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Suleiman M, Abu-Aqil G, Lapidot I, Huleihel M, Salman A. Significant reduction of the culturing time required for bacterial identification and antibiotic susceptibility determination by infrared spectroscopy. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:3745-3756. [PMID: 38818530 DOI: 10.1039/d4ay00604f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Rapid testing of bacteria for antibiotic susceptibility is essential for effective treatment and curbing the emergence of multidrug-resistant bacteria. The misuse of antibiotics, coupled with the time-consuming classical testing methods, intensifies the threat of antibiotic resistance, a major global health concern. In this study, employing infrared spectroscopy-based machine learning techniques, we significantly shortened the time required for susceptibility testing to 10 hours, a significant improvement from the 24 hours in our previous studies as well as the conventional methods that typically take at least 48 hours. This remarkable reduction in turnaround time (from 48 hours to 10 hours), achieved by minimizing the culturing period, offers a game-changing advantage for clinical applications. Our study involves a dataset comprising 400 bacterial samples (200 E. coli, 100 Klebsiella pneumoniae, and 100 Pseudomonas aeruginosa) with an impressive 96% accuracy in the taxonomic classification at the species level and up to 82% accuracy in bacterial susceptibility to various antibiotics.
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Affiliation(s)
- Manal Suleiman
- Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
| | - George Abu-Aqil
- Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
| | - Itshak Lapidot
- Department of Electrical Engineering, ACLP-Afeka Center for Language Processing, Afeka Tel-Aviv Academic College of Engineering, Tel-Aviv 69107, Israel
- Laboratoire Informatique d'Avignon (LIA), Avignon Université, 339 Chemin des Meinajaries, 84000 Avignon, France
| | - Mahmoud Huleihel
- Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
| | - Ahmad Salman
- Department of Physics, SCE - Shamoon College of Engineering, Beer-Sheva 84100, Israel.
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Sami AJ, Bilal S, Alam S, Khalid M, Mangat HA. A Method Based on a Modified Fluorescence In Situ Hybridization (FISH) Approach for the Sensing of Staphylococcus aureus from Nasal Samples. Appl Biochem Biotechnol 2024:10.1007/s12010-024-04892-9. [PMID: 38421570 DOI: 10.1007/s12010-024-04892-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2024] [Indexed: 03/02/2024]
Abstract
Staphylococcus aureus is a major source of bacteremia and develops several complications, causing high morbidity and mortality. Rapid identification and detection of these bacteria have become an important issue for biomedical applications. Herein, an optical method based on a modified fluorescence in situ hybridization (FISH) approach has been established using DNA hybridization technology for the swift detection of pathogenic S. aureus from clinical samples. The platform was constructed with single-stranded genomic DNA and microbial colony by directly immobilizing in agarose-polyvinyl alcohol (AG-PVA) hydrogel on the surface of a glass slide. The probe was based on an elongation factor encoding the tuf gene, which binds with equal affinity to single-stranded DNA targets as well as surface proteins on microbial cells. The probe was labeled with MFP488 fluorophore having excitation wavelength 501 nm. The hybridization of the labeled probe with the target DNA and surface proteins was carried out under optimal FISH conditions, and the detection of bacteria was based on temporary field excitation of the labeled probe under a fluorescence microscope. Positive hybridization signals were detected by high fluorescence intensity. In comparison to genomic DNA, robust signals were observed with microbial cells, perhaps due to the moonlighting effect of the elongation factor Tu (Ef-Tu) expressed on the surface of bacterial cells. The applicability of the developed platform was tested on pediatric nasal samples, and results were verified with real-time qPCR. The designed platform is stable and sensitive, and after detailed optimization, a portable structure for on-site detection of pathogenic bacteria from clinical samples can be produced.
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Affiliation(s)
- Amtul Jamil Sami
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, 54590, Pakistan.
- Center for Biosensor Research and Development, University of the Punjab, Lahore, 54590, Pakistan.
| | - Sehrish Bilal
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, 54590, Pakistan
- Department of Biochemistry, Gulab Devi Educational Complex, Lahore, 54600, Pakistan
| | - Sadaf Alam
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, 54590, Pakistan
| | - Madeeha Khalid
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, 54590, Pakistan
- Department of Biochemistry, University of Okara, Okara, 56300, Pakistan
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Bourceau P, Geier B, Suerdieck V, Bien T, Soltwisch J, Dreisewerd K, Liebeke M. Visualization of metabolites and microbes at high spatial resolution using MALDI mass spectrometry imaging and in situ fluorescence labeling. Nat Protoc 2023; 18:3050-3079. [PMID: 37674095 DOI: 10.1038/s41596-023-00864-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/31/2023] [Indexed: 09/08/2023]
Abstract
Label-free molecular imaging techniques such as matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) enable the direct and simultaneous mapping of hundreds of different metabolites in thin sections of biological tissues. However, in host-microbe interactions it remains challenging to localize microbes and to assign metabolites to the host versus members of the microbiome. We therefore developed a correlative imaging approach combining MALDI-MSI with fluorescence in situ hybridization (FISH) on the same section to identify and localize microbial cells. Here, we detail metaFISH as a robust and easy method for assigning the spatial distribution of metabolites to microbiome members based on imaging of nucleic acid probes, down to single-cell resolution. We describe the steps required for tissue preparation, on-tissue hybridization, fluorescence microscopy, data integration into a correlative image dataset, matrix application and MSI data acquisition. Using metaFISH, we map hundreds of metabolites and several microbial species to the micrometer scale on a single tissue section. For example, intra- and extracellular bacteria, host cells and their associated metabolites can be localized in animal tissues, revealing their complex metabolic interactions. We explain how we identify low-abundance bacterial infection sites as regions of interest for high-resolution MSI analysis, guiding the user to a trade-off between metabolite signal intensities and fluorescence signals. MetaFISH is suitable for a broad range of users from environmental microbiologists to clinical scientists. The protocol requires ~2 work days.
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Affiliation(s)
- Patric Bourceau
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Benedikt Geier
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Stanford University School of Medicine, Stanford, CA, USA
| | | | - Tanja Bien
- Institute of Hygiene, University of Münster, Münster, Germany
- Bruker Daltonics GmbH & Co. KG, Bremen, Germany
| | - Jens Soltwisch
- Institute of Hygiene, University of Münster, Münster, Germany
| | | | - Manuel Liebeke
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- Institute of Human Nutrition and Food Sciences, University of Kiel, Kiel, Germany.
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q-PCR Methodology for Monitoring the Thermophilic Hydrogen Producers Enriched from Elephant Dung. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8100506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
This study aims to create a quantitative polymerase chain reaction (q-PCR) methodology for monitoring the hydrogen-producing mixed cultures enriched from elephant dung using alpha-cellulose as a carbon source through five generations of repetitive sub-culture. The enriched thermophilic mixed cultures from the fifth cultivation cycle gave the highest hydrogen yield of 170.3 mL H2/g cellulose and were used to generate hydrogen from sawdust. Clostridium sp. and Thermoanaerobacterium sp. were the dominant bacteria in thermophilic mixed cultures with high hydrogen yield, according to polymerase chain reaction-denatured gradient gel electrophoresis (PCR-DGGE). q-PCR primers Chis150F and ClostIR, TherF and TherR, and BacdF and BacdR were developed to amplify the 16S rRNA genes of Clostridium sp., Thermoanaerobacterium sp., and Bacillus sp., respectively, for the quantification of hydrogen-producing bacteria in biohydrogen fermentation. Similar q-PCR analysis of Clostridium sp., Thermoanaerobacterium sp., and Bacillus sp. 16S rRNA gene amplification during hydrogen production from cellulose and sawdust revealed increasing gene copy number with time. The molecular approaches developed in this study can be used to monitor microbial communities in hydrogen fermentation processes efficiently.
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Kim G, Ahn D, Kang M, Park J, Ryu D, Jo Y, Song J, Ryu JS, Choi G, Chung HJ, Kim K, Chung DR, Yoo IY, Huh HJ, Min HS, Lee NY, Park Y. Rapid species identification of pathogenic bacteria from a minute quantity exploiting three-dimensional quantitative phase imaging and artificial neural network. LIGHT, SCIENCE & APPLICATIONS 2022; 11:190. [PMID: 35739098 PMCID: PMC9226356 DOI: 10.1038/s41377-022-00881-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 06/03/2022] [Accepted: 06/09/2022] [Indexed: 05/14/2023]
Abstract
The healthcare industry is in dire need of rapid microbial identification techniques for treating microbial infections. Microbial infections are a major healthcare issue worldwide, as these widespread diseases often develop into deadly symptoms. While studies have shown that an early appropriate antibiotic treatment significantly reduces the mortality of an infection, this effective treatment is difficult to practice. The main obstacle to early appropriate antibiotic treatments is the long turnaround time of the routine microbial identification, which includes time-consuming sample growth. Here, we propose a microscopy-based framework that identifies the pathogen from single to few cells. Our framework obtains and exploits the morphology of the limited sample by incorporating three-dimensional quantitative phase imaging and an artificial neural network. We demonstrate the identification of 19 bacterial species that cause bloodstream infections, achieving an accuracy of 82.5% from an individual bacterial cell or cluster. This performance, comparable to that of the gold standard mass spectroscopy under a sufficient amount of sample, underpins the effectiveness of our framework in clinical applications. Furthermore, our accuracy increases with multiple measurements, reaching 99.9% with seven different measurements of cells or clusters. We believe that our framework can serve as a beneficial advisory tool for clinicians during the initial treatment of infections.
