Panserat
- Université de Pau Et Des Pays de L'Adour, E2S UPPA, INRAE, NUMEA, Saint-Pée-Sur-Nivelle, France
| | - Karine Ricaud
- Université de Pau Et Des Pays de L'Adour, E2S UPPA, INRAE, NUMEA, Saint-Pée-Sur-Nivelle, France.
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Comparative Genomics and Physiological Characterization of Two Aerobic Spore Formers Isolated from Human Ileal Samples. Int J Mol Sci 2022; 23:ijms232314946. [PMID: 36499272 PMCID: PMC9739757 DOI: 10.3390/ijms232314946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/25/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022] Open
Abstract
Spore formers are ubiquitous microorganisms commonly isolated from most environments, including the gastro-intestinal tract (GIT) of insects and animals. Spores ingested as food and water contaminants safely transit the stomach and reach the intestine, where some of them germinate and temporarily colonize that niche. In the lower part of the GIT, they re-sporulate and leave the body as spores, therefore passing through their entire life cycle in the animal body. In the intestine, both un-germinated spores and germination-derived cells interact with intestinal and immune cells and have health-beneficial effects, which include the production of useful compounds, protection against pathogenic microorganisms, contribution to the development of an efficient immune system and modulation of the gut microbial composition. We report a genomic and physiological characterization of SF106 and SF174, two aerobic spore former strains previously isolated from ileal biopsies of healthy human volunteers. SF106 and SF174 belong respectively to the B. subtilis and Alkalihalobacillus clausii (formerly Bacillus clausii) species, are unable to produce toxins or other metabolites with cytotoxic activity against cultured human cells, efficiently bind mucin and human epithelial cells in vitro and produce molecules with antimicrobial and antibiofilm activities.
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3
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Begum N, Lee S, Portlock TJ, Pellon A, Nasab SDS, Nielsen J, Uhlen M, Moyes DL, Shoaie S. Integrative functional analysis uncovers metabolic differences between Candida species. Commun Biol 2022; 5:1013. [PMID: 36163459 PMCID: PMC9512779 DOI: 10.1038/s42003-022-03955-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 09/07/2022] [Indexed: 12/02/2022] Open
Abstract
Candida species are a dominant constituent of the human mycobiome and associated with the development of several diseases. Understanding the Candida species metabolism could provide key insights into their ability to cause pathogenesis. Here, we have developed the BioFung database, providing an efficient annotation of protein-encoding genes. Along, with BioFung, using carbohydrate-active enzyme (CAZymes) analysis, we have uncovered core and accessory features across Candida species demonstrating plasticity, adaption to the environment and acquired features. We show a greater importance of amino acid metabolism, as functional analysis revealed that all Candida species can employ amino acid metabolism. However, metabolomics revealed that only a specific cluster of species (AGAu species—C. albicans, C. glabrata and C. auris) utilised amino acid metabolism including arginine, cysteine, and methionine metabolism potentially improving their competitive fitness in pathogenesis. We further identified critical metabolic pathways in the AGAu cluster with biomarkers and anti-fungal target potential in the CAZyme profile, polyamine, choline and fatty acid biosynthesis pathways. This study, combining genomic analysis, and validation with gene expression and metabolomics, highlights the metabolic diversity with AGAu species that underlies their remarkable ability to dominate they mycobiome and cause disease. Metabolic differences between Candida species are uncovered using the BioFung database alongside genomic and metabolic analysis.
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Affiliation(s)
- Neelu Begum
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, SE1 9RT, London, UK
| | - Sunjae Lee
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, SE1 9RT, London, UK
| | - Theo John Portlock
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, SE-171 21, Sweden
| | - Aize Pellon
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, SE1 9RT, London, UK
| | - Shervin Dokht Sadeghi Nasab
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, SE1 9RT, London, UK
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Kemivägen 10, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden.,BioInnovation Institute, Ole Maaløes Vej 3, DK2200, Copenhagen N, Denmark
| | - Mathias Uhlen
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, SE-171 21, Sweden
| | - David L Moyes
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, SE1 9RT, London, UK.
| | - Saeed Shoaie
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, SE1 9RT, London, UK. .,Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, SE-171 21, Sweden.
