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Burguet P, La Rocca R, Kune C, Tellatin D, Stulanovic N, Rigolet A, Far J, Ongena M, Rigali S, Quinton L. Exploiting Differential Signal Filtering (DSF) and Image Structure Filtering (ISF) Methods for Untargeted Mass Spectrometry Imaging of Bacterial Metabolites. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1743-1755. [PMID: 39007645 DOI: 10.1021/jasms.4c00129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) is a label-free technique, producing images where pixels contain mass spectra. The technique allows the visualization of the spatial distribution of (bio)molecules from metabolites to proteins, on surfaces such as tissues sections or bacteria culture media. One particularly exciting example of MALDI-MSI use rests on its potential to localize ionized compounds produced during microbial interactions and chemical communication, offering a molecular snapshot of metabolomes at a given time. The huge size and the complexity of generated MSI data make the processing of the data challenging, which requires the use of computational methods. Despite recent advances, currently available commercial software relies mainly on statistical tools to identify patterns, similarities, and differences within data sets. However, grouping m/z values unique to a given data set according to microbiological contexts, such as coculture experiments, still requires tedious manual analysis. Here we propose a nontargeted method exploiting the differential signals between negative controls and tested experimental conditions, i.e., differential signal filtering (DSF), and a scoring of the ion images using image structure filtering (ISF) coupled with a fold change score between the controls and the conditions of interest. These methods were first applied to coculture experiments involving Escherichia coli and Streptomyces coelicolor, revealing specific MS signals during bacterial interaction. Two case studies were also investigated: (i) cellobiose-mediated induction for the pathogenicity of Streptomyces scabiei, the causative agent of common scab on root and tuber crops, and (ii) iron-repressed production of siderophores of S. scabiei. This report proposes guidelines for MALDI-MSI data treatment applied in the case of microbiology contexts, with enhanced ion peak annotation in specific culture conditions. The strengths and weaknesses of the methods are discussed.
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Affiliation(s)
- Pierre Burguet
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, 4000 Liège, Belgium
| | - Raphaël La Rocca
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, 4000 Liège, Belgium
| | - Christopher Kune
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, 4000 Liège, Belgium
| | - Déborah Tellatin
- InBioS - Center for Protein Engineering, University of Liège, 4000 Liège, Belgium
| | - Nudzejma Stulanovic
- InBioS - Center for Protein Engineering, University of Liège, 4000 Liège, Belgium
| | - Augustin Rigolet
- Gembloux Agro-Bio Tech, University of Liege, 5030 Gembloux, Belgium
| | - Johann Far
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, 4000 Liège, Belgium
| | - Marc Ongena
- Gembloux Agro-Bio Tech, University of Liege, 5030 Gembloux, Belgium
| | - Sébastien Rigali
- InBioS - Center for Protein Engineering, University of Liège, 4000 Liège, Belgium
| | - Loïc Quinton
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, 4000 Liège, Belgium
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Pospíšil J, Sax A, Hubálek M, Krásný L, Vohradský J. Whole proteome analysis of germinating and outgrowing Bacillus subtilis 168. Proteomics 2024:e2400031. [PMID: 39044338 DOI: 10.1002/pmic.202400031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 05/21/2024] [Accepted: 07/08/2024] [Indexed: 07/25/2024]
Abstract
In this study, we present a high-resolution dataset and bioinformatic analysis of the proteome of Bacillus subtilis 168 trp+ (BSB1) during germination and spore outgrowth. Samples were collected at 14 different time points (ranging from 0 to 130 min) in three biological replicates after spore inoculation into germination medium. A total of 2191 proteins were identified and categorized based on their expression kinetics. We observed four distinct clusters that were analyzed for functional categories and KEGG pathways annotations. The examination of newly synthesized proteins between successive time points revealed significant changes, particularly within the first 50 min. The dataset provides an information base that can be used for modeling purposes and inspire the design of new experiments.
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Affiliation(s)
- Jiří Pospíšil
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague 4, Czech Republic
| | - Alice Sax
- Laboratory of Bioinformatics, Institute of Microbiology of the Czech Academy of Sciences, Prague 4, Czech Republic
| | - Martin Hubálek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, Czech Republic
| | - Libor Krásný
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague 4, Czech Republic
| | - Jiří Vohradský
- Laboratory of Bioinformatics, Institute of Microbiology of the Czech Academy of Sciences, Prague 4, Czech Republic
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3
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Montgomery VA, Wood‐Yang AJ, Styczynski MP, Prausnitz MR. Feasibility of engineered Bacillus subtilis for use as a microbiome-based topical drug delivery platform. Bioeng Transl Med 2024; 9:e10645. [PMID: 39036074 PMCID: PMC11256169 DOI: 10.1002/btm2.10645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 12/08/2023] [Accepted: 12/18/2023] [Indexed: 07/23/2024] Open
Abstract
Non-adherence to medication is a major challenge in healthcare that results in worsened treatment outcomes for patients. Reducing the frequency of required administrations could improve adherence but is challenging for topical drug delivery due to the generally short residence time of topical formulations on the skin. In this study, we sought to determine the feasibility of developing a microbiome-based, long-acting, topical delivery platform using Bacillus subtilis for drug production and delivery on the skin, which was assessed using green fluorescent protein as a model heterologous protein for delivery. We developed a computational model of bacteria population dynamics on the skin and used its qualitative predictions to guide experimental design choices. Using an ex vivo pig skin model and a human skin tissue culture model, we saw persistence of delivered bacteria for multiple days and observed little evidence of cytotoxicity to human keratinocyte cells in vitro. Finally, using an in vivo mouse model, we found that the delivered bacteria persisted on the skin for at least 1 day during every-other-day application and did not appear to present safety concerns. Taken together, our results support the feasibility of using engineered B. subtilis for topical drug delivery.
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Affiliation(s)
- Veronica A. Montgomery
- Wallace H. Coulter Department of Biomedical Engineering at Emory University and Georgia TechGeorgia Institute of TechnologyAtlantaGeorgiaUSA
| | - Amy J. Wood‐Yang
- School of Chemical and Biomolecular EngineeringGeorgia Institute of TechnologyAtlantaGeorgiaUSA
| | - Mark P. Styczynski
- School of Chemical and Biomolecular EngineeringGeorgia Institute of TechnologyAtlantaGeorgiaUSA
| | - Mark R. Prausnitz
- Wallace H. Coulter Department of Biomedical Engineering at Emory University and Georgia TechGeorgia Institute of TechnologyAtlantaGeorgiaUSA
- School of Chemical and Biomolecular EngineeringGeorgia Institute of TechnologyAtlantaGeorgiaUSA
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Dhamodiran M, Chinnaperumal K, J D, Venkatesan G, A Alshiekheid M, Suseem SR. Isolation, structural elucidation of bioactive compounds and their wound-healing ability, antibacterial and In silico molecular docking applications. ENVIRONMENTAL RESEARCH 2024; 252:119023. [PMID: 38685295 DOI: 10.1016/j.envres.2024.119023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/13/2024] [Accepted: 04/24/2024] [Indexed: 05/02/2024]
Abstract
Andrographis echioides has been extensively utilized in traditional Indian folk medicines for several skin disorders and other biological actions such as diuretic, antimicrobial, anthelmintic, anti-ulcer, and hepatoprotective properties. Different crude extracts were extracted from A. echioides leaves using various solvents such as methanol and water. The prepared crude extracts were utilized to formulate different herbal ointments. Further, the prepared ointments were examined against wounds and bacterial pathogens. The wound healing ability of the prepared formulations was observed for F1, F2, and F3, to be (89.84%, 95.11%, and 95.75%) respectively. Moreover, wound healing capabilities were compared with standard Betadine which exhibits 98.12%, those results indicating that the prepared herbal ointment also has a promising wound healing ability. The F2 formulations outperform the other two formulations (F1 and F2) in terms of their antibacterial ability to combat Staphylococcus aureus, Klebsiella pneumoniae Bacillus subtilis, and Escherichia coli. Moreover, there are two compounds were successfully isolated and identified from methanolic extract, which are 2-(3,4-dihydroxyphenyl)-3,4-dihydro-2H-chromene-3,5,7-triol and 3-(3,4-Dihydroxyphenyl)-2-propenoic acid. Meanwhile, the molecular docking investigation exposed high binding energy Staphylococcus aureus TyrRS (-8.9 kcal/mol), Isoleucyl-tRNA synthetase (-7.5 kcal/mol), Penicillin-binding protein 2a (-8.0 kcal/mol), S. aureus DNA Gyrase (-7.2 kcal/mol), GSK-3beta (Glycogen synthase kinase-3 beta) (-8.3 kcal/mol) and TGF - Beta Receptor Type 1 Kinase Domain (-8.7 kcal/mol) indicating high degree of interaction between Compound-1 2-(3,4-dihydroxyphenyl)-3,4-dihydro-2H-chromene-3,5,7-triol (DHPDHC) and 7 clinically important skin infective pathogen Staphylococcus aureus proteins at the active sites. Additionally, the standard drug Povidone iodine, Sulphothiazole, and Nitrofurazone (<-8 kcal/mol), displayed low binding affinity on targeted proteins. A molecular dynamics simulation research with high free energy showed stable interaction between the ligand and protein. Which endorses the capabilities of A. echioides derived compounds as a potential wound healer and antibacterial therapeutic candidate for drug development in the future.
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Affiliation(s)
- Mathivanan Dhamodiran
- Department of Chemistry, School of Advanced Sciences, VIT University, Vellore, 632014, Tamil Nadu, India
| | - Kamaraj Chinnaperumal
- Interdisciplinary Institute of Indian System of Medicine (IIISM), Directorate of Research, SRM Institute of Science and Technology (SRMIST), Chengalpattu District, Kattankulathur, 603203, Tamil Nadu, India.
| | - Dhanish J
- Department of Chemistry, School of Advanced Sciences, VIT University, Vellore, 632014, Tamil Nadu, India
| | - Geetha Venkatesan
- Department of Biomaterials, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, 600 077, India
| | - Maha A Alshiekheid
- Department of Botany and Microbiology, College of Science, King Saud University, PO Box -2455, Riyadh - 11451, Saudi Arabia
| | - S R Suseem
- Department of Chemistry, School of Advanced Sciences, VIT University, Vellore, 632014, Tamil Nadu, India.
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Dorfan Y, Nahami A, Morris Y, Shohat B, Kolodkin-Gal I. The Utilization of Bacillus subtilis to Design Environmentally Friendly Living Paints with Anti-Mold Properties. Microorganisms 2024; 12:1226. [PMID: 38930607 PMCID: PMC11205451 DOI: 10.3390/microorganisms12061226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/31/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
The anti-fungal properties of the probiotic bacterium Bacillus subtilis have been studied extensively in agriculture and ecology, but their applications in the built environment remain to be determined. Our work aims to utilize this biological component to introduce new diverse anti-mold properties into paint. "Mold" refers to the ubiquitous fungal species that generate visible multicellular filaments commonly found in household dust. The development of mold leads to severe health problems for occupants, including allergic response, hypersensitivity pneumonitis, and asthma, which have significant economic and clinical outcomes. We here demonstrate the robust effect of a commercial paint enhanced with Bacillus subtilis cells against the common mold agent, Aspergillus niger, and identify three biosynthetic clusters essential for this effect. Our results lay the foundation for bio-convergence and synthetic biology approaches to introduce renewable and environmentally friendly bio-anti-fungal agents into the built environment.
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Affiliation(s)
- Yuval Dorfan
- Faculty of Electrical Engineering, Holon Institute of Technology, Holon 5810201, Israel; (A.N.); (B.S.)
| | - Avichay Nahami
- Faculty of Electrical Engineering, Holon Institute of Technology, Holon 5810201, Israel; (A.N.); (B.S.)