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Affiliation(s)
- Geon Kim
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, 34141, Republic of Korea
| | - Daewoong Ahn
- Tomocube Inc., Daejeon, 34109, Republic of Korea
| | - Minhee Kang
- Smart Healthcare & Device Research Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
| | - Jinho Park
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, 34141, Republic of Korea
| | - DongHun Ryu
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, 34141, Republic of Korea
| | - YoungJu Jo
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, 34141, Republic of Korea
- Tomocube Inc., Daejeon, 34109, Republic of Korea
- Department of Applied Physics, Stanford University, Stanford, CA, 94305, USA
| | - Jinyeop Song
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, 34141, Republic of Korea
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Jea Sung Ryu
- Graduate School of Nanoscience and Technology, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Gunho Choi
- Tomocube Inc., Daejeon, 34109, Republic of Korea
| | - Hyun Jung Chung
- Graduate School of Nanoscience and Technology, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Kyuseok Kim
- Department of Emergency Medicine, Bundang CHA Hospital, Seongnam-si, Gyeonggi-Do, 13496, Korea
| | - Doo Ryeon Chung
- Division of Infectious Diseases, Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
| | - In Young Yoo
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
| | | | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea.
| | - YongKeun Park
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
- KAIST Institute for Health Science and Technology, KAIST, Daejeon, 34141, Republic of Korea.
- Tomocube Inc., Daejeon, 34109, Republic of Korea.
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Suleiman M, Abu-Aqil G, Sharaha U, Riesenberg K, Lapidot I, Salman A, Huleihel M. Infra-red spectroscopy combined with machine learning algorithms enables early determination of Pseudomonas aeruginosa's susceptibility to antibiotics. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 274:121080. [PMID: 35248858 DOI: 10.1016/j.saa.2022.121080] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 06/14/2023]
Abstract
Pseudomonas (P.) aeruginosa is a bacterium responsible for severe infections that have become a real concern in hospital environments. Nosocomial infections caused by P. aeruginosa are often hard to treat because of its intrinsic resistance and remarkable ability to acquire further resistance mechanisms to multiple groups of antimicrobial agents. Thus, rapid determination of the susceptibility of P. aeruginosa isolates to antibiotics is crucial for effective treatment. The current methods used for susceptibility determination are time-consuming; hence the importance of developing a new method. Fourier-transform infra-red (FTIR) spectroscopy is known as a rapid and sensitive diagnostic tool, with the ability to detect minor abnormal molecular changes including those associated with the development of antibiotic- resistant bacteria. The main goal of this study is to evaluate the potential of FTIR spectroscopy together with machine learning algorithms, to determine the susceptibility of P. aeruginosa to different antibiotics in a time span of ∼20 min after the first culture. For this goal, 590 isolates of P. aeruginosa, obtained from different infection sites of various patients, were measured by FTIR spectroscopy and analyzed by machine learning algorithms. We have successfully determined the susceptibility of P. aeruginosa to various antibiotics with an accuracy of 82-90%.
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Affiliation(s)
- Manal Suleiman
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - George Abu-Aqil
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Uraib Sharaha
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | | | - Itshak Lapidot
- Department of Electrical and Electronics Engineering, ACLP-Afeka Center for Language Processing, Afeka Tel-Aviv Academic College of Engineering, Tel-Aviv 69107, Israel
| | - Ahmad Salman
- Department of Physics, SCE - Shamoon College of Engineering, Beer-Sheva 84100, Israel.
| | - Mahmoud Huleihel
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
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Rapid identification of new isolates of Acidipropionibacterium acidipropionici by fluorescence in situ hybridization (FISH). Rev Argent Microbiol 2022; 54:263-267. [DOI: 10.1016/j.ram.2022.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/21/2021] [Accepted: 02/28/2022] [Indexed: 11/17/2022] Open
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Design and Experimental Evaluation of a New RNA-FISH Probe to Detect and Identify Paenibacillus sp. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12052348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Paenibacillus, rod-saped gram-positive endospores forming aerobic or facultative anaerobic bacteria, colonize diverse ecosystems and are involved in the biodegradation of cultural heritage assets. Biodeteriogenic microorganisms can be easily detected/identified by ribonucleic acid- fluorescent in situ hybridization RNA-FISH with specific probes. In this work, probes designed in silico were analyzed to calculate hybridization efficiency and specificity by varying the formamide concentration in the hybridization. The Pab489 probe showed excellent in silico performance with high theoretical maximum efficiency hybridization (99.99%) and specificity and was selected for experimental assays with target Paenibacillus sp. and non-target biodeteriogenic microorganisms. Results assessed by epifluorescence microscopy and flow cytometry revealed that, regardless of the formamide concentration, it was possible to observe that the Pab489-Cy3 probe had a similar signal intensity to the EUB338-Cy3 probe (positive control), so the presence of formamide, a highly toxic and carcinogenic compound used to aid the hybridization process, is not necessary. The designed probe used in FISH assays allows specific in situ identification of Paenibacillus spp. in microbial communities in a culture-independent way. This approach can be employed for screening Paenibacillus spp., showing great potential for future application in biodeterioration of heritage assets, in the search for Paenibacillus strains that produce compounds with biotechnological or medical potential.
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Zand E, Froehling A, Schoenher C, Zunabovic-Pichler M, Schlueter O, Jaeger H. Potential of Flow Cytometric Approaches for Rapid Microbial Detection and Characterization in the Food Industry-A Review. Foods 2021; 10:3112. [PMID: 34945663 PMCID: PMC8701031 DOI: 10.3390/foods10123112] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/14/2021] [Accepted: 11/16/2021] [Indexed: 12/11/2022] Open
Abstract
As microbial contamination is persistent within the food and bioindustries and foodborne infections are still a significant cause of death, the detection, monitoring, and characterization of pathogens and spoilage microorganisms are of great importance. However, the current methods do not meet all relevant criteria. They either show (i) inadequate sensitivity, rapidity, and effectiveness; (ii) a high workload and time requirement; or (iii) difficulties in differentiating between viable and non-viable cells. Flow cytometry (FCM) represents an approach to overcome such limitations. Thus, this comprehensive literature review focuses on the potential of FCM and fluorescence in situ hybridization (FISH) for food and bioindustry applications. First, the principles of FCM and FISH and basic staining methods are discussed, and critical areas for microbial contamination, including abiotic and biotic surfaces, water, and air, are characterized. State-of-the-art non-specific FCM and specific FISH approaches are described, and their limitations are highlighted. One such limitation is the use of toxic and mutagenic fluorochromes and probes. Alternative staining and hybridization approaches are presented, along with other strategies to overcome the current challenges. Further research needs are outlined in order to make FCM and FISH even more suitable monitoring and detection tools for food quality and safety and environmental and clinical approaches.
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Affiliation(s)
- Elena Zand
- Department of Food Science and Technology, Institute of Food Technology, University of Natural Resources and Life Sciences Vienna (BOKU), 1190 Vienna, Austria;
| | - Antje Froehling
- Leibniz Institute for Agricultural Engineering and Bioeconomy, Quality and Safety of Food and Feed, 14469 Potsdam, Germany; (A.F.); (O.S.)
| | - Christoph Schoenher
- Institute of Sanitary Engineering and Water Pollution Control, University of Natural Resources and Life Sciences, 1190 Vienna, Austria; (C.S.); (M.Z.-P.)
| | - Marija Zunabovic-Pichler
- Institute of Sanitary Engineering and Water Pollution Control, University of Natural Resources and Life Sciences, 1190 Vienna, Austria; (C.S.); (M.Z.-P.)
| | - Oliver Schlueter
- Leibniz Institute for Agricultural Engineering and Bioeconomy, Quality and Safety of Food and Feed, 14469 Potsdam, Germany; (A.F.); (O.S.)
| | - Henry Jaeger
- Department of Food Science and Technology, Institute of Food Technology, University of Natural Resources and Life Sciences Vienna (BOKU), 1190 Vienna, Austria;
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Turzynski V, Monsees I, Moraru C, Probst AJ. Imaging Techniques for Detecting Prokaryotic Viruses in Environmental Samples. Viruses 2021; 13:2126. [PMID: 34834933 PMCID: PMC8622608 DOI: 10.3390/v13112126] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 12/28/2022] Open
Abstract
Viruses are the most abundant biological entities on Earth with an estimate of 1031 viral particles across all ecosystems. Prokaryotic viruses-bacteriophages and archaeal viruses-influence global biogeochemical cycles by shaping microbial communities through predation, through the effect of horizontal gene transfer on the host genome evolution, and through manipulating the host cellular metabolism. Imaging techniques have played an important role in understanding the biology and lifestyle of prokaryotic viruses. Specifically, structure-resolving microscopy methods, for example, transmission electron microscopy, are commonly used for understanding viral morphology, ultrastructure, and host interaction. These methods have been applied mostly to cultivated phage-host pairs. However, recent advances in environmental genomics have demonstrated that the majority of viruses remain uncultivated, and thus microscopically uncharacterized. Although light- and structure-resolving microscopy of viruses from environmental samples is possible, quite often the link between the visualization and the genomic information of uncultivated prokaryotic viruses is missing. In this minireview, we summarize the current state of the art of imaging techniques available for characterizing viruses in environmental samples and discuss potential links between viral imaging and environmental genomics for shedding light on the morphology of uncultivated viruses and their lifestyles in Earth's ecosystems.
