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Jo J, Oh J, Park C. Microbial community analysis using high-throughput sequencing technology: a beginner's guide for microbiologists. J Microbiol 2020; 58:176-192. [PMID: 32108314 DOI: 10.1007/s12275-020-9525-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/11/2019] [Accepted: 12/16/2019] [Indexed: 12/19/2022]
Abstract
Microbial communities present in diverse environments from deep seas to human body niches play significant roles in the complex ecosystem and human health. Characterizing their structural and functional diversities is indispensable, and many approaches, such as microscopic observation, DNA fingerprinting, and PCR-based marker gene analysis, have been successfully applied to identify microorganisms. Since the revolutionary improvement of DNA sequencing technologies, direct and high-throughput analysis of genomic DNA from a whole environmental community without prior cultivation has become the mainstream approach, overcoming the constraints of the classical approaches. Here, we first briefly review the history of environmental DNA analysis applications with a focus on profiling the taxonomic composition and functional potentials of microbial communities. To this end, we aim to introduce the shotgun metagenomic sequencing (SMS) approach, which is used for the untargeted ("shotgun") sequencing of all ("meta") microbial genomes ("genomic") present in a sample. SMS data analyses are performed in silico using various software programs; however, in silico analysis is typically regarded as a burden on wet-lab experimental microbiologists. Therefore, in this review, we present microbiologists who are unfamiliar with in silico analyses with a basic and practical SMS data analysis protocol. This protocol covers all the bioinformatics processes of the SMS analysis in terms of data preprocessing, taxonomic profiling, functional annotation, and visualization.
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Affiliation(s)
- Jihoon Jo
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Jooseong Oh
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Chungoo Park
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea.
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52
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López Nadal A, Ikeda-Ohtsubo W, Sipkema D, Peggs D, McGurk C, Forlenza M, Wiegertjes GF, Brugman S. Feed, Microbiota, and Gut Immunity: Using the Zebrafish Model to Understand Fish Health. Front Immunol 2020; 11:114. [PMID: 32117265 PMCID: PMC7014991 DOI: 10.3389/fimmu.2020.00114] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 01/16/2020] [Indexed: 12/12/2022] Open
Abstract
Aquafeed companies aim to provide solutions to the various challenges related to nutrition and health in aquaculture. Solutions to promote feed efficiency and growth, as well as improving the fish health or protect the fish gut from inflammation may include dietary additives such as prebiotics and probiotics. The general assumption is that feed additives can alter the fish microbiota which, in turn, interacts with the host immune system. However, the exact mechanisms by which feed influences host-microbe-immune interactions in fish still remain largely unexplored. Zebrafish rapidly have become a well-recognized animal model to study host-microbe-immune interactions because of the diverse set of research tools available for these small cyprinids. Genome editing technologies can create specific gene-deficient zebrafish that may contribute to our understanding of immune functions. Zebrafish larvae are optically transparent, which allows for in vivo imaging of specific (immune) cell populations in whole transgenic organisms. Germ-free individuals can be reared to study host-microbe interactions. Altogether, these unique zebrafish features may help shed light on the mechanisms by which feed influences host-microbe-immune interactions and ultimately fish health. In this review, we first describe the anatomy and function of the zebrafish gut: the main surface where feed influences host-microbe-immune interactions. Then, we further describe what is currently known about the molecular pathways that underlie this interaction in the zebrafish gut. Finally, we summarize and critically review most of the recent research on prebiotics and probiotics in relation to alterations of zebrafish microbiota and immune responses. We discuss the advantages and disadvantages of the zebrafish as an animal model for other fish species to study feed effects on host-microbe-immune interactions.