- The Scojen Institute for Synthetic Biology, Reichman University, Herzliya 4610101, Israel
| | - Yael Morris
- Faculty of Electrical Engineering, Holon Institute of Technology, Holon 5810201, Israel; (A.N.); (B.S.)
| | - Benny Shohat
- Faculty of Electrical Engineering, Holon Institute of Technology, Holon 5810201, Israel; (A.N.); (B.S.)
| | - Ilana Kolodkin-Gal
- The Scojen Institute for Synthetic Biology, Reichman University, Herzliya 4610101, Israel
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Del'Duca A, de Paiva Oliveira GF, de Andrade Faustino M, Borges LA, Sixel ES, Miranda CAS, Rodrigues EM, Medeiros JD, de Sá Guimarães A, Mendonça LC, Cesar DE. Biocontrol capacity of bacteria isolated from sawdust of the dairy cattle production environment. Res Vet Sci 2024; 166:105103. [PMID: 38061143 DOI: 10.1016/j.rvsc.2023.105103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/29/2023] [Accepted: 12/01/2023] [Indexed: 01/01/2024]
Abstract
This research paper aimed to find endemic bacteria from the cattle production system to control the growth of mastitis pathogens. Bacteria were isolated from compost barn sawdust of two dairy cattle systems and later tested to verify their ability to control the growth of Staphylococcus aureus isolates obtained from cattle with mastitis. Bacterial isolates from these systems were tested to verify biocontrol capacity using the double-layer method. A total of 189 isolates were obtained from all samples by considering the morphology of the different bacterial colonies, with 30 isolates showing positive results for the growth control of at least one S. aureus strain and 19 isolates showing the ability to control more than one pathogen strain. The ability to control more than one pathogen and present a significant halo of inhibition in our isolates represents positive traits in the search for cattle mastitis biocontrol microorganisms. Thus, the results obtained represent the range of bacteria capable of controlling the pathogens without the use of antibiotics.
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Wang Z, Zhu H, Xiong W. Advances in mass spectrometry-based multi-scale metabolomic methodologies and their applications in biological and clinical investigations. Sci Bull (Beijing) 2023; 68:2268-2284. [PMID: 37666722 DOI: 10.1016/j.scib.2023.08.047] [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: 06/15/2023] [Revised: 07/25/2023] [Accepted: 08/22/2023] [Indexed: 09/06/2023]
Abstract
Metabolomics is a nascent field of inquiry that emerged in the late 20th century. It encompasses the comprehensive profiling of metabolites across a spectrum of organisms, ranging from bacteria and cells to tissues. The rapid evolution of analytical methods and data analysis has greatly accelerated progress in this dynamic discipline over recent decades. Sophisticated techniques such as liquid chromatograph mass spectrometry (MS), gas chromatograph MS, capillary electrophoresis MS, and nuclear magnetic resonance serve as the cornerstone of metabolomic analysis. Building upon these methods, a plethora of modifications and combinations have emerged to propel the advancement of metabolomics. Despite this progress, scrutinizing metabolism at the single-cell or single-organelle level remains an arduous task over the decades. Some of the most thrilling advancements, such as single-cell and single-organelle metabolic profiling techniques, offer profound insights into the intricate mechanisms within cells and organelles. This allows for a comprehensive study of metabolic heterogeneity and its pivotal role in multiple biological processes. The progress made in MS imaging has enabled high-resolution in situ metabolic profiling of tissue sections and even individual cells. Spatial reconstruction techniques enable the direct representation of metabolic distribution and alteration in three-dimensional space. The application of novel metabolomic techniques has led to significant breakthroughs in biological and clinical studies, including the discovery of novel metabolic pathways, determination of cell fate in differentiation, anti-aging intervention through modulating metabolism, metabolomics-based clinicopathologic analysis, and surgical decision-making based on on-site intraoperative metabolic analysis. This review presents a comprehensive overview of both conventional and innovative metabolomic techniques, highlighting their applications in groundbreaking biological and clinical studies.
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Affiliation(s)
- Ziyi Wang
- Department of Neurology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
| | - Hongying Zhu
- Department of Neurology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China; Anhui Province Key Laboratory of Biomedical Imaging and Intelligent Processing, Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China; CAS Key Laboratory of Brain Function and Disease, Hefei 230026, China; Anhui Province Key Laboratory of Biomedical Aging Research, Hefei 230026, China.
| | - Wei Xiong
- Department of Neurology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China; Anhui Province Key Laboratory of Biomedical Imaging and Intelligent Processing, Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China; CAS Key Laboratory of Brain Function and Disease, Hefei 230026, China; Anhui Province Key Laboratory of Biomedical Aging Research, Hefei 230026, China.
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Parker GD, Hanley L, Yu XY. Mass Spectral Imaging to Map Plant-Microbe Interactions. Microorganisms 2023; 11:2045. [PMID: 37630605 PMCID: PMC10459445 DOI: 10.3390/microorganisms11082045] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/23/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Plant-microbe interactions are of rising interest in plant sustainability, biomass production, plant biology, and systems biology. These interactions have been a challenge to detect until recent advancements in mass spectrometry imaging. Plants and microbes interact in four main regions within the plant, the rhizosphere, endosphere, phyllosphere, and spermosphere. This mini review covers the challenges within investigations of plant and microbe interactions. We highlight the importance of sample preparation and comparisons among time-of-flight secondary ion mass spectroscopy (ToF-SIMS), matrix-assisted laser desorption/ionization (MALDI), laser desorption ionization (LDI/LDPI), and desorption electrospray ionization (DESI) techniques used for the analysis of these interactions. Using mass spectral imaging (MSI) to study plants and microbes offers advantages in understanding microbe and host interactions at the molecular level with single-cell and community communication information. More research utilizing MSI has emerged in the past several years. We first introduce the principles of major MSI techniques that have been employed in the research of microorganisms. An overview of proper sample preparation methods is offered as a prerequisite for successful MSI analysis. Traditionally, dried or cryogenically prepared, frozen samples have been used; however, they do not provide a true representation of the bacterial biofilms compared to living cell analysis and chemical imaging. New developments such as microfluidic devices that can be used under a vacuum are highly desirable for the application of MSI techniques, such as ToF-SIMS, because they have a subcellular spatial resolution to map and image plant and microbe interactions, including the potential to elucidate metabolic pathways and cell-to-cell interactions. Promising results due to recent MSI advancements in the past five years are selected and highlighted. The latest developments utilizing machine learning are captured as an important outlook for maximal output using MSI to study microorganisms.
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Affiliation(s)
- Gabriel D. Parker
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA
| | - Luke Hanley
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA
| | - Xiao-Ying Yu
- Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
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Gasparek M, Steel H, Papachristodoulou A. Deciphering mechanisms of production of natural compounds using inducer-producer microbial consortia. Biotechnol Adv 2023; 64:108117. [PMID: 36813010 DOI: 10.1016/j.biotechadv.2023.108117] [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: 07/21/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/22/2023]
Abstract
Living organisms produce a wide range of metabolites. Because of their potential antibacterial, antifungal, antiviral, or cytostatic properties, such natural molecules are of high interest to the pharmaceutical industry. In nature, these metabolites are often synthesized via secondary metabolic biosynthetic gene clusters that are silent under the typical culturing conditions. Among different techniques used to activate these silent gene clusters, co-culturing of "producer" species with specific "inducer" microbes is a particularly appealing approach due to its simplicity. Although several "inducer-producer" microbial consortia have been reported in the literature and hundreds of different secondary metabolites with attractive biopharmaceutical properties have been described as a result of co-cultivating inducer-producer consortia, less attention has been devoted to the understanding of the mechanisms and possible means of induction for production of secondary metabolites in co-cultures. This lack of understanding of fundamental biological functions and inter-species interactions significantly limits the diversity and yield of valuable compounds using biological engineering tools. In this review, we summarize and categorize the known physiological mechanisms of production of secondary metabolites in inducer-producer consortia, and then discuss approaches that could be exploited to optimize the discovery and production of secondary metabolites.
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Affiliation(s)
- Miroslav Gasparek
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, United Kingdom.
| | - Harrison Steel
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, United Kingdom
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Wang Y, Xu Y, Cao G, Zhou X, Wang Q, Fu A, Zhan X. Bacillus subtilis DSM29784 attenuates Clostridium perfringens-induced intestinal damage of broilers by modulating intestinal microbiota and the metabolome. Front Microbiol 2023; 14:1138903. [PMID: 37007491 PMCID: PMC10060821 DOI: 10.3389/fmicb.2023.1138903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 02/22/2023] [Indexed: 03/18/2023] Open
Abstract
Necrotic enteritis (NE), especially subclinical NE (SNE), without clinical symptoms, in chicks has become one of the most threatening problems to the poultry industry. Therefore, increasing attention has been focused on the research and application of effective probiotic strains as an alternative to antibiotics to prevent SNE in broilers. In the present study, we evaluated the effects of Bacillus subtilis DSM29784 (BS) on the prevention of subclinical necrotic enteritis (SNE) in broilers. A total of 480 1-day-old broiler chickens were randomly assigned to four dietary treatments, each with six replicates pens of twenty birds for 63 d. The negative (Ctr group) and positive (SNE group) groups were only fed a basal diet, while the two treatment groups received basal diets supplemented with BS (1 × 109 colony-forming units BS/kg) (BS group) and 10mg/kg enramycin (ER group), respectively. On days 15, birds except those in the Ctr group were challenged with 20-fold dose coccidiosis vaccine, and then with 1 ml of C. perfringens (2 × 108) at days 18 to 21 for SNE induction. BS, similar to ER, effectively attenuated CP-induced poor growth performance. Moreover, BS pretreatment increased villi height, claudin-1 expression, maltase activity, and immunoglobulin abundance, while decreasing lesional scores, as well as mucosal IFN-γ and TNF-α concentrations. In addition, BS pretreatment increased the relative abundance of beneficial bacteria and decreased that of pathogenic species; many lipid metabolites were enriched in the cecum of treated chickens. These results suggest that BS potentially provides active ingredients that may serve as an antibiotic substitute, effectively preventing SNE-induced growth decline by enhancing intestinal health in broilers.
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Affiliation(s)
- Yuanyuan Wang
- Key Laboratory of Molecular Animal Nutrition of the Ministry of Education, College of Animal Sciences, Institute of Feed Science, Zhejiang University, Hangzhou, China
| | - Yibin Xu
- Key Laboratory of Molecular Animal Nutrition of the Ministry of Education, College of Animal Sciences, Institute of Feed Science, Zhejiang University, Hangzhou, China
| | | | - Xihong Zhou
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Qian Wang
- Yancheng Biological Engineering Higher Vocational Technology School, Yancheng, China
| | - Aikun Fu
- Key Laboratory of Molecular Animal Nutrition of the Ministry of Education, College of Animal Sciences, Institute of Feed Science, Zhejiang University, Hangzhou, China
- *Correspondence: Xiuan Zhan, ; Aikun Fu,
| | - Xiuan Zhan
- Key Laboratory of Molecular Animal Nutrition of the Ministry of Education, College of Animal Sciences, Institute of Feed Science, Zhejiang University, Hangzhou, China
- *Correspondence: Xiuan Zhan, ; Aikun Fu,
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Bioinformatics Approaches Applied to the Discovery of Antifungal Peptides. Antibiotics (Basel) 2023; 12:antibiotics12030566. [PMID: 36978434 PMCID: PMC10044696 DOI: 10.3390/antibiotics12030566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 03/06/2023] [Accepted: 03/09/2023] [Indexed: 03/16/2023] Open
Abstract
Antifungal peptides (AFPs) comprise a group of substances with a broad spectrum of activities and complex action mechanisms. They develop in nature via an evolutionary process resulting from the interactions between hosts and pathogens. The AFP database is experimentally verified and curated from research articles, patents, and public databases. In this review, we compile information about the primary databases and bioinformatics tools that have been used in the discovery of AFPs during the last 15 years. We focus on the classification and prediction of AFPs using different physicochemical properties, such as polarity, hydrophobicity, hydrophilicity, mass, acidic, basic, and isoelectric indices, and other structural properties. Another method for discovering AFPs is the implementation of a peptidomic approach and bioinformatics filtering, which gave rise to a new family of peptides that exhibit a broad spectrum of antimicrobial activity against Candida albicans with low hemolytic effects. The application of machine intelligence in the sphere of biological sciences has led to the development of automated tools. The progress made in this area has also paved the way for producing new drugs more quickly and effectively. However, we also identified that further advancements are still needed to complete the AFP libraries.