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4
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Liu DM, Huang YY, Liang MH. Analysis of the probiotic characteristics and adaptability of Lactiplantibacillus plantarum DMDL 9010 to gastrointestinal environment by complete genome sequencing and corresponding phenotypes. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113129] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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5
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Hetta HF, Kh Meshaal A, Algammal AM, Yahia R, Makharita RR, Marraiki N, Shah MA, Hassan HAM, Batiha GES. In-vitro Antimicrobial Activity of Essential Oils and Spices Powder of some Medicinal Plants Against Bacillus Species Isolated from Raw and Processed Meat. Infect Drug Resist 2020; 13:4367-4378. [PMID: 33304102 PMCID: PMC7723237 DOI: 10.2147/idr.s277295] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 11/11/2020] [Indexed: 11/23/2022] Open
Abstract
Background and Aim Bacillus species are widely distributed microorganisms in nature that are responsible for outbreaks of food poisoning and a common cause of food spoilage. This study aimed to isolate and identify foodborne Bacillus species from meat and to determine the antimicrobial activities of commercial essential oils and spices powder extracted from certain medicinal plants. Methods Sixty meat samples were collected in Assiut city and subdivided into raw meat and processed meat. Bacillus spp were isolated and identified according to their cultural characters, biochemical reactions, serological typing, and 16S rRNA gene sequencing. The antibacterial activity of essential oils and spices powder was measured by using well-diffusion and microbial count techniques. Results The prevalence of Bacillus spp. in the examined raw meat samples and processed meat samples was 13.34%, and 26.67%, respectively. There was a marked decrease in the total Bacillus species count after treatment of minced beef with essential oils and spices powder compared to the untreated one. Black seed oil was the most potent antibacterial essential oil among the tested oils present in this study. Conclusion Essential oils and spices powder of certain medicinal plants (cumin: Cuminum cyminum, black seeds: Nigella sativa, cloves: Syzygium aromaicum, cinnamon: Cinnamomum zeylanicum, and Marjoram: Origanum majorana) have a potential in vitro antimicrobial activity against Bacillus spp. Furthermore, Nigella sativa oil exhibited the most potent antibacterial activity against Bacillus spp.
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Affiliation(s)
- Helal F Hetta
- Department of Internal Medicine, University of Cincinnati, College of Medicine, Cincinnati, OH 45267-0595, USA.,Department of Medical Microbiology and Immunology, Faculty of Medicine, Assuit University, Assuit 71515, Egypt
| | - Ahmed Kh Meshaal
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Assiut 71524, Egypt
| | - Abdelazeem M Algammal
- Department of Bacteriology, Immunology and Mycology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Ramadan Yahia
- Department of Microbiology and Immunology, Faculty of Pharmacy, Deraya University, Minia, Egypt
| | - Rabab R Makharita
- Biology Department, Faculty of Science and Arts Khulais, University of Jeddah, Jeddah, 21959, Saudi Arabia.,Botany Department, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt
| | - Najat Marraiki
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Muhammad Ajmal Shah
- Department of Pharmacognosy, Faculty of Pharmaceutical Sciences, Government College University, Faisalabad, Pakistan
| | - Hebat-Allah M Hassan
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assuit University, Assuit 71515, Egypt
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicines, Damanhour University, Damanhour 22511, Egypt
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High-Quality Draft Genome Sequences of Marine Fish Gut Bacillus sp. Strains ABP1 and ABP2 with Nonstarch Polysaccharide Hydrolytic Potential. Microbiol Resour Announc 2020; 9:9/15/e00077-20. [PMID: 32273352 PMCID: PMC7380523 DOI: 10.1128/mra.00077-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we present the genome sequences of two environmental Bacillus strains with broad hydrolytic capacity toward different nonstarch polysaccharides (NSPs) that were isolated from the gut of marine fish fed NSP-rich diets. Several genes that may contribute to the NSP-degrading behavior were identified through in silico analysis.