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Affiliation(s)
- Victoria Turzynski
- Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany;
| | - Indra Monsees
- Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany;
| | - Cristina Moraru
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl-von-Ossietzky-University Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26111 Oldenburg, Germany;
| | - Alexander J. Probst
- Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany;
- Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
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11
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Kushkevych I, Hýžová B, Vítězová M, Rittmann SKMR. Microscopic Methods for Identification of Sulfate-Reducing Bacteria from Various Habitats. Int J Mol Sci 2021; 22:4007. [PMID: 33924516 PMCID: PMC8069399 DOI: 10.3390/ijms22084007] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/31/2021] [Accepted: 04/03/2021] [Indexed: 12/01/2022] Open
Abstract
This paper is devoted to microscopic methods for the identification of sulfate-reducing bacteria (SRB). In this context, it describes various habitats, morphology and techniques used for the detection and identification of this very heterogeneous group of anaerobic microorganisms. SRB are present in almost every habitat on Earth, including freshwater and marine water, soils, sediments or animals. In the oil, water and gas industries, they can cause considerable economic losses due to their hydrogen sulfide production; in periodontal lesions and the colon of humans, they can cause health complications. Although the role of these bacteria in inflammatory bowel diseases is not entirely known yet, their presence is increased in patients and produced hydrogen sulfide has a cytotoxic effect. For these reasons, methods for the detection of these microorganisms were described. Apart from selected molecular techniques, including metagenomics, fluorescence microscopy was one of the applied methods. Especially fluorescence in situ hybridization (FISH) in various modifications was described. This method enables visual identification of SRB, determining their abundance and spatial distribution in environmental biofilms and gut samples.
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Affiliation(s)
- Ivan Kushkevych
- Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic; (B.H.); (M.V.)
| | - Blanka Hýžová
- Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic; (B.H.); (M.V.)
| | - Monika Vítězová
- Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic; (B.H.); (M.V.)
| | - Simon K.-M. R. Rittmann
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, 1090 Wien, Austria
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12
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Liu T, Nadaraja AV, Friesen J, Gill K, Lam MI, Roberts DJ. Narrow pH tolerance found for a microbial fuel cell treating winery wastewater. J Appl Microbiol 2021; 131:2280-2293. [PMID: 33843137 DOI: 10.1111/jam.15102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 03/11/2021] [Accepted: 03/31/2021] [Indexed: 11/30/2022]
Abstract
AIMS The use of microbial fuel cells (MFC) to treat winery wastewater is promising; however, an initial acidic pH, fluctuating chemical oxygen demand (COD) levels and a lack of natural buffering in these wastewaters make providing a suitable buffer system at an ideal buffer to COD ratio. METHODS AND RESULTS A lab scale MFC was designed, inoculated with anaerobic winery sludge and fed with synthetic winery wastewater. It was observed that at pH 6·5, the MFC performed best, the maximum output voltage was 0·63 ± 0·01 V for 60 ± 3 h, and the COD removal efficiency reached 77 ± 7%. The electrogens were affected by pH much more than the bulk COD degrading organisms. Fluorescent in situ hybridization suggested Betaproteobacteria played a significant role in electron transfer. CONCLUSIONS A ratio of 1 mmol l-1 phosphate buffer to 100 mg l-1 COD was ideal to maintain a stable pH for MFCs treating synthetic winery wastewater. SIGNIFICANCE AND IMPACT OF THE STUDY The results find the narrow pH tolerance for MFCs treating winery wastewater and demonstrate the significance of pH and buffer to COD ratio for steady performance of MFCs.
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Affiliation(s)
- T Liu
- School of Engineering, The University of British Columbia Okanagan, Kelowna, BC, Canada
| | - A V Nadaraja
- School of Engineering, The University of British Columbia Okanagan, Kelowna, BC, Canada
| | - J Friesen
- School of Engineering, The University of British Columbia Okanagan, Kelowna, BC, Canada
| | - K Gill
- School of Engineering, The University of British Columbia Okanagan, Kelowna, BC, Canada
| | - M I Lam
- School of Engineering, The University of British Columbia Okanagan, Kelowna, BC, Canada
| | - D J Roberts
- School of Engineering, The University of British Columbia Okanagan, Kelowna, BC, Canada.,Faculty of Science and Engineering, University of Northern British Columbia, Prince George, BC, Canada
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Aromokeye DA, Oni OE, Tebben J, Yin X, Richter-Heitmann T, Wendt J, Nimzyk R, Littmann S, Tienken D, Kulkarni AC, Henkel S, Hinrichs KU, Elvert M, Harder T, Kasten S, Friedrich MW. Crystalline iron oxides stimulate methanogenic benzoate degradation in marine sediment-derived enrichment cultures. THE ISME JOURNAL 2021; 15:965-980. [PMID: 33154547 PMCID: PMC8115662 DOI: 10.1038/s41396-020-00824-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 10/09/2020] [Accepted: 10/22/2020] [Indexed: 01/29/2023]
Abstract
Elevated dissolved iron concentrations in the methanic zone are typical geochemical signatures of rapidly accumulating marine sediments. These sediments are often characterized by co-burial of iron oxides with recalcitrant aromatic organic matter of terrigenous origin. Thus far, iron oxides are predicted to either impede organic matter degradation, aiding its preservation, or identified to enhance organic carbon oxidation via direct electron transfer. Here, we investigated the effect of various iron oxide phases with differing crystallinity (magnetite, hematite, and lepidocrocite) during microbial degradation of the aromatic model compound benzoate in methanic sediments. In slurry incubations with magnetite or hematite, concurrent iron reduction, and methanogenesis were stimulated during accelerated benzoate degradation with methanogenesis as the dominant electron sink. In contrast, with lepidocrocite, benzoate degradation, and methanogenesis were inhibited. These observations were reproducible in sediment-free enrichments, even after five successive transfers. Genes involved in the complete degradation of benzoate were identified in multiple metagenome assembled genomes. Four previously unknown benzoate degraders of the genera Thermincola (Peptococcaceae, Firmicutes), Dethiobacter (Syntrophomonadaceae, Firmicutes), Deltaproteobacteria bacteria SG8_13 (Desulfosarcinaceae, Deltaproteobacteria), and Melioribacter (Melioribacteraceae, Chlorobi) were identified from the marine sediment-derived enrichments. Scanning electron microscopy (SEM) and catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) images showed the ability of microorganisms to colonize and concurrently reduce magnetite likely stimulated by the observed methanogenic benzoate degradation. These findings explain the possible contribution of organoclastic reduction of iron oxides to the elevated dissolved Fe2+ pool typically observed in methanic zones of rapidly accumulating coastal and continental margin sediments.
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Affiliation(s)
- David A. Aromokeye
- grid.7704.40000 0001 2297 4381Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany ,grid.7704.40000 0001 2297 4381MARUM—Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Oluwatobi E. Oni
- grid.7704.40000 0001 2297 4381Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Jan Tebben
- grid.10894.340000 0001 1033 7684Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Xiuran Yin
- grid.7704.40000 0001 2297 4381Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany ,grid.7704.40000 0001 2297 4381MARUM—Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Tim Richter-Heitmann
- grid.7704.40000 0001 2297 4381Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Jenny Wendt
- grid.7704.40000 0001 2297 4381MARUM—Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany ,grid.7704.40000 0001 2297 4381Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Rolf Nimzyk
- grid.7704.40000 0001 2297 4381Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Sten Littmann
- grid.419529.20000 0004 0491 3210Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Daniela Tienken
- grid.419529.20000 0004 0491 3210Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Ajinkya C. Kulkarni
- grid.7704.40000 0001 2297 4381Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Susann Henkel
- grid.7704.40000 0001 2297 4381MARUM—Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany ,grid.10894.340000 0001 1033 7684Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Kai-Uwe Hinrichs
- grid.7704.40000 0001 2297 4381MARUM—Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany ,grid.7704.40000 0001 2297 4381Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Marcus Elvert
- grid.7704.40000 0001 2297 4381MARUM—Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany ,grid.7704.40000 0001 2297 4381Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Tilmann Harder
- grid.7704.40000 0001 2297 4381Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany ,grid.10894.340000 0001 1033 7684Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Sabine Kasten
- grid.7704.40000 0001 2297 4381MARUM—Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany ,grid.10894.340000 0001 1033 7684Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany ,grid.7704.40000 0001 2297 4381Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Michael W. Friedrich
- grid.7704.40000 0001 2297 4381Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany ,grid.7704.40000 0001 2297 4381MARUM—Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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14
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Salakkam A, Sittijunda S, Mamimin C, Phanduang O, Reungsang A. Valorization of microalgal biomass for biohydrogen generation: A review. BIORESOURCE TECHNOLOGY 2021; 322:124533. [PMID: 33348113 DOI: 10.1016/j.biortech.2020.124533] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 12/05/2020] [Accepted: 12/08/2020] [Indexed: 05/16/2023]
Abstract
Third generation biomass, i.e. microalgae, has emerged as a promising alternative to first and second generation biomass for biohydrogen production. However, its utilization is still low at present, due to several reasons including the strong and rigidity of the microalgal cell wall that limit the hydrolysis efficiency during dark fermentation (DF) and photofermentation (PF) processes. To improve the utilization efficiency of microalgal biomass, it is crucial that important aspects related to the production of the biomass and the following processes are elaborated. Thus, this article provides detailed overview of algal strains, cultivation, and harvesting. It also presents recent research and detailed information on microalgal biomass pretreatment, and biohydrogen production through DF, PF, and co-digestion of microalgal biomass with organic materials. Furthermore, factors affecting fermentation processes performance and the use of molecular techniques in biohydrogen production are presented. This review also discusses challenges and future prospects towards biohydrogen production from microalgal biomass.
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Affiliation(s)
- Apilak Salakkam
- Department of Biotechnology, Faculty of Technology, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Sureewan Sittijunda
- Faculty of Environment and Resource Studies, Mahidol University, Nakhon Pathom 73170, Thailand
| | - Chonticha Mamimin
- Department of Biotechnology, Faculty of Technology, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Orawan Phanduang
- Department of Biotechnology, Faculty of Technology, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Alissara Reungsang
- Department of Biotechnology, Faculty of Technology, Khon Kaen University, Khon Kaen 40002, Thailand; Research Group for Development of Microbial Hydrogen Production Process from Biomass, Khon Kaen University, Khon Kaen 40002, Thailand; Academy of Science, Royal Society of Thailand, Bangkok 10300, Thailand.