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Luyet C, Elvati P, Vinh J, Violi A. Low-THz Vibrations of Biological Membranes. MEMBRANES 2023; 13:membranes13020139. [PMID: 36837641 PMCID: PMC9965665 DOI: 10.3390/membranes13020139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/04/2023] [Accepted: 01/17/2023] [Indexed: 05/12/2023]
Abstract
A growing body of work has linked key biological activities to the mechanical properties of cellular membranes, and as a means of identification. Here, we present a computational approach to simulate and compare the vibrational spectra in the low-THz region for mammalian and bacterial membranes, investigating the effect of membrane asymmetry and composition, as well as the conserved frequencies of a specific cell. We find that asymmetry does not impact the vibrational spectra, and the impact of sterols depends on the mobility of the components of the membrane. We demonstrate that vibrational spectra can be used to distinguish between membranes and, therefore, could be used in identification of different organisms. The method presented, here, can be immediately extended to other biological structures (e.g., amyloid fibers, polysaccharides, and protein-ligand structures) in order to fingerprint and understand vibrations of numerous biologically-relevant nanoscale structures.
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Affiliation(s)
- Chloe Luyet
- Chemical Engineering, University of Michigan, Ann Arbor, MI 48109-2125, USA
| | - Paolo Elvati
- Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109-2125, USA
| | - Jordan Vinh
- Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109-2125, USA
| | - Angela Violi
- Chemical Engineering, University of Michigan, Ann Arbor, MI 48109-2125, USA
- Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109-2125, USA
- Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109-2125, USA
- Correspondence:
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Sahayasheela VJ, Lankadasari MB, Dan VM, Dastager SG, Pandian GN, Sugiyama H. Artificial intelligence in microbial natural product drug discovery: current and emerging role. Nat Prod Rep 2022; 39:2215-2230. [PMID: 36017693 PMCID: PMC9931531 DOI: 10.1039/d2np00035k] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Covering: up to the end of 2022Microorganisms are exceptional sources of a wide array of unique natural products and play a significant role in drug discovery. During the golden era, several life-saving antibiotics and anticancer agents were isolated from microbes; moreover, they are still widely used. However, difficulties in the isolation methods and repeated discoveries of the same molecules have caused a setback in the past. Artificial intelligence (AI) has had a profound impact on various research fields, and its application allows the effective performance of data analyses and predictions. With the advances in omics, it is possible to obtain a wealth of information for the identification, isolation, and target prediction of secondary metabolites. In this review, we discuss drug discovery based on natural products from microorganisms with the help of AI and machine learning.
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Affiliation(s)
- Vinodh J Sahayasheela
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan.
| | - Manendra B Lankadasari
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Vipin Mohan Dan
- Microbiology Division, Jawaharlal Nehru Tropical Botanic Garden and Research Institute, Thiruvananthapuram, Kerala, India
| | - Syed G Dastager
- NCIM Resource Centre, Division of Biochemical Sciences, CSIR - National Chemical Laboratory, Pune, Maharashtra, India
| | - Ganesh N Pandian
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Ushinomaecho, Sakyo-Ku, Kyoto 606-8501, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-Ku, Kyoto 606-8502, Japan.
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Ushinomaecho, Sakyo-Ku, Kyoto 606-8501, Japan
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14
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Feucherolles M, Frache G. MALDI Mass Spectrometry Imaging: A Potential Game-Changer in a Modern Microbiology. Cells 2022; 11:cells11233900. [PMID: 36497158 PMCID: PMC9738593 DOI: 10.3390/cells11233900] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/11/2022] Open
Abstract
Nowadays, matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) is routinely implemented as the reference method for the swift and straightforward identification of microorganisms. However, this method is not flawless and there is a need to upgrade the current methodology in order to free the routine lab from incubation time and shift from a culture-dependent to an even faster independent culture system. Over the last two decades, mass spectrometry imaging (MSI) gained tremendous popularity in life sciences, including microbiology, due to its ability to simultaneously detect biomolecules, as well as their spatial distribution, in complex samples. Through this literature review, we summarize the latest applications of MALDI-MSI in microbiology. In addition, we discuss the challenges and avenues of exploration for applying MSI to solve current MALDI-TOF MS limits in routine and research laboratories.
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15
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Translocation of subunit PPSE in plipastatin synthase and synthesis of novel lipopeptides. Synth Syst Biotechnol 2022; 7:1173-1180. [PMID: 36204332 PMCID: PMC9519435 DOI: 10.1016/j.synbio.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 08/01/2022] [Accepted: 09/07/2022] [Indexed: 11/20/2022] Open
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16
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Pitchapa R, Dissook S, Putri SP, Fukusaki E, Shimma S. MALDI Mass Spectrometry Imaging Reveals the Existence of an N-Acyl-homoserine Lactone Quorum Sensing System in Pseudomonas putida Biofilms. Metabolites 2022; 12:1148. [PMID: 36422288 PMCID: PMC9697013 DOI: 10.3390/metabo12111148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 02/28/2024] Open
Abstract
Quorum sensing (QS) is generally used to describe the process involving the release and recognition of signaling molecules, such as N-acyl-homoserine lactones, by bacteria to coordinate their response to population density and biofilm development. However, detailed information on the heterogeneity of QS metabolites in biofilms remains largely unknown. Here, we describe the utilization of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) to follow the production of specific metabolites, including QS metabolites, during Pseudomonas putida biofilm development. To do so, a method to grow an agar-based biofilm was first established, and MALDI-MSI was used to detect and visualize the distribution of QS metabolites in biofilms at different cultivation times. This study demonstrated that N-acyl-homoserine lactones are homogeneously produced in the early stages of P. putida biofilm formation. In contrast, the spatial distribution of quinolones and pyochelin correlated with the swarming motility of P. putida in mature biofilms. These two metabolites are involved in the production of extracellular polymeric substances and iron chelators. Our study thus contributes to establishing the specific temporal regulation and spatial distribution of N-acyl-homoserine lactone-related metabolites and quinolone and pyochelin in P. putida biofilms.
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Affiliation(s)
- Rattanaburi Pitchapa
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 5650871, Osaka, Japan
| | - Sivamoke Dissook
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 5650871, Osaka, Japan
| | - Sastia Prama Putri
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 5650871, Osaka, Japan
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 5650871, Osaka, Japan
- Osaka University Shimadzu Analytical Innovation Laboratory, Osaka University, 2-1 Yamadaoka, Suita 5650871, Osaka, Japan
| | - Shuichi Shimma
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 5650871, Osaka, Japan
- Osaka University Shimadzu Analytical Innovation Laboratory, Osaka University, 2-1 Yamadaoka, Suita 5650871, Osaka, Japan
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17
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Li H, Li Z. The Exploration of Microbial Natural Products and Metabolic Interaction Guided by Mass Spectrometry Imaging. Bioengineering (Basel) 2022; 9:707. [PMID: 36421108 PMCID: PMC9687252 DOI: 10.3390/bioengineering9110707] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/02/2022] [Accepted: 11/12/2022] [Indexed: 10/17/2023] Open
Abstract
As an impressive mass spectrometry technology, mass spectrometric imaging (MSI) can provide mass spectra data and spatial distribution of analytes simultaneously. MSI has been widely used in diverse fields such as clinical diagnosis, the pharmaceutical industry and environmental study due to its accuracy, high resolution and developing reproducibility. Natural products (NPs) have been a critical source of leading drugs; almost half of marketed drugs are derived from NPs or their derivatives. The continuous search for bioactive NPs from microorganisms or microbiomes has always been attractive. MSI allows us to analyze and characterize NPs directly in monocultured microorganisms or a microbial community. In this review, we briefly introduce current mainstream ionization technologies for microbial samples and the key issue of sample preparation, and then summarize some applications of MSI in the exploration of microbial NPs and metabolic interaction, especially NPs from marine microbes. Additionally, remaining challenges and future prospects are discussed.
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Affiliation(s)
| | - Zhiyong Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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18
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Dehner CA, Ruff WE, Greiling T, Pereira MS, Redanz S, McNiff J, Girardi M, Kriegel MA. Malignant T Cell Activation by a Bacillus Species Isolated from Cutaneous T-Cell Lymphoma Lesions. JID INNOVATIONS 2022; 2:100084. [PMID: 35199089 PMCID: PMC8844718 DOI: 10.1016/j.xjidi.2021.100084] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 10/05/2021] [Accepted: 10/14/2021] [Indexed: 01/04/2023] Open
Abstract
Cutaneous T-cell lymphoma (CTCL) is a life-debilitating malignancy of lymphocytes homing to the skin. Although CTCL is thought to arise from a combination of genetic, epigenetic, and environmental factors, specific triggers are unclear. The skin is colonized by a unique microbiota and is heavily influenced by its interactions. We hypothesized that adaptive immune responses to skin commensals lead to clonal T-cell proliferation and transformation in the appropriate genetic background. We therefore collected lesional and nonlesional skin microbiota from patients with CTCL to study T cell interactions using skin T cell explants and peripheral, skin-homing CD4+ T cells. By various methods, we identified Bacillus safensis in CTCL lesions, a rare human commensal in healthy skin, and showed that it can induce malignant T cell activation and cytokine secretion. Taken together, our data suggest microbial triggers in the skin microbiota of patients with CTCL as potential instigators of tumorigenesis.
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Affiliation(s)
- Carina A. Dehner
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Pathology & Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - William E. Ruff
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Teri Greiling
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Dermatology, Oregon Health & Science University, Portland, Oregon, USA
| | - Márcia S. Pereira
- Department of Translational Rheumatology and Immunology, Institute of Musculoskeletal Medicine, University of Münster, Münster, Germany
| | - Sylvio Redanz
- Department of Translational Rheumatology and Immunology, Institute of Musculoskeletal Medicine, University of Münster, Münster, Germany
| | - Jennifer McNiff
- Department of Dermatopathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Michael Girardi
- Department of Dermatology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Martin A. Kriegel
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Translational Rheumatology and Immunology, Institute of Musculoskeletal Medicine, University of Münster, Münster, Germany
- Section of Rheumatology and Clinical Immunology, Department of Medicine, University Hospital Münster, Münster, Germany
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19
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Maan H, Itkin M, Malitsky S, Friedman J, Kolodkin-Gal I. Resolving the conflict between antibiotic production and rapid growth by recognition of peptidoglycan of susceptible competitors. Nat Commun 2022; 13:431. [PMID: 35058430 PMCID: PMC8776889 DOI: 10.1038/s41467-021-27904-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 12/16/2021] [Indexed: 11/09/2022] Open
Abstract
Microbial communities employ a variety of complex strategies to compete successfully against competitors sharing their niche, with antibiotic production being a common strategy of aggression. Here, by systematic evaluation of four non-ribosomal peptides/polyketide (NRPs/PKS) antibiotics produced by Bacillus subtilis clade, we revealed that they acted synergistically to effectively eliminate phylogenetically distinct competitors. The production of these antibiotics came with a fitness cost manifested in growth inhibition, rendering their synthesis uneconomical when growing in proximity to a phylogenetically close species, carrying resistance against the same antibiotics. To resolve this conflict and ease the fitness cost, antibiotic production was only induced by the presence of a peptidoglycan cue from a sensitive competitor, a response mediated by the global regulator of cellular competence, ComA. These results experimentally demonstrate a general ecological concept - closely related communities are favoured during competition, due to compatibility in attack and defence mechanisms.