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Affiliation(s)
- Adrià López Nadal
- Cell Biology and Immunology Group, Wageningen University and Research, Wageningen, Netherlands.,Aquaculture and Fisheries Group, Wageningen University and Research, Wageningen, Netherlands
| | - Wakako Ikeda-Ohtsubo
- Laboratory of Animal Products Chemistry, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Detmer Sipkema
- Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - David Peggs
- Skretting Aquaculture Research Centre, Stavanger, Norway
| | - Charles McGurk
- Skretting Aquaculture Research Centre, Stavanger, Norway
| | - Maria Forlenza
- Cell Biology and Immunology Group, Wageningen University and Research, Wageningen, Netherlands
| | - Geert F Wiegertjes
- Aquaculture and Fisheries Group, Wageningen University and Research, Wageningen, Netherlands
| | - Sylvia Brugman
- Cell Biology and Immunology Group, Wageningen University and Research, Wageningen, Netherlands
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53
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Katani R, Schilling MA, Lyimo B, Tonui T, Cattadori IM, Eblate E, Martin A, Estes AB, Buza T, Rentsch D, Davenport KW, Hovde BT, Lyimo S, Munuo L, Stomeo F, Tiambo C, Radzio-Basu J, Mosha F, Hudson PJ, Buza JJ, Kapur V. Microbial Diversity in Bushmeat Samples Recovered from the Serengeti Ecosystem in Tanzania. Sci Rep 2019; 9:18086. [PMID: 31792246 PMCID: PMC6888819 DOI: 10.1038/s41598-019-53969-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 11/05/2019] [Indexed: 01/01/2023] Open
Abstract
Bushmeat, the meat and organs derived from wildlife species, is a common source of animal protein in the diets of those living in sub-Saharan Africa and is frequently associated with zoonotic spillover of dangerous pathogens. Given the frequent consumption of bushmeat in this region and the lack of knowledge about the microbial communities associated with this meat, the microbiome of 56 fresh and processed bushmeat samples ascertained from three districts in the Western Serengeti ecosystem in Tanzania was characterized using 16S rRNA metagenomic sequencing. The results show that the most abundant phyla present in bushmeat samples include Firmicutes (67.8%), Proteobacteria (18.4%), Cyanobacteria (8.9%), and Bacteroidetes (3.1%). Regardless of wildlife species, sample condition, season, or region, the microbiome is diverse across all samples, with no significant difference in alpha or beta diversity. The findings also suggest the presence of DNA signatures of potentially dangerous zoonotic pathogens, including those from the genus Bacillus, Brucella, Coxiella, and others, in bushmeat. Together, this investigation provides a better understanding of the microbiome associated with this major food source in samples collected from the Western Serengeti in Tanzania and highlights a need for future investigations on the potential health risks associated with the harvesting, trade, and consumption of bushmeat in Sub-Saharan Africa.
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Affiliation(s)
- Robab Katani
- Applied Biological and Biosecurity Research Laboratory, Pennsylvania State University, University Park, Pennsylvania, USA.,The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Megan A Schilling
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA.,Department of Animal Science, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Beatus Lyimo
- Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Triza Tonui
- Biosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
| | - Isabella M Cattadori
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA.,Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Ernest Eblate
- Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania.,Tanzania Wildlife Research Institute, Arusha, Tanzania
| | - Andimile Martin
- Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Anna B Estes
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA.,Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Teresia Buza
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | | | | | - Blake T Hovde
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Samson Lyimo
- Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Lydia Munuo
- Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Francesca Stomeo
- Biosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
| | - Christian Tiambo
- Biosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
| | - Jessica Radzio-Basu
- Applied Biological and Biosecurity Research Laboratory, Pennsylvania State University, University Park, Pennsylvania, USA.,The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Fausta Mosha
- Ministry of Health Community Development Gender Elderly and Children, Dar es Salaam, Tanzania
| | - Peter J Hudson
- Applied Biological and Biosecurity Research Laboratory, Pennsylvania State University, University Park, Pennsylvania, USA.,The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Joram J Buza
- Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Vivek Kapur
- Applied Biological and Biosecurity Research Laboratory, Pennsylvania State University, University Park, Pennsylvania, USA. .,The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA. .,Department of Animal Science, Pennsylvania State University, University Park, Pennsylvania, USA. .,Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania.