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7
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Ega SL, Drendel G, Petrovski S, Egidi E, Franks AE, Muddada S. Comparative Analysis of Structural Variations Due to Genome Shuffling of Bacillus Subtilis VS15 for Improved Cellulase Production. Int J Mol Sci 2020; 21:ijms21041299. [PMID: 32075107 PMCID: PMC7072954 DOI: 10.3390/ijms21041299] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 10/29/2019] [Accepted: 10/29/2019] [Indexed: 12/23/2022] Open
Abstract
Cellulose is one of the most abundant and renewable biomass products used for the production of bioethanol. Cellulose can be efficiently hydrolyzed by Bacillus subtilis VS15, a strain isolate obtained from decomposing logs. A genome shuffling approach was implemented to improve the cellulase activity of Bacillus subtilis VS15. Mutant strains were created using ethyl methyl sulfonate (EMS), N-Methyl-N′ nitro-N-nitrosoguanidine (NTG), and ultraviolet light (UV) followed by recursive protoplast fusion. After two rounds of shuffling, the mutants Gb2, Gc8, and Gd7 were produced that had an increase in cellulase activity of 128%, 148%, and 167%, respectively, in comparison to the wild type VS15. The genetic diversity of the shuffled strain Gd7 and wild type VS15 was compared at whole genome level. Genomic-level comparisons identified a set of eight genes, consisting of cellulase and regulatory genes, of interest for further analyses. Various genes were identified with insertions and deletions that may be involved in improved celluase production in Gd7. Strain Gd7 maintained the capability of hydrolyzing wheatbran to glucose and converting glucose to ethanol by fermentation with Saccharomyces cerevisiae of the wild type VS17. This ability was further confirmed by the acidified potassium dichromate (K2Cr2O7) method.
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Affiliation(s)
| | - Gene Drendel
- Department of Physiology, Anatomy and Microbiology, College of Science, Health and Engineering, La Trobe University, Melbourne, Victoria 3086, Australia; (G.D.); (S.P.); (E.E.); (A.E.F.)
| | - Steve Petrovski
- Department of Physiology, Anatomy and Microbiology, College of Science, Health and Engineering, La Trobe University, Melbourne, Victoria 3086, Australia; (G.D.); (S.P.); (E.E.); (A.E.F.)
| | - Eleonora Egidi
- Department of Physiology, Anatomy and Microbiology, College of Science, Health and Engineering, La Trobe University, Melbourne, Victoria 3086, Australia; (G.D.); (S.P.); (E.E.); (A.E.F.)
- Hawkesbury Institute for the Environment, Western Sydney University, Sydney, NSW 2750, Australia
| | - Ashley E. Franks
- Department of Physiology, Anatomy and Microbiology, College of Science, Health and Engineering, La Trobe University, Melbourne, Victoria 3086, Australia; (G.D.); (S.P.); (E.E.); (A.E.F.)