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Affiliation(s)
- Harsh Maan
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl Street, Rehovot, Israel
| | - Maxim Itkin
- Life Science Core Facilities Weizmann Institute of Science, 234 Herzl Street, Rehovot, Israel
| | - Sergey Malitsky
- Life Science Core Facilities Weizmann Institute of Science, 234 Herzl Street, Rehovot, Israel
| | - Jonathan Friedman
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food & Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Ilana Kolodkin-Gal
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food & Environment, The Hebrew University of Jerusalem, Rehovot, Israel.
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20
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Abstract
Bacillus subtilis is a soil bacterium that can form biofilms, which are communities of cells encased by an extracellular matrix. In these complex communities, cells perform numerous metabolic processes and undergo differentiation into functionally distinct phenotypes as a survival strategy. Because biofilms are often studied in bulk, it remains unclear how metabolite production spatially correlates with B. subtilis phenotypes within biofilm structures. In many cases, we still do not know where these biological processes are occurring in the biofilm. Here, we developed a method to analyze the localization of molecules within sagittal thin sections of B. subtilis biofilms using high-resolution mass spectrometry imaging. We correlated the organization of specific molecules to the localization of well-studied B. subtilis phenotypic reporters determined by confocal laser scanning fluorescence microscopy within analogous biofilm thin sections. The correlations between these two data sets suggest the role of surfactin as a signal for extracellular matrix gene expression in the biofilm periphery and the role of bacillibactin as an iron-scavenging molecule. Taken together, this method will help us generate hypotheses to discover relationships between metabolites and phenotypic cell states in B. subtilis and other biofilm-forming bacteria. IMPORTANCE Bacterial biofilms are complex and heterogeneous structures. Cells within biofilms carry out numerous metabolic processes in a nuanced and organized manner, details of which are still being discovered. Here, we used multimodal imaging to analyze B. subtilis biofilm processes at the metabolic and gene expression levels in biofilm sagittal thin sections. Often, imaging techniques analyze only the top of the surface of the biofilm and miss the multifaceted interactions that occur deep within the biofilm. Our analysis of the sagittal planes of B. subtilis biofilms revealed the distributions of metabolic processes throughout the depths of these structures and allowed us to draw correlations between metabolites and phenotypically important subpopulations of B. subtilis cells. This technique provides a platform to generate hypotheses about the role of specific molecules and their relationships to B. subtilis subpopulations of cells.
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21
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Combined Application of Citric Acid and Cr Resistant Microbes Improved Castor Bean Growth and Photosynthesis while It Alleviated Cr Toxicity by Reducing Cr +6 to Cr 3. Microorganisms 2021; 9:microorganisms9122499. [PMID: 34946101 PMCID: PMC8705206 DOI: 10.3390/microorganisms9122499] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/23/2021] [Accepted: 11/29/2021] [Indexed: 01/24/2023] Open
Abstract
Chromium is highly harmful to plants because of its detrimental effects on the availability of vital nutrients and secondary metabolites required for proper plant growth and development. A hydroponic experiment was carried out to analyze the effect of citric acid on castor bean plants under chromium stress. Furthermore, the role of two chromium-resistant microorganisms, Bacillus subtilis and Staphylococcus aureus, in reducing Cr toxicity was investigated. Different amounts of chromium (0 µM, 100 µM, 200 µM) and citric acid (0 mM, 2.5 mM, and 5 mM) were used both alone and in combination to analyze the remediation potential. Results showed that elevated amounts of chromium (specifically 200 µM) minimized the growth and biomass because the high concentration of Cr induced the oxidative markers. Exogenous citric acid treatment boosted plant growth and development by improving photosynthesis via enzymes such as superoxide dismutase, guaiacol peroxidase, catalase, and ascorbate peroxidase, which decreased Cr toxicity. The application of citric acid helped the plants to produce a high concentration of antioxidants which countered the oxidants produced due to chromium stress. It revealed that castor bean plants treated with citric acid could offset the stress injuries by decreasing the H2O2, electrolyte leakage, and malondialdehyde levels. The inoculation of plants with bacteria further boosted the plant growth parameters by improving photosynthesis and reducing the chromium-induced toxicity in the plants. The findings demonstrated that the combination of citric acid and metal-resistant bacteria could be a valuable technique for heavy metal remediation and mediating the adverse effects of metal toxicity on plants.
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22
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Khan S, Vancuren SJ, Hill JE. A Generalist Lifestyle Allows Rare Gardnerella spp. to Persist at Low Levels in the Vaginal Microbiome. MICROBIAL ECOLOGY 2021; 82:1048-1060. [PMID: 33219399 PMCID: PMC7678777 DOI: 10.1007/s00248-020-01643-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 11/12/2020] [Indexed: 06/11/2023]
Abstract
Gardnerella spp. are considered a hallmark of bacterial vaginosis, a dysbiosis of the vaginal microbiome. There are four cpn60 sequence-based subgroups within the genus (A, B, C and D), and thirteen genome species have been defined recently. Gardnerella spp. co-occur in the vaginal microbiome with varying abundance, and these patterns are shaped by a resource-dependent, exploitative competition, which affects the growth rate of subgroups A, B and C negatively. The growth rate of rarely abundant subgroup D, however, increases with the increasing number of competitors, negatively affecting the growth rate of others. We hypothesized that a nutritional generalist lifestyle and minimal niche overlap with the other more abundant Gardnerella spp. facilitate the maintenance of subgroup D in the vaginal microbiome through negative frequency-dependent selection. Using 40 whole-genome sequences from isolates representing all four subgroups, we found that they could be distinguished based on the content of their predicted proteomes. Proteins associated with carbohydrate and amino acid uptake and metabolism were significant contributors to the separation of subgroups. Subgroup D isolates had significantly more of their proteins assigned to amino acid metabolism than the other subgroups. Subgroup D isolates were also significantly different from others in terms of number and type of carbon sources utilized in a phenotypic assay, while the other three could not be distinguished. Overall, the results suggest that a generalist lifestyle and lack of niche overlap with other Gardnerella spp. leads to subgroup D being favoured by negative frequency-dependent selection in the vaginal microbiome.
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Affiliation(s)
- Salahuddin Khan
- Department of Veterinary Microbiology, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK S7N 5B4 Canada
| | - Sarah J. Vancuren
- Present Address: Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON Canada
| | - Janet E. Hill
- Department of Veterinary Microbiology, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK S7N 5B4 Canada
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23
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Maan H, Gilhar O, Porat Z, Kolodkin-Gal I. Bacillus subtilis Colonization of Arabidopsis thaliana Roots Induces Multiple Biosynthetic Clusters for Antibiotic Production. Front Cell Infect Microbiol 2021; 11:722778. [PMID: 34557426 PMCID: PMC8454505 DOI: 10.3389/fcimb.2021.722778] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/16/2021] [Indexed: 12/01/2022] Open
Abstract
Beneficial and probiotic bacteria play an important role in conferring immunity of their hosts to a wide range of bacterial, viral, and fungal diseases. Bacillus subtilis is a Gram-positive bacterium that protects the plant from various pathogens due to its capacity to produce an extensive repertoire of antibiotics. At the same time, the plant microbiome is a highly competitive niche, with multiple microbial species competing for space and resources, a competition that can be determined by the antagonistic potential of each microbiome member. Therefore, regulating antibiotic production in the rhizosphere is of great importance for the elimination of pathogens and establishing beneficial host-associated communities. In this work, we used B. subtilis as a model to investigate the role of plant colonization in antibiotic production. Flow cytometry and imaging flow cytometry (IFC) analysis supported the notion that Arabidopsis thaliana specifically induced the transcription of the biosynthetic clusters for the non-ribosomal peptides surfactin, bacilysin, plipastatin, and the polyketide bacillaene. IFC was more robust in quantifying the inducing effects of A. thaliana, considering the overall heterogeneity of the population. Our results highlight IFC as a useful tool to study the effect of association with a plant host on bacterial gene expression. Furthermore, the common regulation of multiple biosynthetic clusters for antibiotic production by the plant can be translated to improve the performance and competitiveness of beneficial members of the plant microbiome.
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Affiliation(s)
- Harsh Maan
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Omri Gilhar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ziv Porat
- Flow Cytometry Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Ilana Kolodkin-Gal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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24
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Moskovicz V, Ben-El R, Horev G, Mizrahi B. Skin microbiota dynamics following B. subtilis formulation challenge: an in vivo study in mice. BMC Microbiol 2021; 21:231. [PMID: 34418955 PMCID: PMC8379746 DOI: 10.1186/s12866-021-02295-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 08/12/2021] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Modulating the microbiota is a leading-edge strategy for the restoration and maintenance of a healthy, balanced environment. The use of health-promoting bacteria has demonstrated some potential benefits as an alternative for skin microbiota intervention. Here, we investigate the manipulation of mice skin microbiota using B. subtilis incorporated into a supportive Pluronic F-127 hydrogel formulation. The formula plays an important role in delivering the bacteria to the desired action site. RESULTS The B. subtilis challenge induced a shift in the composition and abundance of the skin microbiota. Containment of B. subtilis in the Pluronic F-127 hydrogel accelerated bacterial modulation compared with free B. subtilis. The abundance of both Staphylococcus and Corynebacterium spp. was altered as a result of the live bacterial intervention: the abundance of Corynebacterium increased while that of Staphylococcus decreased. Four days after last application of the B. subtilis formulation, B. subtilis counts returned to its initial level. CONCLUSIONS B. subtilis intervention can induce a shift in the skin microbiota, influencing the abundance of commensal, beneficial, and pathogenic bacteria. Containment of B. subtilis in Pluronic hydrogel accelerates the microbial alteration, probably by facilitating bacterial attachment and supporting continuous growth. Our results reveal the ability of B. subtilis in Pluronic to modulate the skin microbiota composition, suggesting that the formulation holds therapeutic potential for skin disease treatment.
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Affiliation(s)
- Veronica Moskovicz
- Faculty of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, 3200003, Haifa, Israel
| | - Rina Ben-El
- Bioinformatics Knowledge Unit, The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering, Technion - Israel Institute of Technology, 3200003, Haifa, Israel.,Faculty of Biology, Technion - Israel Institute of Technology, 3200003, Haifa, Israel
| | - Guy Horev
- Bioinformatics Knowledge Unit, The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering, Technion - Israel Institute of Technology, 3200003, Haifa, Israel
| | - Boaz Mizrahi
- Faculty of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, 3200003, Haifa, Israel.
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25
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Ben David N, Mafi M, Nyska A, Gross A, Greiner A, Mizrahi B. Bacillus subtilis in PVA Microparticles for Treating Open Wounds. ACS OMEGA 2021; 6:13647-13653. [PMID: 34095658 PMCID: PMC8173545 DOI: 10.1021/acsomega.1c00790] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 05/07/2021] [Indexed: 05/05/2023]
Abstract
Open wound dressings should provide a moist environment, protect the wound from bacterial contamination, and shield it from further damage. These requirements, however, are hard to accomplish since such wounds are colonized by pathogenic bacteria, including resistant species such as methicillin-resistant Staphylococcus aureus (MRSA). A new approach for treating open wounds that is based on sticky and dissolvable polyvinyl alcohol (PVA) microparticles containing live Bacillus subtilis (B. subtilis) is described. Microparticles, fabricated by the spray-drying technique, were administered directly to an open wound while B. subtilis continuously produced and secreted antimicrobial molecules. B. subtilis in PVA microparticles demonstrated remarkable antibacterial activity against MRSA and S. aureus. In in vivo experiments, both B. subtilis and empty PVA microparticles were effective in decreasing healing time; however, B. subtilis microparticles were more effective during the first week. There was no evidence of skin irritation, infection, or other adverse effects during the 15 day postoperative observation period. This concept of combining live secreting bacteria within a supportive delivery system shows great promise as a therapeutic agent for open wounds and other infectious skin disorders.