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54
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Fonseca F, Cerqueira R, Fuentes J. Impact of Ocean Acidification on the Intestinal Microbiota of the Marine Sea Bream ( Sparus aurata L.). Front Physiol 2019; 10:1446. [PMID: 31849701 PMCID: PMC6893888 DOI: 10.3389/fphys.2019.01446] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 11/08/2019] [Indexed: 02/06/2023] Open
Abstract
Within a scenario of increasing atmospheric CO2 and ocean acidification (OA), it is highly relevant to investigate its impacts not only on fish performance but also on fish intestinal microbiome and how that reflects on host performance and health. The main objective of this study was to establish if the intestinal microbiota of the sea bream (Sparus aurata) was affected by high level of CO2 in line with the predictions for this century. The bacterial communities of the intestinal fluid were characterized in animals kept at the present-day level of CO2 (400 μatm) and in animals switched to high CO2 (1200 μatm) for 1 month. Bacterial taxa identification was based on molecular methods, using the DNA coding for the 16S ribosomal RNA and primers targeting the regions V1-V3. Amplicons obtained from DNA samples of animals in the same tank were combined, cloned to obtain a bacterial DNA library, and the clones were sequenced. No significant differences were found between the two treatments for alpha diversity. However, beta diversity analysis revealed distinct dysbiosis in response to hypercapnia, with phylum Firmicutes absent from the bacterial communities of fish exposed to 1200 μatm CO2, whereas Proteobacteria relative abundance was increased at elevated CO2, due to the presence of Gammaproteobacteria (Vibrionaceae and Alteromonadaceae), a class not present in the control samples. This study provides a first glimpse at the impact of OA in fish intestinal microbiota and highlights potential downstream effects to the general condition of fishes under hypercapnia.
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Affiliation(s)
- Filomena Fonseca
- Centro de Investigação Marinha e Ambiental, Universidade do Algarve, Faro, Portugal
| | - Ricardo Cerqueira
- Centro de Investigação Marinha e Ambiental, Universidade do Algarve, Faro, Portugal
- Centre of Marine Sciences, Universidade do Algarve, Faro, Portugal
| | - Juan Fuentes
- Centre of Marine Sciences, Universidade do Algarve, Faro, Portugal
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55
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Adhikari B, Hernandez-Patlan D, Solis-Cruz B, Kwon YM, Arreguin MA, Latorre JD, Hernandez-Velasco X, Hargis BM, Tellez-Isaias G. Evaluation of the Antimicrobial and Anti-inflammatory Properties of Bacillus-DFM (Norum™) in Broiler Chickens Infected With Salmonella Enteritidis. Front Vet Sci 2019; 6:282. [PMID: 31508436 PMCID: PMC6718558 DOI: 10.3389/fvets.2019.00282] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 08/07/2019] [Indexed: 12/18/2022] Open
Abstract
Restrictions of in-feed antibiotics use in poultry has pushed research toward finding appropriate alternatives such as Direct-Fed Microbials (DFM). In this study, previously tested Bacillus isolates (B. subtilis and B. amyloliquefaciens) were used to evaluate their therapeutic and prophylactic effects against Salmonella enterica serovar Enteritidis (S. Enteritidis) in broiler chickens. For this purpose, initial antibacterial activity of Bacillus-DFM (104 spores/g or 106 spores/g) against S. Enteritidis colonization in crop, proventriculus and intestine was investigated using an in vitro digestive model. Furthermore, to evaluate therapeutic and prophylactic effects of Bacillus-DFM (104 spores/g) against S. Enteritidis colonization, altogether 60 (n = 30/group) and 30 (n = 15/group) 1-day-old broiler chickens were randomly allocated to either DFM or control group (without Bacillus-DFM), respectively. Chickens were orally gavaged with 104 cfu of S. Enteritidis per chicken at 1-day old, and cecal tonsils (CT) and crop were collected 3 and 10 days later during the therapeutic study, whereas they were orally gavaged with 107 cfu of S. Enteritidis per chicken at 6-day-old, and CT and crop were collected 24 h later from two independent trials during the prophylactic study. Serum superoxide dismutase (SOD), FITC-d and intestinal IgA levels were reported for both chicken studies, in addition cecal microbiota analysis was performed during the therapeutic study. DFM significantly reduced S. Enteritidis concentration in the intestine compartment, and in both proventriculus and intestine compartments as compared to the control when used at 104 spores/g and 106 spores/g, respectively (p < 0.05). DFM significantly reduced FITC-d and IgA as well as SOD and IgA levels (p < 0.05) compared to the control in therapeutic and prophylactic studies, respectively. Interestingly, in the therapeutic study, there were significant differences in bacterial community structure and predicted metabolic pathways between DFM and control. Likewise, phylum Actinobacteria and the genera Bifidobacterium, Roseburia, Proteus, and cc_115 were decreased, while the genus Streptococcus was enriched significantly in the DFM group as compared to the control (MetagenomeSeq, p < 0.05). Thus, the overall results suggest that the Bacillus-DFM can reduce S. Enteritidis colonization and improve the intestinal health in chickens through mechanism(s) that might involve the modulation of gut microbiota and their metabolic pathways.