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15
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Matturro B, Rossetti S, Leitão P. CAtalyzed Reporter Deposition Fluorescence In Situ Hybridization (CARD-FISH) for Complex Environmental Samples. Methods Mol Biol 2021; 2246:129-140. [PMID: 33576987 DOI: 10.1007/978-1-0716-1115-9_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
CARD-FISH technique allows us to increase microbial cell detection compared to traditional FISH assays. Specific nonfluorescent oligonucleotide probes targeting 16S rRNA genes are employed and are chemically activated by the binding of tyramide molecules, with the latter able to generate a cascade of fluorescence signals, improving sensitivity and reducing background noise. The technique has been successfully applied for the detection of microorganisms in different environmental matrices and under different growth conditions (including those where cells are characterized by low physiological activity and low ribosome content). This chapter presents a straightforward procedure to execute CARD-FISH analysis, from sample preparation and fixation, to microscopic visualization, along with relevant technical notes.
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Affiliation(s)
- Bruna Matturro
- Water Research Institute (IRSA), National Research Council (CNR), Monterotondo St. (RM), 00015, Italy.
| | - Simona Rossetti
- Water Research Institute (IRSA), National Research Council (CNR), Monterotondo St. (RM), 00015, Italy
| | - Patrícia Leitão
- Cento de Recursos Naturais e Ambiente (CERENA), Faculty of Engineering, University of Porto, Porto, Portugal
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16
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Teixeira H, Sousa AL, Azevedo AS. Bioinformatic Tools and Guidelines for the Design of Fluorescence In Situ Hybridization Probes. Methods Mol Biol 2021; 2246:35-50. [PMID: 33576981 DOI: 10.1007/978-1-0716-1115-9_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Fluorescence in situ hybridization (FISH) is a well-established technique that allows the detection of microorganisms in diverse types of samples (e.g., clinical, food, environmental samples, and biofilm communities). The FISH probe design is an essential step in this technique. For this, two strategies can be used, the manual form based on multiple sequence alignment to identify conserved regions and programs/software specifically developed for the selection of the sequence of the probe. Additionally, databases/software for the theoretical evaluation of the probes in terms of specificity, sensitivity, and thermodynamic parameters (melting temperature and Gibbs free energy change) are used. The purpose of this chapter is to describe the essential steps and guidelines for the design of FISH probes (e.g., DNA and Nucleic Acid Mimic (NAM) probes), and its theoretical evaluation through the application of diverse bioinformatic tools.
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Affiliation(s)
- Helena Teixeira
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Ana L Sousa
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal.,INIAV - National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, Lugar da Madalena, Vairão, Vila do Conde, Portugal
| | - Andreia S Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal. .,i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal. .,IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal. .,CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal.
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17
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Phosphate-Solubilizing Fungi: Current Perspective and Future Need for Agricultural Sustainability. Fungal Biol 2021. [DOI: 10.1007/978-3-030-60659-6_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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18
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Foladori P, Petrini S, Bruni L, Andreottola G. Bacteria and photosynthetic cells in a photobioreactor treating real municipal wastewater: Analysis and quantification using flow cytometry. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101969] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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19
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Branco P, Candeias A, Caldeira AT, González-Pérez M. A simple procedure for detecting Dekkera bruxellensis in wine environment by RNA-FISH using a novel probe. Int J Food Microbiol 2020; 314:108415. [PMID: 31707175 DOI: 10.1016/j.ijfoodmicro.2019.108415] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 09/30/2019] [Accepted: 10/28/2019] [Indexed: 11/30/2022]
Abstract
Dekkera bruxellensis, considered the major microbial contaminant in wine production, produces 4-ethylphenol, a cause of unpleasant odors. Thus, identification of this yeast before wine spoilage is crucial. Although challenging, it could be achieved using a simple technique: RNA-FISH. To reach it is necessary to design probes that allow specific detection/identification of D. bruxellensis among the wine microorganisms and in the wine environment and, if possible, using low formamide concentrations. Therefore, this study was focused on: a) designing a DNA-FISH probe to identify D. bruxellensis that matches these requirements and b) determining the applicability of the RNA-FISH procedure after the end of the alcoholic fermentation and in wine. A novel DNA-FISH D. bruxellensis probe with good performance and specificity was designed. The application of this probe using an in-suspension RNA-FISH protocol (applying only 5% of formamide) allowed the early detection/identification of D. bruxellensis at low cell densities (5 × 102 cell/mL). This was possible by flow cytometry independently of the growth stage of the target cells, both at the end of the alcoholic fermentation and in wine even in the presence of high S. cerevisiae cell densities. Thus, this study aims to contribute to facilitate the identification of D. bruxellensis before wine spoilage occurs, preventing economic losses to the wine industry.
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Affiliation(s)
- Patrícia Branco
- HERCULES Laboratory, Évora University, Largo Marquês de Marialva 8, 7000-809 Évora, Portugal
| | - António Candeias
- HERCULES Laboratory, Évora University, Largo Marquês de Marialva 8, 7000-809 Évora, Portugal; Chemistry Department, School of Sciences and Technology, Évora University, Rua Romão Ramalho 59, 7000-671 Évora, Portugal
| | - Ana Teresa Caldeira
- HERCULES Laboratory, Évora University, Largo Marquês de Marialva 8, 7000-809 Évora, Portugal; Chemistry Department, School of Sciences and Technology, Évora University, Rua Romão Ramalho 59, 7000-671 Évora, Portugal
| | - Marina González-Pérez
- HERCULES Laboratory, Évora University, Largo Marquês de Marialva 8, 7000-809 Évora, Portugal.
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20
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Giaretta PR, Suchodolski JS, Jergens AE, Steiner JM, Lidbury JA, Cook AK, Hanifeh M, Spillmann T, Kilpinen S, Syrjä P, Rech RR. Bacterial Biogeography of the Colon in Dogs With Chronic Inflammatory Enteropathy. Vet Pathol 2020; 57:258-265. [PMID: 31916499 DOI: 10.1177/0300985819891259] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The intestinal microbiota is believed to play a role in the pathogenesis of inflammatory bowel disease in humans and chronic inflammatory enteropathy (CIE) in dogs. While most previous studies have described the gut microbiota using sequencing methods, it is fundamental to assess the spatial distribution of the bacteria for a better understanding of their relationship with the host. The microbiota in the colonic mucosa of 22 dogs with CIE and 11 control dogs was investigated using fluorescence in situ hybridization (FISH) with a universal eubacterial probe (EUB338) and specific probes for select bacterial groups. The number of total bacteria labeled with EUB338 probe was lower within the colonic crypts of dogs with CIE compared to controls. Helicobacter spp. and Akkermansia spp. were decreased on the colonic surface and in the crypts of dogs with CIE. Dogs with CIE had increased number of Escherichia coli/Shigella spp. on the colonic surface and within the crypts compared to control dogs. In conclusion, the bacterial microbiota in the colonic mucosa differed between dogs with and without CIE, with depletion of the crypt bacteria in dogs with CIE. The crypt bacterial species that was intimately associated with the host mucosa in control dogs was composed mainly of Helicobacter spp.
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Affiliation(s)
- Paula R Giaretta
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Jan S Suchodolski
- Department of Small Animal Clinical Sciences, Gastrointestinal Laboratory, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Albert E Jergens
- Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Jörg M Steiner
- Department of Small Animal Clinical Sciences, Gastrointestinal Laboratory, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Jonathan A Lidbury
- Department of Small Animal Clinical Sciences, Gastrointestinal Laboratory, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Audrey K Cook
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Mohsen Hanifeh
- Faculty of Veterinary Medicine, Department of Equine and Small Animal Medicine, University of Helsinki, Helsinki, Finland
| | - Thomas Spillmann
- Faculty of Veterinary Medicine, Department of Equine and Small Animal Medicine, University of Helsinki, Helsinki, Finland
| | - Susanne Kilpinen
- Faculty of Veterinary Medicine, Department of Equine and Small Animal Medicine, University of Helsinki, Helsinki, Finland
| | - Pernilla Syrjä
- Faculty of Veterinary Medicine, Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Raquel R Rech
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
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21
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Fluorescence in situ hybridization (FISH) and cell sorting of living bacteria. Sci Rep 2019; 9:18618. [PMID: 31819112 PMCID: PMC6901588 DOI: 10.1038/s41598-019-55049-2] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 11/21/2019] [Indexed: 01/09/2023] Open
Abstract
Despite the development of several cultivation methods, the rate of discovery of microorganisms that are yet-to-be cultivated outpaces the rate of isolating and cultivating novel species in the laboratory. Furthermore, no current cultivation technique is capable of selectively isolating and cultivating specific bacterial taxa or phylogenetic groups independently of morphological or physiological properties. Here, we developed a new method to isolate living bacteria solely based on their 16S rRNA gene sequence. We showed that bacteria can survive a modified version of the standard fluorescence in situ hybridization (FISH) procedure, in which fixation is omitted and other factors, such as centrifugation and buffers, are optimized. We also demonstrated that labelled DNA probes can be introduced into living bacterial cells by means of chemical transformation and that specific hybridization occurs. This new method, which we call live-FISH, was then combined with fluorescence-activated cell sorting (FACS) to sort specific taxonomic groups of bacteria from a mock and natural bacterial communities and subsequently culture them. Live-FISH represents the first attempt to systematically optimize conditions known to affect cell viability during FISH and then to sort bacterial cells surviving the procedure. No sophisticated probe design is required, making live-FISH a straightforward method to be potentially used in combination with other single-cell techniques and for the isolation and cultivation of new microorganisms.