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Affiliation(s)
- Noa Ben David
- Faculty
of Biotechnology and Food Engineering, Technion
- Israel Institute of Technology, Haifa 3200003, Israel
| | - Mahsa Mafi
- Faculty
of Biology, Chemistry and Earth Sciences, Bayreuth Center for Colloids
and Interfaces, University of Bayreuth, Bayreuth 95440, Germany
| | | | - Adi Gross
- Faculty
of Biotechnology and Food Engineering, Technion
- Israel Institute of Technology, Haifa 3200003, Israel
| | - Andreas Greiner
- Faculty
of Biology, Chemistry and Earth Sciences, Bayreuth Center for Colloids
and Interfaces, University of Bayreuth, Bayreuth 95440, Germany
| | - Boaz Mizrahi
- Faculty
of Biotechnology and Food Engineering, Technion
- Israel Institute of Technology, Haifa 3200003, Israel
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26
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Hou Q, Kolodkin-Gal I. Harvesting the complex pathways of antibiotic production and resistance of soil bacilli for optimizing plant microbiome. FEMS Microbiol Ecol 2021; 96:5872479. [PMID: 32672816 DOI: 10.1093/femsec/fiaa142] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/13/2020] [Indexed: 01/04/2023] Open
Abstract
A sustainable future increasing depends on our capacity to utilize beneficial plant microbiomes to meet our growing needs. Plant microbiome symbiosis is a hallmark of the beneficial interactions between bacteria and their host. Specifically, colonization of plant roots by biocontrol agents and plant growth-promoting bacteria can play an important role in maintaining the optimal rhizosphere environment, supporting plant growth and promoting its fitness. Rhizosphere communities confer immunity against a wide range of foliar diseases by secreting antibiotics and activating plant defences. At the same time, the rhizosphere is a highly competitive niche, with multiple microbial species competing for space and resources, engaged in an arms race involving the production of a vast array of antibiotics and utilization of a variety of antibiotic resistance mechanisms. Therefore, elucidating the mechanisms that govern antibiotic production and resistance in the rhizosphere is of great significance for designing beneficial communities with enhanced biocontrol properties. In this review, we used Bacillus subtilis and B. amyloliquefaciens as models to investigate the genetics of antibiosis and the potential for its translation of into improved plant microbiome performance.
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Affiliation(s)
- Qihui Hou
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ilana Kolodkin-Gal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
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Kim G, Kim M, Kim M, Park C, Yoon Y, Lim DH, Yeo H, Kang S, Lee YG, Beak NI, Lee J, Kim S, Kwon JY, Choi WW, Lee C, Yoon KW, Park H, Lee DG. Spermidine-induced recovery of human dermal structure and barrier function by skin microbiome. Commun Biol 2021; 4:231. [PMID: 33608630 PMCID: PMC7895926 DOI: 10.1038/s42003-020-01619-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 12/17/2020] [Indexed: 01/31/2023] Open
Abstract
An unbalanced microbial ecosystem on the human skin is closely related to skin diseases and has been associated with inflammation and immune responses. However, little is known about the role of the skin microbiome on skin aging. Here, we report that the Streptococcus species improved the skin structure and barrier function, thereby contributing to anti-aging. Metagenomic analyses showed the abundance of Streptococcus in younger individuals or those having more elastic skin. Particularly, we isolated Streptococcus pneumoniae, Streptococcus infantis, and Streptococcus thermophilus from face of young individuals. Treatment with secretions of S. pneumoniae and S. infantis induced the expression of genes associated with the formation of skin structure and the skin barrier function in human skin cells. The application of culture supernatant including Streptococcal secretions on human skin showed marked improvements on skin phenotypes such as elasticity, hydration, and desquamation. Gene Ontology analysis revealed overlaps in spermidine biosynthetic and glycogen biosynthetic processes. Streptococcus-secreted spermidine contributed to the recovery of skin structure and barrier function through the upregulation of collagen and lipid synthesis in aged cells. Overall, our data suggest the role of skin microbiome into anti-aging and clinical applications.
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Affiliation(s)
- Gihyeon Kim
- grid.61221.360000 0001 1033 9831Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Misun Kim
- R&I Center, COSMAX BTI, Pangyo-ro 255, Bundang-gu, 13486 Seoungnam-si, Gyeonggi-do Republic of Korea
| | - Minji Kim
- R&I Center, COSMAX BTI, Pangyo-ro 255, Bundang-gu, 13486 Seoungnam-si, Gyeonggi-do Republic of Korea
| | - Changho Park
- grid.508753.cGenome and Company, Pangyo-ro 253, Bundang-gu, 13486 Seoungnam-si, Gyeonggi-do Republic of Korea
| | - Youngmin Yoon
- grid.61221.360000 0001 1033 9831Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Doo-Hyeon Lim
- R&I Center, COSMAX BTI, Pangyo-ro 255, Bundang-gu, 13486 Seoungnam-si, Gyeonggi-do Republic of Korea
| | - Hyeonju Yeo
- R&I Center, COSMAX BTI, Pangyo-ro 255, Bundang-gu, 13486 Seoungnam-si, Gyeonggi-do Republic of Korea
| | - Seunghyun Kang
- R&I Center, COSMAX BTI, Pangyo-ro 255, Bundang-gu, 13486 Seoungnam-si, Gyeonggi-do Republic of Korea
| | - Yeong-Geun Lee
- grid.289247.20000 0001 2171 7818Graduate School of Biotechnology and Department of Oriental Medicine Biotechnology, Kyung Hee University, 17104 Yongin, Republic of Korea
| | - Nam-In Beak
- grid.289247.20000 0001 2171 7818Graduate School of Biotechnology and Department of Oriental Medicine Biotechnology, Kyung Hee University, 17104 Yongin, Republic of Korea
| | - Jongsung Lee
- grid.264381.a0000 0001 2181 989XDermatology Laboratory, Department of Integrative Biotechnology & Biocosmetics Research Center, College of Biotechnology and Bioengineering, Sungkyunkwan University, 16419 Suwon City, Gyeonggi-do Republic of Korea
| | - Sujeong Kim
- grid.61221.360000 0001 1033 9831Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Jee Young Kwon
- grid.249880.f0000 0004 0374 0039The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA
| | - Won Woo Choi
- Wells Dermatology Clinic, 583 Shinsa-dong, Gangnam-ku, Seoul, Republic of Korea
| | - Charles Lee
- grid.249880.f0000 0004 0374 0039The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA ,grid.255649.90000 0001 2171 7754Department of Life Science, Ewha Womans University, 03760 Seoul, Republic of Korea ,grid.452438.cThe First Affiliated Hospital of Xi’an Jiaotong University, 710061 Xi’an, China
| | - Kyoung Wan Yoon
- grid.508753.cGenome and Company, Pangyo-ro 253, Bundang-gu, 13486 Seoungnam-si, Gyeonggi-do Republic of Korea ,grid.412238.e0000 0004 0532 7053Department of Biotechnology, Hoseo University, Asan, 31499 Republic of Korea
| | - Hansoo Park
- grid.61221.360000 0001 1033 9831Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea ,grid.508753.cGenome and Company, Pangyo-ro 253, Bundang-gu, 13486 Seoungnam-si, Gyeonggi-do Republic of Korea
| | - Dong-Geol Lee
- R&I Center, COSMAX BTI, Pangyo-ro 255, Bundang-gu, 13486 Seoungnam-si, Gyeonggi-do Republic of Korea
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Joshi RV, Gunawan C, Mann R. We Are One: Multispecies Metabolism of a Biofilm Consortium and Their Treatment Strategies. Front Microbiol 2021; 12:635432. [PMID: 33584635 PMCID: PMC7876221 DOI: 10.3389/fmicb.2021.635432] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/11/2021] [Indexed: 12/12/2022] Open
Abstract
The ecological and medical significance of bacterial biofilms have been well recognized. Biofilms are harder to control than their planktonic free-living counterparts and quite recently, the focus of the study has shifted to the multispecies consortia, which represent the vast majority of real-case infection scenarios. Studies have begun to explore the complex interspecies interactions within these biofilms. However, only little attention is currently given to the role of cellular metabolites in the cell-to-cell communication. The concentration gradients of metabolic substrates and products affect the spatial growth of bacteria in multispecies biofilm. This, if looked into more deeply, can lead to identification of potential therapies targeting the specific metabolites and hence the coordinated protection in the bacterial community. Herein, we review the interspecies communications, including their metabolic cross-talking, in multispecies biofilm, to signify the importance of such interactions on the initial formation and subsequent growth of these biofilms. Multispecies biofilms with their species heterogeneity are more resilient to antimicrobial agents than their single species biofilm counterparts and this characteristic is of particular interest when dealing with pathogenic bacteria. In this Review, we also discuss the treatment options available, to include current and emerging avenues to combat pathogenic multispecies biofilms in the clinical, environmental, as well as industrial settings.
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Affiliation(s)
| | - Cindy Gunawan
- iThree Institute, University of Technology Sydney, Sydney, NSW, Australia
- School of Chemical Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Riti Mann
- iThree Institute, University of Technology Sydney, Sydney, NSW, Australia
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29
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Bacillus subtilis extracellular polymeric substances conditioning layers inhibit Escherichia coli adhesion to silicon surfaces: A potential candidate for interfacial antifouling additives. Biointerphases 2021; 16:011003. [PMID: 33706527 DOI: 10.1116/6.0000737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Biofouling on material surfaces is a ubiquitous problem in a variety of fields. In aqueous environments, the process of biofouling initiates with the formation of a layer of macromolecules called the conditioning layer on the solid-liquid interface, followed by the adhesion and colonization of planktonic bacteria and the subsequent biofilm development and maturation. In this study, the extracellular polymeric substances (EPS) secreted by Bacillus subtilis were collected and used to prepare conditioning layers on inert surfaces. The morphologies and antifouling performances of the EPS conditioning layers were investigated. It was found that the initial adhesion of Escherichia coli was inhibited on the surfaces precoated with EPS conditioning layers. To further explore the underlying antifouling mechanisms of the EPS conditioning layers, the respective roles of two constituents of B. subtilis EPS (γ-polyglutamic acid and surfactin) were investigated. This study has provided the possibility of developing a novel interfacial antifouling additive with the advantages of easy preparation, nontoxicity, and environmental friendliness.
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Hou Q, Keren-Paz A, Korenblum E, Oved R, Malitsky S, Kolodkin-Gal I. Weaponizing volatiles to inhibit competitor biofilms from a distance. NPJ Biofilms Microbiomes 2021; 7:2. [PMID: 33402677 PMCID: PMC7785731 DOI: 10.1038/s41522-020-00174-4] [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: 06/04/2020] [Accepted: 11/19/2020] [Indexed: 01/29/2023] Open
Abstract
The soil bacterium Bacillus subtilis forms beneficial biofilms that induce plant defences and prevent the growth of pathogens. It is naturally found in the rhizosphere, where microorganisms coexist in an extremely competitive environment, and thus have evolved a diverse arsenal of defence mechanisms. In this work, we found that volatile compounds produced by B. subtilis biofilms inhibited the development of competing biofilm colonies, by reducing extracellular matrix gene expression, both within and across species. This effect was dose-dependent, with the structural defects becoming more pronounced as the number of volatile-producing colonies increased. This inhibition was mostly mediated by organic volatiles, and we identified the active molecules as 3-methyl-1-butanol and 1-butanol. Similar results were obtained with biofilms formed by phylogenetically distinct bacterium sharing the same niche, Escherichia coli, which produced the biofilm-inhibiting 3-methyl-1-butanol and 2-nonanon. The ability of established biofilms to inhibit the development and spreading of new biofilms from afar might be a general mechanism utilized by bacterial biofilms to protect an occupied niche from the invasion of competing bacteria.