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Affiliation(s)
- Bishnu Adhikari
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Daniel Hernandez-Patlan
- Unidad de Investigación Multidisciplinaria, Laboratorio 5: LEDEFAR, Facultad de Estudios Superiores (FES) Cuautitlán, Universidad Nacional Autónoma de México (UNAM), Cuautitlán Izcalli, Mexico
| | - Bruno Solis-Cruz
- Unidad de Investigación Multidisciplinaria, Laboratorio 5: LEDEFAR, Facultad de Estudios Superiores (FES) Cuautitlán, Universidad Nacional Autónoma de México (UNAM), Cuautitlán Izcalli, Mexico
| | - Young Min Kwon
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | | | - Juan D Latorre
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Xochitl Hernandez-Velasco
- Departamento de Medicina y Zootecnia de Aves, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Billy M Hargis
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
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56
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Splichal I, Donovan SM, Splichalova Z, Neuzil Bunesova V, Vlkova E, Jenistova V, Killer J, Svejstil R, Skrivanova E, Splichalova A. Colonization of Germ-Free Piglets with Commensal Lactobacillus amylovorus, Lactobacillus mucosae, and Probiotic E. coli Nissle 1917 and Their Interference with Salmonella Typhimurium. Microorganisms 2019; 7:microorganisms7080273. [PMID: 31434337 PMCID: PMC6722580 DOI: 10.3390/microorganisms7080273] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/09/2019] [Accepted: 08/19/2019] [Indexed: 01/12/2023] Open
Abstract
Non-typhoid Salmonellae are worldwide spread food-borne pathogens that cause diarrhea in humans and animals. Their multi-drug resistances require alternative ways to combat this enteric pathogen. Mono-colonization of a gnotobiotic piglet gastrointestinal tract with commensal lactobacilli Lactobacillus amylovorus and Lactobacillus mucosae and with probiotic E. coli Nissle 1917 and their interference with S. Typhimurium infection was compared. The impact of bacteria and possible protection against infection with Salmonella were evaluated by clinical signs, bacterial translocation, intestinal histology, mRNA expression of villin, claudin-1, claudin-2, and occludin in the ileum and colon, and local intestinal and systemic levels of inflammatory cytokines IL-8, TNF-α, and IL-10. Both lactobacilli colonized the gastrointestinal tract in approximately 100× lower density compare to E. coli Nissle and S. Typhimurium. Neither L. amylovorus nor L. mucosae suppressed the inflammatory reaction caused by the 24 h infection with S. Typhimurium. In contrast, probiotic E. coli Nissle 1917 was able to suppress clinical signs, histopathological changes, the transcriptions of the proteins, and the inductions of the inflammatory cytokines. Future studies are needed to determine whether prebiotic support of the growth of lactobacilli and multistrain lactobacilli inoculum could show higher protective effects.