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22
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Olowomofe TO, Oluyege JO, Aderiye B, Oluwole OA. Degradation of poly aromatic fractions of crude oil and detection of catabolic genes in hydrocarbon-degrading bacteria isolated from Agbabu bitumen sediments in Ondo State. AIMS Microbiol 2019; 5:308-323. [PMID: 31915745 PMCID: PMC6946641 DOI: 10.3934/microbiol.2019.4.308] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 09/09/2019] [Indexed: 11/29/2022] Open
Abstract
Pollution due to release of Poly aromatic hydrocarbons (PAHs) are a major environmental issue especially in oil producing communities. This study investigates the polyaromatic hydrocarbon degradation potentials of some bacteria: Campylobacter hominis, Bacillus cereus, Dyadobacter koreensis, Pseudomonas aeruginosa and Micrococcus luteus isolated from Agbabu bitumen sediments in Ondo State. The isolates were used singly and in consortium for the degradation of Bonny light crude oil. Concentrations of residual aromatic hydrocarbons in crude oil degraded by these isolates were determined by Gas chromatography/Mass Spectroscopy with flame ionization detector (FID). Detection of catabolic genes (nahH, CatA and AlkB) in the isolates was determined by PCR amplification of their specific primers. The GC-MS analyses showed degradation of poly aromatic hydrocarbons (PAHs) by these isolates. The consortium exhibited the highest PAH reduction (73%) while C. hominis had the least PAH reduction (56%). Dyadobacter koreensis, P. aeruginosa, Micrococcus luteus and B. cereus, displayed 66%, 60%, 59% and 58% PAH reduction respectively. The catabolic gene nahH gene was present in B. cereus, D. koreensis, P. aeruginosa and M. luteus, alkB gene was present in B. cereus, C. hominis, and D. koreensis while CatA was not detected in any of the isolates. The findings of this study affirmed the hydrocarbon-degrading abilities and presence of catabolic genes in these bacteria, these make them potential tools in oil prospecting and cleaning up of hydrocarbon contaminated sites.
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Affiliation(s)
| | - J. O. Oluyege
- Department of Microbiology, Ekiti State University, Ado-Ekiti
| | - B.I. Aderiye
- Department of Microbiology, Ekiti State University, Ado-Ekiti
| | - O. A. Oluwole
- Department of Science and Laboratory Technology, Ekiti State University, Ado-Ekiti
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23
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Optimizing locked nucleic acid/2'-O-methyl-RNA fluorescence in situ hybridization (LNA/2'OMe-FISH) procedure for bacterial detection. PLoS One 2019; 14:e0217689. [PMID: 31150460 PMCID: PMC6544301 DOI: 10.1371/journal.pone.0217689] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 05/16/2019] [Indexed: 01/23/2023] Open
Abstract
Despite the successful application of LNA/2'OMe-FISH procedures for bacteria detection, there is a lack of knowledge on the properties that affect hybridization. Such information is crucial for the rational design of protocols. Hence, this work aimed to evaluate the effect of three essential factors on the LNA/2'OMe hybridization step-hybridization temperature, NaCl concentration and type and concentration of denaturant (formamide, ethylene carbonate and urea). This optimization was performed for 3 Gram-negative bacteria (Escherichia coli, Pseudomonas aeruginosa and Citrobacter freundii) and 2 Gram-positive bacteria (Enterococcus faecalis and Staphylococcus epidermidis), employing the response surface methodology and a Eubacteria probe. In general, it was observed that a high NaCl concentration is beneficial (from 2 M to 5 M), regardless of the denaturant used. Urea, formamide and ethylene carbonate are suitable denaturants for LNA/2'OMe-FISH applications; but urea provides higher fluorescence intensities among the different bacteria, especially for gram-positive bacteria and for P. aeruginosa. However, a unique optimal protocol was not found for all tested bacteria. Despite this, the results indicate that a hybridization solution with 2 M of urea and 4 M of NaCl would be a proper starting point. Furthermore, a hybridization temperature around 62°C, for 14 bp probes with LNA monomers at every third position of 2'OMe and 64% of GC content, should be use in initial optimization of new LNA/2'OMe-FISH protocols.
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24
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Perera IA, Abinandan S, Subashchandrabose SR, Venkateswarlu K, Naidu R, Megharaj M. Advances in the technologies for studying consortia of bacteria and cyanobacteria/microalgae in wastewaters. Crit Rev Biotechnol 2019; 39:709-731. [PMID: 30971144 DOI: 10.1080/07388551.2019.1597828] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The excessive generation and discharge of wastewaters have been serious concerns worldwide in the recent past. From an environmental friendly perspective, bacteria, cyanobacteria and microalgae, and the consortia have been largely considered for biological treatment of wastewaters. For efficient use of bacteria‒cyanobacteria/microalgae consortia in wastewater treatment, detailed knowledge on their structure, behavior and interaction is essential. In this direction, specific analytical tools and techniques play a significant role in studying these consortia. This review presents a critical perspective on physical, biochemical and molecular techniques such as microscopy, flow cytometry with cell sorting, nanoSIMS and omics approaches used for systematic investigations of the structure and function, particularly nutrient removal potential of bacteria‒cyanobacteria/microalgae consortia. In particular, the use of specific molecular techniques of genomics, transcriptomics, proteomics metabolomics and genetic engineering to develop more stable consortia of bacteria and cyanobacteria/microalgae with their improved biotechnological capabilities in wastewater treatment has been highlighted.
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Affiliation(s)
- Isiri Adhiwarie Perera
- a Global Centre for Environmental Remediation (GCER), Faculty of Science , The University of Newcastle , Callaghan , New South Wales , Australia
| | - Sudharsanam Abinandan
- a Global Centre for Environmental Remediation (GCER), Faculty of Science , The University of Newcastle , Callaghan , New South Wales , Australia
| | - Suresh R Subashchandrabose
- a Global Centre for Environmental Remediation (GCER), Faculty of Science , The University of Newcastle , Callaghan , New South Wales , Australia.,b Cooperative Research Centre for Contamination Assessment and Remediation of Environment (CRC CARE) , The University of Newcastle , Callaghan , New South Wales , Australia
| | - Kadiyala Venkateswarlu
- c Formerly Department of Microbiology , Sri Krishnadevaraya University , Anantapuramu , Andhra Pradesh , India
| | - Ravi Naidu
- a Global Centre for Environmental Remediation (GCER), Faculty of Science , The University of Newcastle , Callaghan , New South Wales , Australia.,b Cooperative Research Centre for Contamination Assessment and Remediation of Environment (CRC CARE) , The University of Newcastle , Callaghan , New South Wales , Australia
| | - Mallavarapu Megharaj
- a Global Centre for Environmental Remediation (GCER), Faculty of Science , The University of Newcastle , Callaghan , New South Wales , Australia.,b Cooperative Research Centre for Contamination Assessment and Remediation of Environment (CRC CARE) , The University of Newcastle , Callaghan , New South Wales , Australia
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25
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Lippmann T, Braubach P, Ettinger M, Kuehnel M, Laenger F, Jonigk D. Fluorescence in Situ Hybridization (FISH) for the Diagnosis of Periprosthetic Joint Infection in Formalin-Fixed Paraffin-Embedded Surgical Tissues. J Bone Joint Surg Am 2019; 101:e5. [PMID: 30653049 DOI: 10.2106/jbjs.18.00243] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
BACKGROUND As the number of arthroplasties performed increases, periprosthetic joint infection (PJI) represents a common and challenging problem. The Musculoskeletal Infection Society (MSIS) recommends diagnosing PJI according to its guidelines. The aim of the current study was to assess whether fluorescence in situ hybridization (FISH) analysis of formalin-fixed paraffin-embedded periprosthetic membranes can successfully improve the diagnosis of infection in patients with orthopaedic implants. METHODS We retrospectively analyzed 88 periprosthetic membranes of joint prostheses using FISH analysis according to a standard protocol, with a probe targeting a sequence found in most bacteria. We compared the results with routine clinical classification according to the guidelines of the MSIS, microbiological culture, and histopathological classification according to Morawietz and Krenn. We additionally performed FISH analysis using 2 species-specific probes for several culture-positive cases. RESULTS FISH successfully detected bacteria in 38 (95%) of 40 periprosthetic membranes that were rated positive by clinical classification. FISH results compared with clinical classification demonstrated a sensitivity of 95% (95% confidence interval [CI], 83.08% to 99.39%), a specificity of 85.42% (95% CI, 72.24% to 93.93%), a positive predictive value of 84.44% (95% CI, 70.55% to 93.50%), and a negative predictive value of 95.35% (95% CI, 84.19% to 99.43%). FISH results compared with histopathological classification demonstrated a sensitivity of 95.12% (95% CI, 83.47% to 99.40%), a specificity of 87.23% (95% CI, 74.26% to 95.17%), a positive predictive value of 86.67% (95% CI, 73.21% to 94.95%), and a negative predictive value of 95.35% (95% CI, 84.19% to 99.43%). We successfully detected Pseudomonas aeruginosa and Staphylococcus aureus with species-specific FISH probes in all cases that were positive for these respective bacteria by microbiological culture. CONCLUSIONS FISH-based diagnosis of PJI is feasible and can be used as an additional diagnostic criterion. FISH not only can detect bacteria in periprosthetic membranes but can also differentiate pathogens at the species level. FISH represents a fast and reliable tool for detecting PJI in periprosthetic membranes, especially in combination with clinical and histopathological classification. LEVEL OF EVIDENCE Diagnostic Level III. See Instructions for Authors for a complete description of levels of evidence.