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Affiliation(s)
- Qihui Hou
- grid.13992.300000 0004 0604 7563Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Alona Keren-Paz
- grid.13992.300000 0004 0604 7563Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Elisa Korenblum
- grid.13992.300000 0004 0604 7563Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Rela Oved
- grid.13992.300000 0004 0604 7563Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Sergey Malitsky
- grid.13992.300000 0004 0604 7563Metabolic Profiling Unit, Weizmann Institute of Science, Rehovot, Israel
| | - Ilana Kolodkin-Gal
- grid.13992.300000 0004 0604 7563Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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31
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Accorsi EK, Franzosa EA, Hsu T, Joice Cordy R, Maayan-Metzger A, Jaber H, Reiss-Mandel A, Kline M, DuLong C, Lipsitch M, Regev-Yochay G, Huttenhower C. Determinants of Staphylococcus aureus carriage in the developing infant nasal microbiome. Genome Biol 2020; 21:301. [PMID: 33308267 PMCID: PMC7731505 DOI: 10.1186/s13059-020-02209-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 11/19/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Staphylococcus aureus is a leading cause of healthcare- and community-associated infections and can be difficult to treat due to antimicrobial resistance. About 30% of individuals carry S. aureus asymptomatically in their nares, a risk factor for later infection, and interactions with other species in the nasal microbiome likely modulate its carriage. It is thus important to identify ecological or functional genetic elements within the maternal or infant nasal microbiomes that influence S. aureus acquisition and retention in early life. RESULTS We recruited 36 mother-infant pairs and profiled a subset of monthly longitudinal nasal samples from the first year after birth using shotgun metagenomic sequencing. The infant nasal microbiome is highly variable, particularly within the first 2 months. It is weakly influenced by maternal nasal microbiome composition, but primarily shaped by developmental and external factors, such as daycare. Infants display distinctive patterns of S. aureus carriage, positively associated with Acinetobacter species, Streptococcus parasanguinis, Streptococcus salivarius, and Veillonella species and inversely associated with maternal Dolosigranulum pigrum. Furthermore, we identify a gene family, likely acting as a taxonomic marker for an unclassified species, that is significantly anti-correlated with S. aureus in infants and mothers. In gene content-based strain profiling, infant S. aureus strains are more similar to maternal strains. CONCLUSIONS This improved understanding of S. aureus colonization is an important first step toward the development of novel, ecological therapies for controlling S. aureus carriage.
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Affiliation(s)
- Emma K. Accorsi
- Harvard T. H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115 USA
| | - Eric A. Franzosa
- Harvard T. H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute, 415 Main St., Cambridge, MA 02142 USA
| | - Tiffany Hsu
- Harvard T. H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute, 415 Main St., Cambridge, MA 02142 USA
| | - Regina Joice Cordy
- Harvard T. H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115 USA
- Wake Forest University, 1834 Wake Forest Rd., Winston-Salem, NC 27109 USA
| | - Ayala Maayan-Metzger
- Sackler Faculty of Medicine, Tel Aviv University, 69978 Ramat Aviv, Tel Aviv, Israel
- Sheba Medical Center, Derech Sheba 2, Ramat Gan, Israel
| | - Hanaa Jaber
- Sheba Medical Center, Derech Sheba 2, Ramat Gan, Israel
| | | | - Madeleine Kline
- Harvard Medical School, 25 Shattuck St., Boston, MA 02115 USA
| | - Casey DuLong
- Harvard T. H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115 USA
| | - Marc Lipsitch
- Harvard T. H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115 USA
| | - Gili Regev-Yochay
- Sackler Faculty of Medicine, Tel Aviv University, 69978 Ramat Aviv, Tel Aviv, Israel
- Sheba Medical Center, Derech Sheba 2, Ramat Gan, Israel
| | - Curtis Huttenhower
- Harvard T. H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute, 415 Main St., Cambridge, MA 02142 USA
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Watson E, Smith BT, Smoak MM, Tatara AM, Shah SR, Pearce HA, Hogan KJ, Shum J, Melville JC, Hanna IA, Demian N, Wenke JC, Bennett GN, van den Beucken JJJP, Jansen JA, Wong ME, Mikos AG. Localized mandibular infection affects remote in vivo bioreactor bone generation. Biomaterials 2020; 256:120185. [PMID: 32599360 PMCID: PMC7423761 DOI: 10.1016/j.biomaterials.2020.120185] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/05/2020] [Accepted: 06/07/2020] [Indexed: 12/30/2022]
Abstract
Mandibular reconstruction requires functional and aesthetic repair and is further complicated by contamination from oral and skin flora. Antibiotic-releasing porous space maintainers have been developed for the local release of vancomycin and to promote soft tissue attachment. In this study, mandibular defects in six sheep were inoculated with 106 colony forming units of Staphylococcus aureus; three sheep were implanted with unloaded porous space maintainers and three sheep were implanted with vancomycin-loaded space maintainers within the defect site. During the same surgery, 3D-printed in vivo bioreactors containing autograft or xenograft were implanted adjacent to rib periosteum. After 9 weeks, animals were euthanized, and tissues were analyzed. Antibiotic-loaded space maintainers were able to prevent dehiscence of soft tissue overlying the space maintainer, reduce local inflammatory cells, eliminate the persistence of pathogens, and prevent the increase in mandibular size compared to unloaded space maintainers in this sheep model. Animals with an untreated mandibular infection formed bony tissues with greater density and maturity within the distal bioreactors. Additionally, tissues grown in autograft-filled bioreactors had higher compressive moduli and higher maximum screw pull-out forces than xenograft-filled bioreactors. In summary, we demonstrated that antibiotic-releasing space maintainers are an innovative approach to preserve a robust soft tissue pocket while clearing infection, and that local infections can increase local and remote bone growth.
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Affiliation(s)
- Emma Watson
- Department of Bioengineering, Rice University, Houston, TX, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
| | - Brandon T Smith
- Department of Bioengineering, Rice University, Houston, TX, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
| | - Mollie M Smoak
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Alexander M Tatara
- Department of Bioengineering, Rice University, Houston, TX, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
| | - Sarita R Shah
- Department of Bioengineering, Rice University, Houston, TX, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
| | - Hannah A Pearce
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Katie J Hogan
- Department of Bioengineering, Rice University, Houston, TX, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
| | - Jonathan Shum
- Department of Oral and Maxillofacial Surgery, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - James C Melville
- Department of Oral and Maxillofacial Surgery, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Issa A Hanna
- Department of Oral and Maxillofacial Surgery, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Nagi Demian
- Department of Oral and Maxillofacial Surgery, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Joseph C Wenke
- Extremity Trauma & Regenerative Medicine, U.S. Army Institute of Surgical Research, San Antonio, TX, USA
| | | | | | - John A Jansen
- Department of Biomaterials, Radboudumc, Nijmegen, the Netherlands
| | - Mark E Wong
- Department of Oral and Maxillofacial Surgery, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Antonios G Mikos
- Department of Bioengineering, Rice University, Houston, TX, USA.
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Hernandez-Valdes JA, Zhou L, de Vries MP, Kuipers OP. Impact of spatial proximity on territoriality among human skin bacteria. NPJ Biofilms Microbiomes 2020; 6:30. [PMID: 32764612 PMCID: PMC7413532 DOI: 10.1038/s41522-020-00140-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 07/14/2020] [Indexed: 12/30/2022] Open
Abstract
Bacteria display social behavior and establish cooperative or competitive interactions in the niches they occupy. The human skin is a densely populated environment where many bacterial species live. Thus, bacterial inhabitants are expected to find a balance in these interactions, which eventually defines their spatial distribution and the composition of our skin microbiota. Unraveling the physiological basis of the interactions between bacterial species in organized environments requires reductionist analyses using functionally relevant species. Here, we study the interaction between two members of our skin microbiota, Bacillus subtilis and Staphylococcus epidermidis. We show that B. subtilis actively responds to the presence of S. epidermidis in its proximity by two strategies: antimicrobial production and development of a subpopulation with migratory response. The initial response of B. subtilis is production of chlorotetain, which degrades the S. epidermidis at the colony level. Next, a subpopulation of B. subtilis motile cells emerges. Remarkably this subpopulation slides towards the remaining S. epidermidis colony and engulfs it. A slow response back from S. epidermidis cells give origin to resistant cells that prevent both attacks from B. subtilis. We hypothesized that this niche conquering and back-down response from B. subtilis and S. epidermidis, respectively, which resembles other conflicts in nature as the ones observed in animals, may play a role in defining the presence of certain bacterial species in the specific microenvironments that these bacteria occupy on our skin.
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Affiliation(s)
- Jhonatan A Hernandez-Valdes
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Lu Zhou
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Marcel P de Vries
- Department of Biomedical Engineering Antonius Deusinglaan 1, University Medical Center Groningen, Groningen University, 9713 AW, Groningen, Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
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Liu R, Khan RAA, Yue Q, Jiao Y, Yang Y, Li Y, Xie B. Discovery of a new antifungal lipopeptaibol from Purpureocillium lilacinum using MALDI-TOF-IMS. Biochem Biophys Res Commun 2020; 527:689-695. [PMID: 32423807 DOI: 10.1016/j.bbrc.2020.05.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 05/04/2020] [Indexed: 10/24/2022]
Abstract
Fungi are considered to be rich in biologically active natural products for agricultural and medicinal purposes. The discovery and accurate identification of the bioactive fungal natural products is important for their efficient utilization. During the course of our continuing search for the new natural products from the fungal agents, we found the well-known bio-control fungus Purpureocillium lilacinum showed in vitro activity against Botrytis cinerea, an airborne plant pathogenic fungus causing gray mold disease in many vegetables and fruits. The co-culture of two fungi on agar plate showed that P. lilacinum inhibited the growth of B. cinerea which means P. lilacinum has potential to produce some bioactive secondary metabolites against B. cinerea. In this study, we applied matrix-assisted laser desorption ionization-time of flight mass spectrometry imaging mass spectrometry (MALDI-TOF-IMS), as a fast identification tool, for the discovery of a new antifungal lipopeptaibol (leucinostatin Z) from P. lilacinum against B. cinerea. The planar structure of leucinostatin Z was further established by using the LC-HRESI-MS-MS analysis. MALDI-TOF-IMS is becoming a new approach that allows us to observe the bioactive natural products directly on growth media between the colonies of two fungi, which is faster and more effective than the traditional techniques to discover new bioactive compounds in fungi.