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Affiliation(s)
- Igor Splichal
- Laboratory of Gnotobiology, Institute of Microbiology, Czech Academy of Sciences, 549 22 Novy Hradek, Czech Republic
| | - Sharon M Donovan
- Department of Food Science and Human Nutrition, University of Illinois, Urbana, IL 61801, USA
| | - Zdislava Splichalova
- Laboratory of Gnotobiology, Institute of Microbiology, Czech Academy of Sciences, 549 22 Novy Hradek, Czech Republic
| | - Vera Neuzil Bunesova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, 165 00 Prague, Czech Republic
| | - Eva Vlkova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, 165 00 Prague, Czech Republic
| | - Vera Jenistova
- Laboratory of Gnotobiology, Institute of Microbiology, Czech Academy of Sciences, 549 22 Novy Hradek, Czech Republic
| | - Jiri Killer
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, 165 00 Prague, Czech Republic
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Roman Svejstil
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, 165 00 Prague, Czech Republic
| | - Eva Skrivanova
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, 165 00 Prague, Czech Republic
| | - Alla Splichalova
- Laboratory of Gnotobiology, Institute of Microbiology, Czech Academy of Sciences, 549 22 Novy Hradek, Czech Republic.
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57
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Stringlis IA, de Jonge R, Pieterse CMJ. The Age of Coumarins in Plant-Microbe Interactions. PLANT & CELL PHYSIOLOGY 2019; 60:1405-1419. [PMID: 31076771 PMCID: PMC6915228 DOI: 10.1093/pcp/pcz076] [Citation(s) in RCA: 144] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Accepted: 04/23/2019] [Indexed: 05/05/2023]
Abstract
Coumarins are a family of plant-derived secondary metabolites that are produced via the phenylpropanoid pathway. In the past decade, coumarins have emerged as iron-mobilizing compounds that are secreted by plant roots and aid in iron uptake from iron-deprived soils. Members of the coumarin family are found in many plant species. Besides their role in iron uptake, coumarins have been extensively studied for their potential to fight infections in both plants and animals. Coumarin activities range from antimicrobial and antiviral to anticoagulant and anticancer. In recent years, studies in the model plant species tobacco and Arabidopsis have significantly increased our understanding of coumarin biosynthesis, accumulation, secretion, chemical modification and their modes of action against plant pathogens. Here, we review current knowledge on coumarins in different plant species. We focus on simple coumarins and provide an overview on their biosynthesis and role in environmental stress responses, with special attention for the recently discovered semiochemical role of coumarins in aboveground and belowground plant-microbe interactions and the assembly of the root microbiome.
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Affiliation(s)
- Ioannis A Stringlis
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
- Corresponding author: E-mail, ; Fax,+31 30 253 2837
| | - Ronnie de Jonge
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Corn� M J Pieterse
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
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58
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Auguste M, Lasa A, Pallavicini A, Gualdi S, Vezzulli L, Canesi L. Exposure to TiO 2 nanoparticles induces shifts in the microbiota composition of Mytilus galloprovincialis hemolymph. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 670:129-137. [PMID: 30903888 DOI: 10.1016/j.scitotenv.2019.03.133] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/07/2019] [Accepted: 03/09/2019] [Indexed: 06/09/2023]
Abstract
It is now recognized that host microbiome, the community of microorganisms that colonize the animal body (e.g. microbiota) and their genomes, play an important role in the health status of all organisms, from nutrient processing to protection from disease. In particular, the complex, bilateral interactions between the host innate immune system and the microbiota are crucial in maintaining whole body homeostasis. The development of nanotechnology is raising concern on the potential impact of nanoparticles-NPs on human and environmental health. Titanium dioxide-nTiO2, one of the most widely NP in use, has been shown to affect the gut microbiota of mammals and fish, as well as to potentially alter microbial communities. In the marine bivalve Mytilus galloprovincialis, nTiO2 has been previously shown to interact with hemolymph components, thus resulting in immunomodulation. However, no information is available on the possible impact of NPs on the microbiome of marine organisms. Bivalves host high microbial abundance and diversity, and alteration of their microbiota, in both tissues and hemolymph, in response to stressful conditions has been linked to a compromised health status and susceptibility to diseases. In this work, the effects of nTiO2 exposure (100 μg/L, 4 days) on Mytilus hemolymph microbiota were investigated by 16S rRNA gene-based profiling. Immune parameters were also evaluated. Although hemolymph microbiota of control and nTiO2-treated mussels revealed a similar core composition, nTiO2 exposure affected the abundance of different genera, with decreases in some (e.g. Shewanella, Kistimonas, Vibrio) and increases in others (e.g. Stenotrophomonas). The immunomodulatory effects of nTiO2 were confirmed by the increase in the bactericidal activity of whole hemolymph. These represent the first data on the effects of NPs on the microbiome of marine invertebrates, and suggest that the shift in hemolymph microbiome composition induced by nTiO2 may result from the interplay between the microbiota and the immune system.