- Centre for Future Landscapes, College of Science, Health and Engineering, La Trobe University, Melbourne, VI 3086, Australia
| | - Sudhamani Muddada
- Department of Biotechnology, K L E F University, Guntur 522 502, India;
- Correspondence: ; Tel.: +91-970-3470-598
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8
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Kotowicz N, Bhardwaj R, Ferreira W, Hong H, Olender A, Ramirez J, Cutting S. Safety and probiotic evaluation of two Bacillus strains producing antioxidant compounds. Benef Microbes 2019; 10:759-771. [DOI: 10.3920/bm2019.0040] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Bacillus species are becoming increasingly relevant for use as probiotics or feed additives where their heat stability can ensure survival in the food matrix or enable long-term storage at ambient temperature. Some Bacillus species are pigmented and in this study, we have examined two strains, one Bacillus pumilus (pigmented red) and the other Bacillus megaterium (pigmented yellow) for their safety for potential use in humans as dietary supplements. In addition, we have set out to determine if they might confer any potential health benefits. Both strains produce C30 carotenoids while the B. pumilus strain also produced large quantities of riboflavin equivalent to genetically modified Bacillus strains and most probably contributing to this strain’s pigmentation. Riboflavin’s and carotenoids are antioxidants, and we have evaluated the ability of vegetative cells and/or spores to influence populations of Faecalibacterium prausnitzii in the colon of mice. While both strains increased levels of F. prausnitzii, spores of the B. pumilus strain produced a significant increase in F. prausnitzii levels. If found to be reproducible in humans such an effect might, potentially, confer health benefits particularly for those suffering from inflammatory bowel disease.
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Affiliation(s)
- N. Kotowicz
- SporeGen Ltd., Bourne Labs, Egham, Surrey, TW20 OEX, United Kingdom
| | - R.K. Bhardwaj
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 OEX, United Kingdom
| | - W.T. Ferreira
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 OEX, United Kingdom
| | - H.A. Hong
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 OEX, United Kingdom
| | - A. Olender
- Department of Medical Microbiology, Medical University of Lublin, Chodzki 1 Street, Lublin, 20-093, Poland
| | - J. Ramirez
- Enviromedica, 2301 Scarbrough Drive, Suite 300, Austin, TX 78728, USA
| | - S.M. Cutting
- SporeGen Ltd., Bourne Labs, Egham, Surrey, TW20 OEX, United Kingdom
- School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 OEX, United Kingdom
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9
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Serra CR, Almeida EM, Guerreiro I, Santos R, Merrifield DL, Tavares F, Oliva-Teles A, Enes P. Selection of carbohydrate-active probiotics from the gut of carnivorous fish fed plant-based diets. Sci Rep 2019; 9:6384. [PMID: 31011158 PMCID: PMC6476879 DOI: 10.1038/s41598-019-42716-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 03/25/2019] [Indexed: 02/06/2023] Open
Abstract
The gastrointestinal microbiota plays a critical role on host health and metabolism. This is particularly important in teleost nutrition, because fish do not possess some of the necessary enzymes to cope with the dietary challenges of aquaculture production. A main difficulty within fish nutrition is its dependence on fish meal, an unsustainable commodity and a source of organic pollutants. The most obvious sustainable alternatives to fish meal are plant feedstuffs, but their nutritive value is limited by the presence of high levels of non-starch polysaccharides (NSP), which are not metabolized by fish. The composition of fish-gut microbial communities have been demonstrated to adapt when the host is fed different ingredients. Thus, we hypothesized that a selective pressure of plant-based diets on fish gut microbiota, could be a beneficial strategy for an enrichment of bacteria with a secretome able to mobilize dietary NSP. By targeting bacterial sporulating isolates with diverse carbohydrase activities from the gut of European sea bass, we have obtained isolates with high probiotic potential. By inferring the adaptive fitness to the fish gut and the amenability to industrial processing, we identified the best two candidates to become industrially valuable probiotics. This potential was confirmed in vivo, since one of the select isolates lead to a better growth and feed utilization efficiency in fish fed probiotic-supplemented plant-based diets, thus contributing for sustainable and more cost-effective aquaculture practices.