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Affiliation(s)
- Rui Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Raja Asad Ali Khan
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qun Yue
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yang Jiao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yuhong Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yan Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Bingyan Xie
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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35
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Chen Y, Wang X, Zhang X, Xu D, Zhang W, Qiu J, Liu Q, Dong Q. Modeling the interactions among
Salmonella
enteritidis,
Pseudomonas aeruginosa
, and
Lactobacillus plantarum. J Food Saf 2020. [DOI: 10.1111/jfs.12811] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Yuanmei Chen
- School of Medical Instrument and Food EngineeringUniversity of Shanghai for Science and Technology Shanghai China
| | - Xiang Wang
- School of Medical Instrument and Food EngineeringUniversity of Shanghai for Science and Technology Shanghai China
| | - Xibin Zhang
- Lab of Beef Processing and Quality Control, College of Food Science and EngineeringShandong Agricultural University Taian Shandong China
- New Hope Liuhe Co., Ltd. Beijing China
| | - Dongpo Xu
- School of Medical Instrument and Food EngineeringUniversity of Shanghai for Science and Technology Shanghai China
| | - Wenmin Zhang
- School of Medical Instrument and Food EngineeringUniversity of Shanghai for Science and Technology Shanghai China
| | - Jingxuan Qiu
- School of Medical Instrument and Food EngineeringUniversity of Shanghai for Science and Technology Shanghai China
| | - Qing Liu
- School of Medical Instrument and Food EngineeringUniversity of Shanghai for Science and Technology Shanghai China
| | - Qingli Dong
- School of Medical Instrument and Food EngineeringUniversity of Shanghai for Science and Technology Shanghai China
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36
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Vrouvaki I, Koutra E, Kornaros M, Avgoustakis K, Lamari FN, Hatziantoniou S. Polymeric Nanoparticles of Pistacia lentiscus var. chia Essential Oil for Cutaneous Applications. Pharmaceutics 2020; 12:E353. [PMID: 32295134 PMCID: PMC7238218 DOI: 10.3390/pharmaceutics12040353] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 04/08/2020] [Accepted: 04/09/2020] [Indexed: 01/25/2023] Open
Abstract
Polymeric nanoparticles (NPs) encapsulating Pistacia lentiscus L. var. chia essential oil (EO) were prepared by a solvent evaporation method, in order to obtain a novel carrier for administration on the skin. The specific EO exhibits antimicrobial and anti-inflammatory properties thus stimulating considerable interest as a novel agent for the treatment of minor skin inflammations. The incorporation into nanoparticles could overcome the administration limitations that inserts the nature of the EO. Nanoparticles were prepared, utilizing poly(lactic acid) (PLA) as shell material, due to its biocompatibility and biodegradability, while the influence of surfactant type on NPs properties was examined. Two surfactants were selected, namely poly(vinyl alcohol) (PVA) and lecithin (LEC) and NPs' physicochemical characteristics i.e. size, polydispersity index (PdI) and ζ-potential were determined, not indicating significant differences (p > 0.05) between PLA/PVA-NPs (239.9 nm, 0.081, -29.1 mV) and PLA/LEC-NPs (286.1 nm, 0.167, -34.5 mV). However, encapsulation efficiency (%EE) measured by GC-MS, was clearly higher for PLA/PVA-NPs than PLA/LEC-NPs (37.45% vs. 9.15%, respectively). Moreover PLA/PVA-NPs remained stable over a period of 60 days. The in vitro release study indicated gradual release of the EO from PLA/PVA-NPs and more immediate from PLA/LEC-NPs. The above findings, in addition to the SEM images of the particles propose a potential structure of nanocapsules for PLA/PVA-NPs, where shell material is mainly consisted of PLA, enclosing the EO in the core. However, this does not seem to be the case for PLA/LEC-NPs, as the results indicated low EO content, rapid release and a considerable percentage of humidity detected by SEM. Furthermore, the Minimum Inhibitory Concentration (MIC) of the EO was determined against Escherichia coli and Bacillus subtilis, while NPs, however did not exhibit considerable activity in the concentration range applied. In conclusion, the surfactant selection may modify the release of EO incorporated in NPs for topical application allowing its action without interfering to the physiological skin microbiota.
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Affiliation(s)
- Ilianna Vrouvaki
- Laboratory of Pharmaceutical Technology, Department of Pharmacy, University of Patras, 26504 Patras, Greece; (I.V.); (K.A.)
| | - Eleni Koutra
- Laboratory of Biochemical Engineering and Environmental Technology (LBEET), Department of Chemical Engineering, University of Patras, 26504 Patras, Greece; (E.K.); (M.K.)
| | - Michael Kornaros
- Laboratory of Biochemical Engineering and Environmental Technology (LBEET), Department of Chemical Engineering, University of Patras, 26504 Patras, Greece; (E.K.); (M.K.)
- INVALOR: Research Infrastructure for Waste Valorization and Sustainable Management, University Campus, 26504 Patras, Greece
| | - Konstantinos Avgoustakis
- Laboratory of Pharmaceutical Technology, Department of Pharmacy, University of Patras, 26504 Patras, Greece; (I.V.); (K.A.)
| | - Fotini N. Lamari
- Laboratory of Pharmacognosy and Chemistry of Natural Products, Department of Pharmacy, University of Patras, 26504 Patras, Greece;
| | - Sophia Hatziantoniou
- Laboratory of Pharmaceutical Technology, Department of Pharmacy, University of Patras, 26504 Patras, Greece; (I.V.); (K.A.)
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Brockmann EU, Steil D, Bauwens A, Soltwisch J, Dreisewerd K. Advanced Methods for MALDI-MS Imaging of the Chemical Communication in Microbial Communities. Anal Chem 2019; 91:15081-15089. [DOI: 10.1021/acs.analchem.9b03772] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Eike Ulrich Brockmann
- Institute of Hygiene, University of Münster, Münster 48149, Germany
- Interdisciplinary Center for Clinical Research (IZKF), University of Münster, Münster 48149, Germany
| | - Daniel Steil
- Institute of Hygiene, University of Münster, Münster 48149, Germany
- Interdisciplinary Center for Clinical Research (IZKF), University of Münster, Münster 48149, Germany
| | - Andreas Bauwens
- Institute of Hygiene, University of Münster, Münster 48149, Germany
| | - Jens Soltwisch
- Institute of Hygiene, University of Münster, Münster 48149, Germany
- Interdisciplinary Center for Clinical Research (IZKF), University of Münster, Münster 48149, Germany
| | - Klaus Dreisewerd
- Institute of Hygiene, University of Münster, Münster 48149, Germany
- Interdisciplinary Center for Clinical Research (IZKF), University of Münster, Münster 48149, Germany
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Temkin MI, Carlson CM, Stubbendieck AL, Currie CR, Stubbendieck RM. High Throughput Co-culture Assays for the Investigation of Microbial Interactions. J Vis Exp 2019:10.3791/60275. [PMID: 31680681 PMCID: PMC7380114 DOI: 10.3791/60275] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The study of interactions between microorganisms has led to numerous discoveries, from novel antimicrobials to insights in microbial ecology. Many approaches used for the study of microbial interactions require specialized equipment and are expensive and time intensive. This paper presents a protocol for co-culture interaction assays that are inexpensive, scalable to large sample numbers, and easily adaptable to numerous experimental designs. Microorganisms are cultured together, with each well representing one pairwise combination of microorganisms. A test organism is cultured on one side of each well and first incubated in monoculture. Subsequently, target organisms are simultaneously inoculated onto the opposite side of each well using a 3D-printed inoculation stamp. After co-culture, the completed assays are scored for visual phenotypes, such as growth or inhibition. These assays can be used to confirm phenotypes or identify patterns among isolates of interest. Using this simple and effective method, users can analyze combinations of microorganisms rapidly and efficiently. This co-culture approach is applicable to antibiotic discovery as well as culture-based microbiome research and has already been successfully applied to both applications.
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Affiliation(s)
- Mia I Temkin
- Department of Bacteriology, University of Wisconsin-Madison
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Kumar KV, Pal A, Bai P, Kour A, E S, P R, Kausar A, Chatterjee M, Prasad G, Balayan S, Dutta P, Wijesekera K. Co-aggregation of bacterial flora isolated from the human skin surface. Microb Pathog 2019; 135:103630. [DOI: 10.1016/j.micpath.2019.103630] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 06/27/2019] [Accepted: 07/16/2019] [Indexed: 12/21/2022]
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Probiotic Bifunctionality of Bacillus subtilis-Rescuing Lactic Acid Bacteria from Desiccation and Antagonizing Pathogenic Staphylococcus aureus. Microorganisms 2019; 7:microorganisms7100407. [PMID: 31569575 PMCID: PMC6843919 DOI: 10.3390/microorganisms7100407] [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: 08/29/2019] [Revised: 09/20/2019] [Accepted: 09/23/2019] [Indexed: 12/28/2022] Open
Abstract
Live probiotic bacteria obtained with food are thought to have beneficial effects on a mammalian host, including their ability to reduce intestinal colonization by pathogens. To ensure the beneficial effects, the probiotic cells must survive processing and storage of food, its passage through the upper gastrointestinal tract (GIT), and subsequent chemical ingestion processes until they reach their target organ. However, there is considerable loss of viability of the probiotic bacteria during the drying process, in the acidic conditions of the stomach, and in the high bile concentration in the small intestine. Bacillus subtilis, a spore-forming probiotic bacterium, can effectively maintain a favorable balance of microflora in the GIT. B. subtilis produces a protective extracellular matrix (ECM), which is shared with other probiotic bacteria; thus, it was suggested that this ECM could potentially protect an entire community of probiotic cells against unfavorable environmental conditions. Consequently, a biofilm-based bio-coating system was developed that would enable a mutual growth of B. subtilis with different lactic acid bacteria (LAB) through increasing the ECM production. Results of the study demonstrate a significant increase in the survivability of the bio-coated LAB cells during the desiccation process and passage through the acidic environment. Thus, it provides evidence about the ability of B. subtilis in rescuing the desiccation-sensitive LAB, for instance, Lactobacillus rhamnosus, from complete eradication. Furthermore, this study demonstrates the antagonistic potential of the mutual probiotic system against pathogenic bacteria such as Staphylococcus aureus. The data show that the cells of B. subtilis possess robust anti-biofilm activity against S. aureus through activating the antimicrobial lipopeptide production pathway.
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Rampelotto PH, Sereia AF, de Oliveira LFV, Margis R. Exploring the Hospital Microbiome by High-Resolution 16S rRNA Profiling. Int J Mol Sci 2019; 20:ijms20123099. [PMID: 31242612 PMCID: PMC6696720 DOI: 10.3390/ijms20123099] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/19/2019] [Accepted: 06/20/2019] [Indexed: 02/07/2023] Open
Abstract
The aim of this work was to analyze and compare the bacterial communities of 663 samples from a Brazilian hospital by using high-throughput sequencing of the 16S rRNA gene. To increase taxonomic profiling and specificity of 16S-based identification, a strict sequence quality filtering process was applied for the accurate identification of clinically relevant bacterial taxa. Our results indicate that the hospital environment is predominantly inhabited by closely related species. A massive dominance of a few taxa in all taxonomic levels down to the genera was observed, where the ten most abundant genera in each facility represented 64.4% of all observed taxa, with a major predominance of Acinetobacter and Pseudomonas. The presence of several nosocomial pathogens was revealed. Co-occurrence analysis indicated that the present hospital microbial network had low connectedness, forming a clustered topology, but not structured among groups of nodes (i.e., modules). Furthermore, we were able to detect ecologically relevant relationships between specific microbial taxa, in particular, potential competition between pathogens and non-pathogens. Overall, these results provide new insight into different aspects of a hospital microbiome and indicate that 16S rRNA sequencing may serve as a robust one-step tool for microbiological identification and characterization of a wide range of clinically relevant bacterial taxa in hospital settings with a high resolution.
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Affiliation(s)
- Pabulo H. Rampelotto
- PPGBCM, Center of Biotechnology, Federal University of Rio Grande do Sul, 9500, Porto Alegre, RS 91501-970, Brazil;
- Laboratory of Experimental Hepatology and Gastroenterology, Hospital de Clínicas de Porto Alegre (HCPA), 2350, Porto Alegre, RS 90035-903, Brazil
| | - Aline F.R. Sereia
- Neoprospecta Microbiome Technologies, 1302, Florianópolis, SC 88057-260, Brazil; (A.F.R.S.); (L.F.d.V.O.)
| | - Luiz Felipe V. de Oliveira
- Neoprospecta Microbiome Technologies, 1302, Florianópolis, SC 88057-260, Brazil; (A.F.R.S.); (L.F.d.V.O.)
| | - Rogério Margis
- PPGBCM, Center of Biotechnology, Federal University of Rio Grande do Sul, 9500, Porto Alegre, RS 91501-970, Brazil;
- Correspondence:
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Luzzatto-Knaan T, Melnik AV, Dorrestein PC. Mass Spectrometry Uncovers the Role of Surfactin as an Interspecies Recruitment Factor. ACS Chem Biol 2019; 14:459-467. [PMID: 30763059 DOI: 10.1021/acschembio.8b01120] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Microbes use metabolic exchange to sense and respond to their changing environment. Surfactins, produced by Bacillus subtilis, have been extensively studied for their role in biofilm formation, biosurfactant properties, and antimicrobial activity, affecting the surrounding microbial consortia. Using mass spectrometry, we reveal that Paenibacillus dendritiformis, originally isolated with B. subtilis, is not antagonized by the presence of surfactins and is actually attracted to them. We demonstrate here for the first time that P. dendritiformis is also actively degrading surfactins produced by B. subtilis and accumulating the degradation products that serve as territorial markers. This new attribute as an attractant of selected microbes and the conversion into a deterrent highlight the diverse role natural products have in shaping the environment and establishing mixed communities.