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Affiliation(s)
- Torsten Lippmann
- Institute of Pathology (T.L., P.B., M.K., F.L., and D.J.) and Department of Orthopaedic Surgery (M.E.), Hannover Medical School (MHH), Hannover, Germany
| | - Peter Braubach
- Institute of Pathology (T.L., P.B., M.K., F.L., and D.J.) and Department of Orthopaedic Surgery (M.E.), Hannover Medical School (MHH), Hannover, Germany
| | - Max Ettinger
- Institute of Pathology (T.L., P.B., M.K., F.L., and D.J.) and Department of Orthopaedic Surgery (M.E.), Hannover Medical School (MHH), Hannover, Germany
| | - Mark Kuehnel
- Institute of Pathology (T.L., P.B., M.K., F.L., and D.J.) and Department of Orthopaedic Surgery (M.E.), Hannover Medical School (MHH), Hannover, Germany
| | - Florian Laenger
- Institute of Pathology (T.L., P.B., M.K., F.L., and D.J.) and Department of Orthopaedic Surgery (M.E.), Hannover Medical School (MHH), Hannover, Germany.,Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (Deutsches Zentrum für Lungenforschung [DZL]), Hannover, Germany
| | - Danny Jonigk
- Institute of Pathology (T.L., P.B., M.K., F.L., and D.J.) and Department of Orthopaedic Surgery (M.E.), Hannover Medical School (MHH), Hannover, Germany.,Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (Deutsches Zentrum für Lungenforschung [DZL]), Hannover, Germany
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Pala C, Molari M, Nizzoli D, Bartoli M, Viaroli P, Manini E. Environmental Drivers Controlling Bacterial and Archaeal Abundance in the Sediments of a Mediterranean Lagoon Ecosystem. Curr Microbiol 2018; 75:1147-1155. [PMID: 29766233 PMCID: PMC6096605 DOI: 10.1007/s00284-018-1503-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 04/27/2018] [Indexed: 02/02/2023]
Abstract
The environmental factors controlling the abundance of Bacteria and Archaea in lagoon ecosystems are poorly understood. Here, an integrated physico-chemical, biogeochemical, and microbiological survey was applied in the Sacca di Goro lagoon (Po River Delta, Italy) to investigate the variation of bacterial and archaeal abundance, as assessed by Fluorescence In Situ Hybridization, along winter and summer environmental gradients. We hypothesised that bacterial and archaeal cells respond differentially to physico-chemical parameters of the sediment, which can be manifested in variations of total cells number. Our results suggest that Archaea are an important component of microbial communities (up to 20%) and they are also quite constant along the sediment depth investigated, while Bacteria tend to decrease in the subsurface sediments. The abiotic (i.e. temperature, ammonium, pH) and trophic parameters (i.e. chlorophyll a) explain differentially the variations of bacterial and archaeal distribution, and raise interesting questions about the ecological significance of the microbial composition in this area.
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Affiliation(s)
- Claudia Pala
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.
- Institute for Marine Science - ISMAR, National Research Council of Italy - CNR, Ancona, Italy.
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359, Bremen, Germany.
| | - Massimiliano Molari
- Institute for Marine Science - ISMAR, National Research Council of Italy - CNR, Ancona, Italy
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359, Bremen, Germany
| | - Daniele Nizzoli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Marco Bartoli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Pierluigi Viaroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Elena Manini
- Institute for Marine Science - ISMAR, National Research Council of Italy - CNR, Ancona, Italy
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Invasive pulmonary aspergillosis: current diagnostic methodologies and a new molecular approach. Eur J Clin Microbiol Infect Dis 2018; 37:1393-1403. [DOI: 10.1007/s10096-018-3251-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Accepted: 04/05/2018] [Indexed: 12/11/2022]
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28
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Khan MA, Patel PG, Ganesh AG, Rais N, Faheem SM, Khan ST. Assessing Methanogenic Archaeal Community in Full Scale Anaerobic Sludge Digester Systems in Dubai, United Arab Emirates. Open Microbiol J 2018; 12:123-134. [PMID: 29785219 PMCID: PMC5960743 DOI: 10.2174/1874285801812010123] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 04/18/2018] [Accepted: 04/19/2018] [Indexed: 11/22/2022] Open
Abstract
Introduction: Anaerobic digestion for methane production comprises of an exceptionally diverse microbial consortium, a profound understanding about which is still constrained. In this study, the methanogenic archaeal communities in three full-scale anaerobic digesters of a Municipal Wastewater Treatment Plant were analyzed by Fluorescence in situ hybridization and quantitative real-time Polymerase Chain Reaction (qPCR) technique. Methods & Materials: Fluorescence in situ hybridization (FISH) was performed to detect and quantify the methanogenic Archaea in the sludge samples whereas qPCR was carried out to support the FISH analysis. Multiple probes targeting domain archaea, different orders and families of Archaea were used for the studies. Results and Discussion: In general, the aceticlastic organisms (Methanosarcinaceae & Methanosaetaceae) were more abundant than the hydrogenotrophic organisms (Methanobacteriales, Methanomicrobiales, Methanobacteriaceae & Methanococcales). Both FISH and qPCR indicated that family Methanosaetaceae was the most abundant suggesting that aceticlastic methanogenesis is probably the dominant methane production pathway in these digesters. Conclusion: Future work involving high-throughput sequencing methods and correlating archaeal communities with the main operational parameters of anaerobic digesters will help to obtain a better understanding of the dynamics of the methanogenic archaeal community in wastewater treatment plants in United Arab Emirates (UAE) which in turn would lead to improved performance of anaerobic sludge digesters.
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Affiliation(s)
- Munawwar A Khan
- Department of Life and Environmental Sciences, College of Natural and Health Sciences, Zayed University, P.O.Box: 19282, Dubai, UAE
| | - Poojabahen G Patel
- School of Life Sciences, Manipal University, Dubai International Academic City, P.O.Box 345050, Dubai, UAE
| | - Arpitha G Ganesh
- Department of Life and Environmental Sciences, College of Natural and Health Sciences, Zayed University, P.O.Box: 19282, Dubai, UAE
| | - Naushad Rais
- School of Life Sciences, Manipal University, Dubai International Academic City, P.O.Box 345050, Dubai, UAE
| | - Sultan M Faheem
- School of Life Sciences, Manipal University, Dubai International Academic City, P.O.Box 345050, Dubai, UAE
| | - Shams T Khan
- Department of Agricultural Microbiology, Aligarh Muslim University, Aligarh, 2002002, UP. India
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Jiang B, Jin N, Xing Y, Su Y, Zhang D. Unraveling uncultivable pesticide degraders via stable isotope probing (SIP). Crit Rev Biotechnol 2018; 38:1025-1048. [DOI: 10.1080/07388551.2018.1427697] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Bo Jiang
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing, PR China
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing, PR China
| | - Naifu Jin
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Yi Xing
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing, PR China
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, University of Science & Technology Beijing, Beijing, PR China
| | - Yuping Su
- Environmental Science and Engineering College, Fujian Normal University, Fuzhou, PR China
| | - Dayi Zhang
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
- Environmental Science and Engineering College, Fujian Normal University, Fuzhou, PR China
- School of Environment, Tsinghua University, Beijing, PR China
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30
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Methods for Collection and Characterization of Samples From Icy Environments. METHODS IN MICROBIOLOGY 2018. [DOI: 10.1016/bs.mim.2018.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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31
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Shankar M, Rampure S, Siddini V, Ballal HS. Outbreak of Ralstonia mannitolilytica in Hemodialysis Unit: A Case Series. Indian J Nephrol 2018; 28:323-326. [PMID: 30158756 PMCID: PMC6094832 DOI: 10.4103/ijn.ijn_77_17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Ralstonia mannitolilytica is a Gram-negative soil bacteria. It is an emerging opportunistic pathogen in hospital-acquired infections. Maintenance hemodialysis patients at Manipal Hospital Outpatient Haemodialysis unit, Bengaluru, witnessed an outbreak of R. mannitolilytica infection between October 2016 and November 2016. Five patients were infected and one of them presented with infective endocarditis. All patients were successfully treated with antibiotic according to culture and sensitivity pattern. Immediately following the outbreak, environmental sampling was done. The culture from sterile water was positive for R. mannitolilytica growth. The Department of Infection Control ordered for discarding the whole batch of sterile water followed by water treatment with shock chlorination and room disinfection. Following implementation of the same, the outbreak of R. mannitolilytica infection was controlled. R. mannitolilytica infections are hospital acquired, affecting mainly immunocompromised patients. The disease onset and progression is rapid. Early identification of the organism and treatment with appropriate antibiotics is important.
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Affiliation(s)
- M Shankar
- Department of Nephrology, Manipal Hospital, Bengaluru, Karnataka, India
| | - S Rampure
- Department of Nephrology, Manipal Hospital, Bengaluru, Karnataka, India
| | - V Siddini
- Department of Nephrology, Manipal Hospital, Bengaluru, Karnataka, India
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32
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Sharaha U, Rodriguez-Diaz E, Riesenberg K, Bigio IJ, Huleihel M, Salman A. Using Infrared Spectroscopy and Multivariate Analysis to Detect Antibiotics' Resistant Escherichia coli Bacteria. Anal Chem 2017; 89:8782-8790. [PMID: 28731324 DOI: 10.1021/acs.analchem.7b01025] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacterial pathogens are one of the primary causes of human morbidity worldwide. Historically, antibiotics have been highly effective against most bacterial pathogens; however, the increasing resistance of bacteria to a broad spectrum of commonly used antibiotics has become a global health-care problem. Early and rapid determination of bacterial susceptibility to antibiotics has become essential in many clinical settings and, sometimes, can save lives. Currently classical procedures require at least 48 h for determining bacterial susceptibility, which can constitute a life-threatening delay for effective treatment. Infrared (IR) microscopy is a rapid and inexpensive technique, which has been used successfully for the detection and identification of various biological samples; nonetheless, its true potential in routine clinical diagnosis has not yet been established. In this study, we evaluated the potential of this technique for rapid identification of bacterial susceptibility to specific antibiotics based on the IR spectra of the bacteria. IR spectroscopy was conducted on bacterial colonies, obtained after 24 h culture from patients' samples. An IR microscope was utilized, and a computational classification method was developed to analyze the IR spectra by novel pattern-recognition and statistical tools, to determine E. coli susceptibility within a few minutes to different antibiotics, gentamicin, ceftazidime, nitrofurantoin, nalidixic acid, ofloxacin. Our results show that it was possible to classify the tested bacteria into sensitive and resistant types, with success rates as high as 85% for a number of examined antibiotics. These promising results open the potential of this technique for faster determination of bacterial susceptibility to certain antibiotics.