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Affiliation(s)
- Cláudia R Serra
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal.
| | - Eduarda M Almeida
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, Ed. FC4, 4169-007, Porto, Portugal.,CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - Inês Guerreiro
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, Ed. FC4, 4169-007, Porto, Portugal
| | - Rafaela Santos
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, Ed. FC4, 4169-007, Porto, Portugal
| | - Daniel L Merrifield
- School of Biomedical and Biological Sciences, Plymouth University, 401 Davy Building, Drake Circus, Plymouth, PL4 8AA, Devon, UK
| | - Fernando Tavares
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, Ed. FC4, 4169-007, Porto, Portugal.,CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - Aires Oliva-Teles
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, Ed. FC4, 4169-007, Porto, Portugal
| | - Paula Enes
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal
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10
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Ferreira Filho JA, Horta MAC, Beloti LL, Dos Santos CA, de Souza AP. Carbohydrate-active enzymes in Trichoderma harzianum: a bioinformatic analysis bioprospecting for key enzymes for the biofuels industry. BMC Genomics 2017; 18:779. [PMID: 29025413 PMCID: PMC5639747 DOI: 10.1186/s12864-017-4181-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Accepted: 10/05/2017] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Trichoderma harzianum is used in biotechnology applications due to its ability to produce powerful enzymes for the conversion of lignocellulosic substrates into soluble sugars. Active enzymes involved in carbohydrate metabolism are defined as carbohydrate-active enzymes (CAZymes), and the most abundant family in the CAZy database is the glycoside hydrolases. The enzymes of this family play a fundamental role in the decomposition of plant biomass. RESULTS In this study, the CAZymes of T. harzianum were identified and classified using bioinformatic approaches after which the expression profiles of all annotated CAZymes were assessed via RNA-Seq, and a phylogenetic analysis was performed. A total of 430 CAZymes (3.7% of the total proteins for this organism) were annotated in T. harzianum, including 259 glycoside hydrolases (GHs), 101 glycosyl transferases (GTs), 6 polysaccharide lyases (PLs), 22 carbohydrate esterases (CEs), 42 auxiliary activities (AAs) and 46 carbohydrate-binding modules (CBMs). Among the identified T. harzianum CAZymes, 47% were predicted to harbor a signal peptide sequence and were therefore classified as secreted proteins. The GH families were the CAZyme class with the greatest number of expressed genes, including GH18 (23 genes), GH3 (17 genes), GH16 (16 genes), GH2 (13 genes) and GH5 (12 genes). A phylogenetic analysis of the proteins in the AA9/GH61, CE5 and GH55 families showed high functional variation among the proteins. CONCLUSIONS Identifying the main proteins used by T. harzianum for biomass degradation can ensure new advances in the biofuel production field. Herein, we annotated and characterized the expression levels of all of the CAZymes from T. harzianum, which may contribute to future studies focusing on the functional and structural characterization of the identified proteins.
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Affiliation(s)
- Jaire Alves Ferreira Filho
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil.,Graduate Program in Genetics and Molecular Biology, Institute of Biology, UNICAMP, Campinas, SP, Brazil
| | | | - Lilian Luzia Beloti
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Clelton Aparecido Dos Santos
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Anete Pereira de Souza
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil. .,Department of Plant Biology, Institute of Biology, UNICAMP, Campinas, SP, Brazil.