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Affiliation(s)
- Manon Auguste
- DISTAV, Dept. of Environmental, Earth and Life Sciences, University of Genoa, Italy.
| | - Aide Lasa
- DISTAV, Dept. of Environmental, Earth and Life Sciences, University of Genoa, Italy; Department of Microbiology and Parasitology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | | | - Stefano Gualdi
- Department of Plant and Microbial Biology, University of Zürich, Switzerland
| | - Luigi Vezzulli
- DISTAV, Dept. of Environmental, Earth and Life Sciences, University of Genoa, Italy
| | - Laura Canesi
- DISTAV, Dept. of Environmental, Earth and Life Sciences, University of Genoa, Italy
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59
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Vamanu E. Polyphenolic Nutraceuticals to Combat Oxidative Stress Through Microbiota Modulation. Front Pharmacol 2019; 10:492. [PMID: 31130865 PMCID: PMC6509743 DOI: 10.3389/fphar.2019.00492] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 04/18/2019] [Indexed: 01/26/2023] Open
Abstract
Due to their direct relationship with the activity of the gut microbiota, nutraceuticals are, at present, an effective alternative for the mitigation and alleviation of the dysfunctions governed by oxidative stress. The escalation in the number of the target group patients (diabetes, cardiovascular dysfunction, cancer, etc.) has spurred the quest for alternative action methods. The therapeutic value is determined through in vitro and in vivo methods, and involves the analysis of the therapeutic index. As the adverse outcomes are decreased, the pharmacological potential is assessed by the mechanisms, including biotransformation and the identification of the relevant biomarkers. Inflammatory action is among the principal effects that need to be reduced because it favors the presence of free radicals and dysbiosis. This article aimed at highlighting the action of the nutraceuticals in minimizing the oxidative stress by directly influencing the microbiota and slowing down the inflammatory progression. The pharmacological aspects as a therapeutic indicator of the use of nutraceuticals in improving the population health.
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Affiliation(s)
- Emanuel Vamanu
- Faculty of Biotechnology, University of Agronomic Sciences and Veterinary Medicine of Bucharest, Bucharest, Romania
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60
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New frontiers in agriculture productivity: Optimised microbial inoculants and in situ microbiome engineering. Biotechnol Adv 2019; 37:107371. [PMID: 30890361 DOI: 10.1016/j.biotechadv.2019.03.010] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 02/20/2019] [Accepted: 03/11/2019] [Indexed: 01/07/2023]
Abstract
Increasing agricultural productivity is critical to feed the ever-growing human population. Being linked intimately to plant health, growth and productivity, harnessing the plant microbiome is considered a potentially viable approach for the next green revolution, in an environmentally sustainable way. In recent years, our understanding of drivers, roles, mechanisms, along with knowledge to manipulate the plant microbiome, have significantly advanced. Yet, translating this knowledge to expand farm productivity and sustainability requires the development of solutions for a number of technological and logistic challenges. In this article, we propose new and emerging strategies to improve the survival and activity of microbial inoculants, including using selected indigenous microbes and optimising microbial delivery methods, as well as modern gene editing tools to engineer microbial inoculants. In addition, we identify multiple biochemical and molecular mechanisms and/approaches which can be exploited for microbiome engineering in situ to optimise plant-microbiome interactions for improved farm yields. These novel biotechnological approaches can provide effective tools to attract and maintain activities of crop beneficial microbiota that increase crop performance in terms of nutrient acquisition, and resistance to biotic and abiotic stresses, resulting in an increased agricultural productivity and sustainability.