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Affiliation(s)
- Uraib Sharaha
- Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev , Beer-Sheva 84105, Israel
| | - Eladio Rodriguez-Diaz
- Department of Medicine, Section of Gastroenterology, Boston University School of Medicine , Boston, Massachusetts 02118, United States.,USA 2 Section of Gastroenterology, VA Boston Healthcare System , Boston, Massachusetts 02130, United States
| | | | - Irving J Bigio
- Department of Biomedical Engineering, Boston University , Boston, Massachusetts 02215, United States.,Department of Electrical & Computer Engineering, Boston University , Boston, Massachusetts 02215, United States
| | - Mahmoud Huleihel
- Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev , Beer-Sheva 84105, Israel
| | - Ahmad Salman
- Department of Physics, SCE-Shamoon College of Engineering , Beer-Sheva 84100, Israel
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Braubach P, Lippmann T, Raoult D, Lagier JC, Anagnostopoulos I, Zender S, Länger FP, Kreipe HH, Kühnel MP, Jonigk D. Fluorescence In Situ Hybridization for Diagnosis of Whipple's Disease in Formalin-Fixed Paraffin-Embedded Tissue. Front Med (Lausanne) 2017; 4:87. [PMID: 28691008 PMCID: PMC5479881 DOI: 10.3389/fmed.2017.00087] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 06/07/2017] [Indexed: 12/12/2022] Open
Abstract
Whipple’s disease (WD) is a rare chronic systemic infection with a wide range of clinical symptoms, routinely diagnosed in biopsies from the small intestine and other tissues by periodic acid–Schiff (PAS) diastase staining and immunohistological analysis with specific antibodies. The aim of our study was to improve the pathological diagnosis of WD. Therefore, we analyzed the potential of fluorescence in situ hybridization (FISH) for diagnosing WD, using a Tropheryma (T.) whipplei-specific probe. 19 formalin-fixed paraffin-embedded (FFPE) duodenal biopsy specimens of 12 patients with treated (6/12) and untreated (6/12) WD were retrospectively examined using PAS diastase staining, immunohistochemistry, and FISH. 20 biopsy specimens with normal intestinal mucosa, Helicobacter pylori, or mycobacterial infection, respectively, served as controls. We successfully detected T. whipplei in tissue biopsies with a sensitivity of 83% in untreated (5/6) and 40% in treated (4/10) cases of WD. In our study, we show that FISH-based diagnosis of individual vital T. whipplei in FFPE specimens is feasible and can be considered as ancillary diagnostic tool for the diagnosis of WD in FFPE material. We show that FISH not only detect active WD but also be helpful as an indicator for the efficiency of antibiotic treatment and for detection of recurrence of disease when the signal of PAS diastase and immunohistochemistry lags behind the recurrence of disease, especially if the clinical course of the patient and antimicrobial treatment is considered.
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Affiliation(s)
- Peter Braubach
- Institute of Pathology, Hannover Medical School (MHH), Hanover, Germany
| | - Torsten Lippmann
- Institute of Pathology, Hannover Medical School (MHH), Hanover, Germany
| | - Didier Raoult
- Aix Marseille University, CNRS, IRD, INSERM, AP-HM, URMITE, IHU Méditerranée Infection, Marseille, France
| | - Jean-Christophe Lagier
- Aix Marseille University, CNRS, IRD, INSERM, AP-HM, URMITE, IHU Méditerranée Infection, Marseille, France
| | | | - Steffen Zender
- Department of Gastroenterology, Hepatology, and Endocrinology, Centre for Internal Medicine, Hannover Medical School (MHH), Hanover, Germany
| | | | | | | | - Danny Jonigk
- Institute of Pathology, Hannover Medical School (MHH), Hanover, Germany
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Borrero-Santiago AR, Bautista-Chamizo E, DelValls TÁ, Riba I. A possible CO 2 leakage event: Can the marine microbial community be recovered? MARINE POLLUTION BULLETIN 2017; 117:380-385. [PMID: 28202276 DOI: 10.1016/j.marpolbul.2017.02.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 01/24/2017] [Accepted: 02/09/2017] [Indexed: 06/06/2023]
Abstract
Bacterial communities have been studied to a much lesser degree than macrofauna in the case of a CO2 release. The resistance capacity of marine bacteria is well known, but their possible responses and their ability to recover after a CO2 release has not been investigated. Therefore, this work evaluated the responses of a marine bacterial community after 96h of CO2 exposure under diverse pH treatments (7.8 as control without CO2, 7.0, 6.5, and 6.0) and 24h after CO2 exposure. Results showed that the respiration activity and the diversity of the community were affected in all pH treatments. However, after 24h without CO2 enrichment, the respiration activity and diversity increased, showing a partial recovery. Consequently, bacterial responses have the potential to be used as a monitoring tool for risk assessment related to carbon capture and storage techniques or in any similar CO2 enrichment situations.
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Affiliation(s)
- A R Borrero-Santiago
- UNESCO/UNITWIN Wicop. Departamento de Química-Física, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz. Av. República Saharaui S/N. Polígono Río San Pedro s/n, Puerto Real 11510, Cádiz, Spain.
| | - E Bautista-Chamizo
- UNESCO/UNITWIN Wicop. Departamento de Química-Física, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz. Av. República Saharaui S/N. Polígono Río San Pedro s/n, Puerto Real 11510, Cádiz, Spain
| | - T Á DelValls
- UNESCO/UNITWIN Wicop. Departamento de Química-Física, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz. Av. República Saharaui S/N. Polígono Río San Pedro s/n, Puerto Real 11510, Cádiz, Spain
| | - I Riba
- UNESCO/UNITWIN Wicop. Departamento de Química-Física, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz. Av. República Saharaui S/N. Polígono Río San Pedro s/n, Puerto Real 11510, Cádiz, Spain
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Azevedo AS, Almeida C, Melo LF, Azevedo NF. Impact of polymicrobial biofilms in catheter-associated urinary tract infections. Crit Rev Microbiol 2016; 43:423-439. [PMID: 28033847 DOI: 10.1080/1040841x.2016.1240656] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Recent reports have demonstrated that most biofilms involved in catheter-associated urinary tract infections are polymicrobial communities, with pathogenic microorganisms (e.g. Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae) and uncommon microorganisms (e.g. Delftia tsuruhatensis, Achromobacter xylosoxidans) frequently co-inhabiting the same urinary catheter. However, little is known about the interactions that occur between different microorganisms and how they impact biofilm formation and infection outcome. This lack of knowledge affects CAUTIs management as uncommon bacteria action can, for instance, influence the rate at which pathogens adhere and grow, as well as affect the overall biofilm resistance to antibiotics. Another relevant aspect is the understanding of factors that drive a single pathogenic bacterium to become prevalent in a polymicrobial community and subsequently cause infection. In this review, a general overview about the IMDs-associated biofilm infections is provided, with an emphasis on the pathophysiology and the microbiome composition of CAUTIs. Based on the available literature, it is clear that more research about the microbiome interaction, mechanisms of biofilm formation and of antimicrobial tolerance of the polymicrobial consortium are required to better understand and treat these infections.
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Affiliation(s)
- Andreia S Azevedo
- a Department of Chemical Engineering, Faculty of Engineering , Laboratory for Process Engineering, Environment, and Energy and Biotechnology Engineering (LEPABE), University of Porto , Porto , Portugal
| | - Carina Almeida
- a Department of Chemical Engineering, Faculty of Engineering , Laboratory for Process Engineering, Environment, and Energy and Biotechnology Engineering (LEPABE), University of Porto , Porto , Portugal.,b Institute for Biotechnology and Bioengineering (IBB), Centre of Biological Engineering, Universidade do Minho , Braga , Portugal
| | - Luís F Melo
- a Department of Chemical Engineering, Faculty of Engineering , Laboratory for Process Engineering, Environment, and Energy and Biotechnology Engineering (LEPABE), University of Porto , Porto , Portugal
| | - Nuno F Azevedo
- a Department of Chemical Engineering, Faculty of Engineering , Laboratory for Process Engineering, Environment, and Energy and Biotechnology Engineering (LEPABE), University of Porto , Porto , Portugal
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Spatial Molecular Architecture of the Microbial Community of a Peltigera Lichen. mSystems 2016; 1:mSystems00139-16. [PMID: 28028548 PMCID: PMC5183598 DOI: 10.1128/msystems.00139-16] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 11/17/2016] [Indexed: 11/25/2022] Open
Abstract
Microbial communities have evolved over centuries to live symbiotically. The direct visualization of such communities at the chemical and functional level presents a challenge. Overcoming this challenge may allow one to visualize the spatial distributions of specific molecules involved in symbiosis and to define their functional roles in shaping the community structure. In this study, we examined the diversity of microbial genes and taxa and the presence of biosynthetic gene clusters by metagenomic sequencing and the compartmentalization of organic chemical components within a lichen using mass spectrometry. This approach allowed the identification of chemically distinct sections within this composite organism. Using our multipronged approach, various fungal natural products, not previously reported from lichens, were identified and two different fungal layers were visualized at the chemical level. Microbes are commonly studied as individual species, but they exist as mixed assemblages in nature. At present, we know very little about the spatial organization of the molecules, including natural products that are produced within these microbial networks. Lichens represent a particularly specialized type of symbiotic microbial assemblage in which the component microorganisms exist together. These composite microbial assemblages are typically comprised of several types of microorganisms representing phylogenetically diverse life forms, including fungi, photosymbionts, bacteria, and other microbes. Here, we employed matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) imaging mass spectrometry to characterize the distributions of small molecules within a Peltigera lichen. In order to probe how small molecules are organized and localized within the microbial consortium, analytes were annotated and assigned to their respective producer microorganisms using mass spectrometry-based molecular networking and metagenome sequencing. The spatial analysis of the molecules not only reveals an ordered layering of molecules within the lichen but also supports the compartmentalization of unique functions attributed to various layers. These functions include chemical defense (e.g., antibiotics), light-harvesting functions associated with the cyanobacterial outer layer (e.g., chlorophyll), energy transfer (e.g., sugars) surrounding the sun-exposed cyanobacterial layer, and carbohydrates that may serve a structural or storage function and are observed with higher intensities in the non-sun-exposed areas (e.g., complex carbohydrates). IMPORTANCE Microbial communities have evolved over centuries to live symbiotically. The direct visualization of such communities at the chemical and functional level presents a challenge. Overcoming this challenge may allow one to visualize the spatial distributions of specific molecules involved in symbiosis and to define their functional roles in shaping the community structure. In this study, we examined the diversity of microbial genes and taxa and the presence of biosynthetic gene clusters by metagenomic sequencing and the compartmentalization of organic chemical components within a lichen using mass spectrometry. This approach allowed the identification of chemically distinct sections within this composite organism. Using our multipronged approach, various fungal natural products, not previously reported from lichens, were identified and two different fungal layers were visualized at the chemical level.