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11
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Biotechnological production of value-added compounds by ustilaginomycetous yeasts. Appl Microbiol Biotechnol 2017; 101:7789-7809. [DOI: 10.1007/s00253-017-8516-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 09/03/2017] [Accepted: 09/04/2017] [Indexed: 11/30/2022]
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12
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Disturbance of the intestinal microbial community by ursolic acid contributes to its function as a regulator of fat deposition. J Funct Foods 2015. [DOI: 10.1016/j.jff.2015.02.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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13
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Corfield AP. Mucins: A biologically relevant glycan barrier in mucosal protection. Biochim Biophys Acta Gen Subj 2015; 1850:236-52. [DOI: 10.1016/j.bbagen.2014.05.003] [Citation(s) in RCA: 265] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 04/05/2014] [Accepted: 05/02/2014] [Indexed: 02/08/2023]
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14
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Steiger S, Perez-Fons L, Cutting SM, Fraser PD, Sandmann G. Annotation and functional assignment of the genes for the C30 carotenoid pathways from the genomes of two bacteria: Bacillus indicus and Bacillus firmus. Microbiology (Reading) 2015; 161:194-202. [DOI: 10.1099/mic.0.083519-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Sabine Steiger
- Biosynthesis Group, Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Laura Perez-Fons
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey, UK
| | - Simon M. Cutting
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey, UK
| | - Paul D. Fraser
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey, UK
| | - Gerhard Sandmann
- Biosynthesis Group, Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
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15
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Stecher B, Berry D, Loy A. Colonization resistance and microbial ecophysiology: using gnotobiotic mouse models and single-cell technology to explore the intestinal jungle. FEMS Microbiol Rev 2013; 37:793-829. [PMID: 23662775 DOI: 10.1111/1574-6976.12024] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 04/11/2013] [Accepted: 04/18/2013] [Indexed: 12/14/2022] Open
Abstract
The highly diverse intestinal microbiota forms a structured community engaged in constant communication with itself and its host and is characterized by extensive ecological interactions. A key benefit that the microbiota affords its host is its ability to protect against infections in a process termed colonization resistance (CR), which remains insufficiently understood. In this review, we connect basic concepts of CR with new insights from recent years and highlight key technological advances in the field of microbial ecology. We present a selection of statistical and bioinformatics tools used to generate hypotheses about synergistic and antagonistic interactions in microbial ecosystems from metagenomic datasets. We emphasize the importance of experimentally testing these hypotheses and discuss the value of gnotobiotic mouse models for investigating specific aspects related to microbiota-host-pathogen interactions in a well-defined experimental system. We further introduce new developments in the area of single-cell analysis using fluorescence in situ hybridization in combination with metabolic stable isotope labeling technologies for studying the in vivo activities of complex community members. These approaches promise to yield novel insights into the mechanisms of CR and intestinal ecophysiology in general, and give researchers the means to experimentally test hypotheses in vivo at varying levels of biological and ecological complexity.
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Affiliation(s)
- Bärbel Stecher
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Ludwig-Maximilians-University of Munich, Munich, Germany.
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16
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Manzo N, Di Luccia B, Isticato R, D’Apuzzo E, De Felice M, Ricca E. Pigmentation and sporulation are alternative cell fates in Bacillus pumilus SF214. PLoS One 2013; 8:e62093. [PMID: 23634224 PMCID: PMC3636246 DOI: 10.1371/journal.pone.0062093] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 03/15/2013] [Indexed: 11/19/2022] Open
Abstract
Bacillus pumilus SF214 is a spore forming bacterium, isolated from a marine sample, able to produce a matrix and a orange-red, water soluble pigment. Pigmentation is strictly regulated and high pigment production was observed during the late stationary growth phase in a minimal medium and at growth temperatures lower than the optimum. Only a subpopulation of stationary phase cells produced the pigment, indicating that the stationary culture contains a heterogeneous cell population and that pigment synthesis is a bimodal phenomenon. The fraction of cells producing the pigment varied in the different growth conditions and occured only in cells not devoted to sporulation. Only some of the pigmented cells were also able to produce a matrix. Pigment and matrix production in SF214 appear then as two developmental fates both alternative to sporulation. Since the pigment had an essential role in the cell resistance to oxidative stress conditions, we propose that within the heterogeneous population different survival strategies can be followed by the different cells.
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Affiliation(s)
- Nicola Manzo
- Department of Biology, Federico II University, Napoli, Italy
| | | | | | - Enrica D’Apuzzo
- Department of Biology, Federico II University, Napoli, Italy
| | | | - Ezio Ricca
- Department of Biology, Federico II University, Napoli, Italy
- * E-mail:
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17
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Lee YJ, Lee SJ, Jeong H, Kim HJ, Ryu N, Kim BC, Lee HS, Lee DW, Lee SJ. Draft genome sequence of Bacillus oceanisediminis 2691. J Bacteriol 2012; 194:6351-2. [PMID: 23105082 PMCID: PMC3486353 DOI: 10.1128/jb.01643-12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 09/12/2012] [Indexed: 11/20/2022] Open
Abstract
Bacillus oceanisediminis 2691 is an aerobic, Gram-positive, spore-forming, and moderately halophilic bacterium that was isolated from marine sediment of the Yellow Sea coast of South Korea. Here, we report the draft genome sequence of B. oceanisediminis 2691 that may have an important role in the bioremediation of marine sediment.