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Affiliation(s)
- Tal Luzzatto-Knaan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Alexey V. Melnik
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Pieter C. Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
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Liu S, Zuo J, Lu Y, Gao L, Zhai Y, Xu W. Direct bacteria analysis using laserspray ionization miniature mass spectrometry. Anal Bioanal Chem 2018; 411:4031-4040. [DOI: 10.1007/s00216-018-1385-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 08/15/2018] [Accepted: 09/17/2018] [Indexed: 01/29/2023]
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Cameron SJ, Takáts Z. Mass spectrometry approaches to metabolic profiling of microbial communities within the human gastrointestinal tract. Methods 2018; 149:13-24. [DOI: 10.1016/j.ymeth.2018.04.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/05/2018] [Accepted: 04/22/2018] [Indexed: 12/14/2022] Open
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Raffatellu M. Learning from bacterial competition in the host to develop antimicrobials. Nat Med 2018; 24:1097-1103. [DOI: 10.1038/s41591-018-0145-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 05/24/2018] [Accepted: 07/03/2018] [Indexed: 02/07/2023]
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Parrot D, Papazian S, Foil D, Tasdemir D. Imaging the Unimaginable: Desorption Electrospray Ionization - Imaging Mass Spectrometry (DESI-IMS) in Natural Product Research. PLANTA MEDICA 2018; 84:584-593. [PMID: 29388184 PMCID: PMC6053038 DOI: 10.1055/s-0044-100188] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 12/15/2017] [Accepted: 12/27/2017] [Indexed: 05/06/2023]
Abstract
Imaging mass spectrometry (IMS) has recently established itself in the field of "spatial metabolomics." Merging the sensitivity and fast screening of high-throughput mass spectrometry with spatial and temporal chemical information, IMS visualizes the production, location, and distribution of metabolites in intact biological models. Since metabolite profiling and morphological features are combined in single images, IMS offers an unmatched chemical detail on complex biological and microbiological systems. Thus, IMS-type "spatial metabolomics" emerges as a powerful and complementary approach to genomics, transcriptomics, and classical metabolomics studies. In this review, we summarize the current state-of-the-art IMS methods with a strong focus on desorption electrospray ionization (DESI)-IMS. DESI-IMS utilizes the original principle of electrospray ionization, but in this case solvent droplets are rastered and desorbed directly on the sample surface. The rapid and minimally destructive DESI-IMS chemical screening is achieved at ambient conditions and enables the accurate view of molecules in tissues at the µm-scale resolution. DESI-IMS analysis does not require complex sample preparation and allows repeated measurements on samples from different biological sources, including microorganisms, plants, and animals. Thanks to its easy workflow and versatility, DESI-IMS has successfully been applied to many different research fields, such as clinical analysis, cancer research, environmental sciences, microbiology, chemical ecology, and drug discovery. Herein we discuss the present applications of DESI-IMS in natural product research.
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Affiliation(s)
- Delphine Parrot
- GEOMAR Centre for Marine Biotechnology, Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany
| | - Stefano Papazian
- GEOMAR Centre for Marine Biotechnology, Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany
| | - Daniel Foil
- GEOMAR Centre for Marine Biotechnology, Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany
| | - Deniz Tasdemir
- GEOMAR Centre for Marine Biotechnology, Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany
- Kiel University, Kiel, Germany
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Hug JJ, Bader CD, Remškar M, Cirnski K, Müller R. Concepts and Methods to Access Novel Antibiotics from Actinomycetes. Antibiotics (Basel) 2018; 7:E44. [PMID: 29789481 PMCID: PMC6022970 DOI: 10.3390/antibiotics7020044] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 05/14/2018] [Accepted: 05/17/2018] [Indexed: 12/25/2022] Open
Abstract
Actinomycetes have been proven to be an excellent source of secondary metabolites for more than half a century. Exhibiting various bioactivities, they provide valuable approved drugs in clinical use. Most microorganisms are still untapped in terms of their capacity to produce secondary metabolites, since only a small fraction can be cultured in the laboratory. Thus, improving cultivation techniques to extend the range of secondary metabolite producers accessible under laboratory conditions is an important first step in prospecting underexplored sources for the isolation of novel antibiotics. Currently uncultured actinobacteria can be made available by bioprospecting extreme or simply habitats other than soil. Furthermore, bioinformatic analysis of genomes reveals most producers to harbour many more biosynthetic gene clusters than compounds identified from any single strain, which translates into a silent biosynthetic potential of the microbial world for the production of yet unknown natural products. This review covers discovery strategies and innovative methods recently employed to access the untapped reservoir of natural products. The focus is the order of actinomycetes although most approaches are similarly applicable to other microbes. Advanced cultivation methods, genomics- and metagenomics-based approaches, as well as modern metabolomics-inspired methods are highlighted to emphasise the interplay of different disciplines to improve access to novel natural products.
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Affiliation(s)
- Joachim J Hug
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| | - Chantal D Bader
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| | - Maja Remškar
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| | - Katarina Cirnski
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| | - Rolf Müller
- Department Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
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García-Pérez AN, de Jong A, Junker S, Becher D, Chlebowicz MA, Duipmans JC, Jonkman MF, van Dijl JM. From the wound to the bench: exoproteome interplay between wound-colonizing Staphylococcus aureus strains and co-existing bacteria. Virulence 2018; 9:363-378. [PMID: 29233035 PMCID: PMC5955179 DOI: 10.1080/21505594.2017.1395129] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 10/09/2017] [Accepted: 10/15/2017] [Indexed: 11/16/2022] Open
Abstract
Wound-colonizing microorganisms can form complex and dynamic polymicrobial communities where pathogens and commensals may co-exist, cooperate or compete with each other. The present study was aimed at identifying possible interactions between different bacteria isolated from the same chronic wound of a patient with the genetic blistering disease epidermolysis bullosa (EB). Specifically, this involved two different isolates of the human pathogen Staphylococcus aureus, and isolates of Bacillus thuringiensis and Klebsiella oxytoca. Particular focus was attributed to interactions of S. aureus with the two other species, because of the high staphylococcal prevalence among chronic wounds. Intriguingly, upon co-cultivation, none of the wound isolates inhibited each other's growth. Since the extracellular proteome of bacterial pathogens is a reservoir of virulence factors, the exoproteomes of the staphylococcal isolates in monoculture and co-culture with B. thuringiensis and K. oxytoca were characterized by Mass Spectrometry to explore the inherent relationships between these co-exisiting bacteria. This revealed a massive reduction in the number of staphylococcal exoproteins upon co-culturing with K. oxytoca or B. thuringiensis. Interestingly, this decrease was particularly evident for extracellular proteins with a predicted cytoplasmic localization, which were recently implicated in staphylococcal virulence and epidemiology. Furthermore, our exoproteome analysis uncovered potential cooperativity between the two different S. aureus isolates. Altogether, the observed exoproteome variations upon co-culturing are indicative of unprecedented adaptive mechanisms that set limits to the production of secreted staphylococcal virulence factors.
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Affiliation(s)
- Andrea N. García-Pérez
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen, the Netherlands
| | - Anne de Jong
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, AG Groningen, the Netherlands
| | - Sabryna Junker
- Institute for Microbiology, Ernst-Moritz-Arndt Universität Greifswald, Friedrich-Ludwig-Jahn-Str. 15, Greifswald, Germany
| | - Dörte Becher
- Institute for Microbiology, Ernst-Moritz-Arndt Universität Greifswald, Friedrich-Ludwig-Jahn-Str. 15, Greifswald, Germany
| | - Monika A. Chlebowicz
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen, the Netherlands
| | - José C. Duipmans
- Department of Dermatology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, RB Groningen, the Netherlands
| | - Marcel F. Jonkman
- Department of Dermatology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, RB Groningen, the Netherlands
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen, the Netherlands
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Zuñiga C, Zaramela L, Zengler K. Elucidation of complexity and prediction of interactions in microbial communities. Microb Biotechnol 2017; 10:1500-1522. [PMID: 28925555 PMCID: PMC5658597 DOI: 10.1111/1751-7915.12855] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/10/2017] [Accepted: 08/11/2017] [Indexed: 12/11/2022] Open
Abstract
Microorganisms engage in complex interactions with other members of the microbial community, higher organisms as well as their environment. However, determining the exact nature of these interactions can be challenging due to the large number of members in these communities and the manifold of interactions they can engage in. Various omic data, such as 16S rRNA gene sequencing, shotgun metagenomics, metatranscriptomics, metaproteomics and metabolomics, have been deployed to unravel the community structure, interactions and resulting community dynamics in situ. Interpretation of these multi-omic data often requires advanced computational methods. Modelling approaches are powerful tools to integrate, contextualize and interpret experimental data, thus shedding light on the underlying processes shaping the microbiome. Here, we review current methods and approaches, both experimental and computational, to elucidate interactions in microbial communities and to predict their responses to perturbations.
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Affiliation(s)
- Cristal Zuñiga
- Department of PediatricsUniversity of California, San Diego9500 Gilman DriveLa JollaCA92093‐0760USA
| | - Livia Zaramela
- Department of PediatricsUniversity of California, San Diego9500 Gilman DriveLa JollaCA92093‐0760USA
| | - Karsten Zengler
- Department of PediatricsUniversity of California, San Diego9500 Gilman DriveLa JollaCA92093‐0760USA
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50
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Covington BC, McLean JA, Bachmann BO. Comparative mass spectrometry-based metabolomics strategies for the investigation of microbial secondary metabolites. Nat Prod Rep 2017; 34:6-24. [PMID: 27604382 PMCID: PMC5214543 DOI: 10.1039/c6np00048g] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Covering: 2000 to 2016The labor-intensive process of microbial natural product discovery is contingent upon identifying discrete secondary metabolites of interest within complex biological extracts, which contain inventories of all extractable small molecules produced by an organism or consortium. Historically, compound isolation prioritization has been driven by observed biological activity and/or relative metabolite abundance and followed by dereplication via accurate mass analysis. Decades of discovery using variants of these methods has generated the natural pharmacopeia but also contributes to recent high rediscovery rates. However, genomic sequencing reveals substantial untapped potential in previously mined organisms, and can provide useful prescience of potentially new secondary metabolites that ultimately enables isolation. Recently, advances in comparative metabolomics analyses have been coupled to secondary metabolic predictions to accelerate bioactivity and abundance-independent discovery work flows. In this review we will discuss the various analytical and computational techniques that enable MS-based metabolomic applications to natural product discovery and discuss the future prospects for comparative metabolomics in natural product discovery.
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Affiliation(s)
- Brett C Covington
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Nashville, TN 37235, USA.
| | - John A McLean
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Nashville, TN 37235, USA. and Center for Innovative Technology, Vanderbilt University, 5401 Stevenson Center, Nashville, TN 37235, USA
| | - Brian O Bachmann
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Nashville, TN 37235, USA.
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