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61
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Probiotics and Prebiotics for the Amelioration of Type 1 Diabetes: Present and Future Perspectives. Microorganisms 2019; 7:microorganisms7030067. [PMID: 30832381 PMCID: PMC6463158 DOI: 10.3390/microorganisms7030067] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 02/19/2019] [Accepted: 02/25/2019] [Indexed: 12/18/2022] Open
Abstract
Type 1-diabetes (T1D) is an autoimmune disease characterized by immune-mediated destruction of pancreatic beta (β)-cells. Genetic and environmental interactions play an important role in immune system malfunction by priming an aggressive adaptive immune response against β-cells. The microbes inhabiting the human intestine closely interact with the enteric mucosal immune system. Gut microbiota colonization and immune system maturation occur in parallel during early years of life; hence, perturbations in the gut microbiota can impair the functions of immune cells and vice-versa. Abnormal gut microbiota perturbations (dysbiosis) are often detected in T1D subjects, particularly those diagnosed as multiple-autoantibody-positive as a result of an aggressive and adverse immunoresponse. The pathogenesis of T1D involves activation of self-reactive T-cells, resulting in the destruction of β-cells by CD8⁺ T-lymphocytes. It is also becoming clear that gut microbes interact closely with T-cells. The amelioration of gut dysbiosis using specific probiotics and prebiotics has been found to be associated with decline in the autoimmune response (with diminished inflammation) and gut integrity (through increased expression of tight-junction proteins in the intestinal epithelium). This review discusses the potential interactions between gut microbiota and immune mechanisms that are involved in the progression of T1D and contemplates the potential effects and prospects of gut microbiota modulators, including probiotic and prebiotic interventions, in the amelioration of T1D pathology, in both human and animal models.
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Ikeda-Ohtsubo W, Brugman S, Warden CH, Rebel JMJ, Folkerts G, Pieterse CMJ. How Can We Define "Optimal Microbiota?": A Comparative Review of Structure and Functions of Microbiota of Animals, Fish, and Plants in Agriculture. Front Nutr 2018; 5:90. [PMID: 30333981 PMCID: PMC6176000 DOI: 10.3389/fnut.2018.00090] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 09/07/2018] [Indexed: 12/21/2022] Open
Abstract
All multicellular organisms benefit from their own microbiota, which play important roles in maintaining the host nutritional health and immunity. Recently, the number of studies on the microbiota of animals, fish, and plants of economic importance is rapidly expanding and there are increasing expectations that productivity and sustainability in agricultural management can be improved by microbiota manipulation. However, optimizing microbiota is still a challenging task because of the lack of knowledge on the dominant microorganisms or significant variations between microbiota, reflecting sampling biases, different agricultural management as well as breeding backgrounds. To offer a more generalized view on microbiota in agriculture, which can be used for defining criteria of “optimal microbiota” as the goal of manipulation, we summarize here current knowledge on microbiota on animals, fish, and plants with emphasis on bacterial community structure and metabolic functions, and how microbiota can be affected by domestication, conventional agricultural practices, and use of antimicrobial agents. Finally, we discuss future tasks for defining “optimal microbiota,” which can improve host growth, nutrition, and immunity and reduce the use of antimicrobial agents in agriculture.
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Affiliation(s)
- Wakako Ikeda-Ohtsubo
- Laboratory of Animal Products Chemistry, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Sylvia Brugman
- Cell Biology and Immunology Group, Wageningen University and Research, Wageningen, Netherlands
| | - Craig H Warden
- Departments of Pediatrics, Neurobiology Physiology and Behavior, University of California, Davis, Davis, CA, United States
| | - Johanna M J Rebel
- Wageningen Livestock Research, Wageningen University and Research, Wageningen, Netherlands
| | - Gert Folkerts
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Corné M J Pieterse
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, Netherlands
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