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Affiliation(s)
- Yong-Jik Lee
- Systems and Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Sang-Jae Lee
- Systems and Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Haeyoung Jeong
- Systems and Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Biosystems and Bioengineering Program, University of Science and Technology, Daejeon, Republic of Korea
| | - Hyun Ju Kim
- Systems and Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Biosystems and Bioengineering Program, University of Science and Technology, Daejeon, Republic of Korea
| | - Naeun Ryu
- College of Medical and Life Sciences, Silla University, Busan, Republic of Korea
| | - Byoung-Chan Kim
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Han-Seung Lee
- College of Medical and Life Sciences, Silla University, Busan, Republic of Korea
| | - Dong-Woo Lee
- Division of Applied Biology and Chemistry, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Sang Jun Lee
- Systems and Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Biosystems and Bioengineering Program, University of Science and Technology, Daejeon, Republic of Korea
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18
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Steiger S, Perez-Fons L, Fraser P, Sandmann G. Biosynthesis of a novel C30 carotenoid in Bacillus firmus isolates. J Appl Microbiol 2012; 113:888-95. [DOI: 10.1111/j.1365-2672.2012.05377.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Revised: 06/13/2012] [Accepted: 06/16/2012] [Indexed: 11/30/2022]
Affiliation(s)
- S. Steiger
- Biosynthesis Group, Molecular Biosciences; Goethe University Frankfurt; Frankfurt; Germany
| | - L. Perez-Fons
- School of Biological Sciences; Royal Holloway; University of London; Egham; Surrey; UK
| | - P.D. Fraser
- School of Biological Sciences; Royal Holloway; University of London; Egham; Surrey; UK
| | - G. Sandmann
- Biosynthesis Group, Molecular Biosciences; Goethe University Frankfurt; Frankfurt; Germany
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19
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Permpoonpattana P, Hong H, Khaneja R, Cutting S. Evaluation of Bacillus subtilis strains as probiotics and their potential as a food ingredient. Benef Microbes 2012; 3:127-35. [DOI: 10.3920/bm2012.0002] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Spores of Bacillus subtilis including one strain used commercially were evaluated for their potential value as a probiotic and as potential food additives. Two isolates of B. subtilis examined here were HU58, a human isolate and PXN21, a strain used in an existing commercial product. Compared to a domesticated laboratory strain of B. subtilis both isolates carried traits that could prove advantageous in the human gastro-intestinal tract. This included full resistance to gastric fluids, rapid sporulation and the formation of robust biofilms. We also showed that PXN21 spores when administered weekly to mice conferred non-specific cellular immune responses, indicative signs of the stimulation of innate immunity. Spores mixed in wholemeal biscuits were found to survive baking at 235 °C for 8 minutes with only a 1-log reduction in viability. That spores can survive the baking process offers the possibility of using spores as probiotic supplements in a range of novel food products.
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Affiliation(s)
- P. Permpoonpattana
- School of Biological Sciences, University of London, Royal Holloway, Egham, Surrey TW20 0EX, United Kingdom
| | - H.A. Hong
- School of Biological Sciences, University of London, Royal Holloway, Egham, Surrey TW20 0EX, United Kingdom
| | - R. Khaneja
- School of Biological Sciences, University of London, Royal Holloway, Egham, Surrey TW20 0EX, United Kingdom
| | - S.M. Cutting
- School of Biological Sciences, University of London, Royal Holloway, Egham, Surrey TW20 0EX, United Kingdom
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