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Gokal J, Awolusi OO, Enitan AM, Kumari S, Bux F. Chapter 4 Molecular Characterization and Quantification of Microbial Communities in Wastewater Treatment Systems. Microb Biotechnol 2016. [DOI: 10.1201/9781315367880-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Nakipoglu M, Yilmaz F, Icgen B. vanA-targeted oligonucleotide DNA probe designed to monitor vancomycin- and teicoplanin-resistant bacteria in surface waters. ENVIRONMENTAL MONITORING AND ASSESSMENT 2016; 188:569. [PMID: 27640164 DOI: 10.1007/s10661-016-5578-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Accepted: 09/07/2016] [Indexed: 06/06/2023]
Abstract
The glycopeptide antibiotics teicoplanin and vancomycin are common to treat severe Gram-positive bacterial infections. The gene vanA confers high-level resistance to these antibiotics, and these phenomena have been shown to be transferable. Release of vancomycin- and teicoplanin-resistant bacteria to surface waters is, therefore, of particular concern since they might proliferate and spread in different environments. Monitoring of the fate of vanA gene in these waters provides information on the exposure and potential threats of those bacteria for the environment and public health. Therefore, this study aimed at preparing a 25-mer-oligonucleotide DNA probe based on the 909 bp BamHI-ClaI fragment from Enterococcus faecium plasmids pVEF1 and pVEF2 through the use of Vector NTI Express Software. The newly designed vanA probe displayed highly specific hybridization with vanA-positive Enterococcus faecalis tested at 46 °C, 55 % formamide, and 0.020 M NaCl stringency conditions. In situ fluorescein hybridizations under the same stringency conditions were also used to monitor river water samples by using fluorescein microscopy. The results showed that the vanA-targeted oligonucleotide DNA probe prepared was not only highly specific but also quantitative tool for monitoring vancomycin- and teicoplanin-resistant bacteria in surface waters.
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Affiliation(s)
- Mustafa Nakipoglu
- Department of Biotechnology, Middle East Technical University, 06800, Ankara, Turkey
| | - Fadime Yilmaz
- Department of Environmental Engineering, Middle East Technical University, 06800, Ankara, Turkey
| | - Bulent Icgen
- Department of Biotechnology, Middle East Technical University, 06800, Ankara, Turkey.
- Department of Environmental Engineering, Middle East Technical University, 06800, Ankara, Turkey.
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Ghosal D, Ghosh S, Dutta TK, Ahn Y. Current State of Knowledge in Microbial Degradation of Polycyclic Aromatic Hydrocarbons (PAHs): A Review. Front Microbiol 2016; 7:1369. [PMID: 27630626 PMCID: PMC5006600 DOI: 10.3389/fmicb.2016.01369] [Citation(s) in RCA: 249] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 08/18/2016] [Indexed: 12/22/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) include a group of organic priority pollutants of critical environmental and public health concern due to their toxic, genotoxic, mutagenic and/or carcinogenic properties and their ubiquitous occurrence as well as recalcitrance. The increased awareness of their various adverse effects on ecosystem and human health has led to a dramatic increase in research aimed toward removing PAHs from the environment. PAHs may undergo adsorption, volatilization, photolysis, and chemical oxidation, although transformation by microorganisms is the major neutralization process of PAH-contaminated sites in an ecologically accepted manner. Microbial degradation of PAHs depends on various environmental conditions, such as nutrients, number and kind of the microorganisms, nature as well as chemical property of the PAH being degraded. A wide variety of bacterial, fungal and algal species have the potential to degrade/transform PAHs, among which bacteria and fungi mediated degradation has been studied most extensively. In last few decades microbial community analysis, biochemical pathway for PAHs degradation, gene organization, enzyme system, genetic regulation for PAH degradation have been explored in great detail. Although, xenobiotic-degrading microorganisms have incredible potential to restore contaminated environments inexpensively yet effectively, but new advancements are required to make such microbes effective and more powerful in removing those compounds, which were once thought to be recalcitrant. Recent analytical chemistry and genetic engineering tools might help to improve the efficiency of degradation of PAHs by microorganisms, and minimize uncertainties of successful bioremediation. However, appropriate implementation of the potential of naturally occurring microorganisms for field bioremediation could be considerably enhanced by optimizing certain factors such as bioavailability, adsorption and mass transfer of PAHs. The main purpose of this review is to provide an overview of current knowledge of bacteria, halophilic archaea, fungi and algae mediated degradation/transformation of PAHs. In addition, factors affecting PAHs degradation in the environment, recent advancement in genetic, genomic, proteomic and metabolomic techniques are also highlighted with an aim to facilitate the development of a new insight into the bioremediation of PAH in the environment.
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Affiliation(s)
- Debajyoti Ghosal
- Environmental Engineering Laboratory, Department of Civil Engineering, Yeungnam UniversityGyeongsan, South Korea
| | - Shreya Ghosh
- Disasters Prevention Research Institute, Yeungnam UniversityGyeongsan, South Korea
| | - Tapan K. Dutta
- Department of Microbiology, Bose InstituteKolkata, India
| | - Youngho Ahn
- Environmental Engineering Laboratory, Department of Civil Engineering, Yeungnam UniversityGyeongsan, South Korea
- Disasters Prevention Research Institute, Yeungnam UniversityGyeongsan, South Korea
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40
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Functional ecology of aquatic phagotrophic protists – Concepts, limitations, and perspectives. Eur J Protistol 2016; 55:50-74. [DOI: 10.1016/j.ejop.2016.03.003] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 03/15/2016] [Accepted: 03/23/2016] [Indexed: 01/02/2023]
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Seyedmonir E, Yilmaz F, Icgen B. Methicillin-Resistant Bacteria Inhabiting Surface Waters Monitored by mecA-Targeted Oligonucleotide Probes. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2016; 97:261-271. [PMID: 27156085 DOI: 10.1007/s00128-016-1815-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 04/27/2016] [Indexed: 06/05/2023]
Abstract
Part of a 20-60 kb staphylococcal chromosome cassette called mecA encodes low-affinity penicillin-binding protein PBP2a and causes methicillin resistance. Among all methicillin-resistant bacteria, methicillin-resistant Staphylococcus aureus is a major pathogen and main concern worldwide. Although the origin of the mecA is not very well-defined, mecA homologues are also ubiquitous in methicillin-resistant non-staphylococcal bacteria. Due to the dissemination of methicillin resistance through the transmission of mecA gene among staphylococcal and non-staphylococcal bacteria inhabiting surface waters, there is a need to monitor mecA gene in these waters for public health safety. Therefore, this study aimed at monitoring mecA harboring bacteria inhabiting surface waters by using fluorescently labelled mecA-targeted oligonucleotide probes. Under the hybridization conditions of 55 % formamide and 0.020 M NaCl at 46°C, the oligonucleotide probe used in the study showed high hybridization stringency to the mecA gene targeted. The strong linear relationships observed between the signal intensity and the target gene were used to assess the population dynamics of mecA harboring isolates over a 2-year-period. The results indicated that mecA-targeted oligonucleotide probes can be effectively used for in situ monitoring of methicillin resistant isolates inhabiting surface waters.
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Affiliation(s)
- Elnaz Seyedmonir
- Department of Biochemistry, Middle East Technical University, 06800, Ankara, Turkey
| | - Fadime Yilmaz
- Department of Environmental Engineering, Middle East Technical University, 06800, Ankara, Turkey
| | - Bulent Icgen
- Department of Biochemistry, Middle East Technical University, 06800, Ankara, Turkey.
- Department of Environmental Engineering, Middle East Technical University, 06800, Ankara, Turkey.
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Ellison MA, McMahon MB, Bonde MR, Palmer CL, Luster DG. In situ hybridization for the detection of rust fungi in paraffin embedded plant tissue sections. PLANT METHODS 2016; 12:37. [PMID: 27471544 PMCID: PMC4964054 DOI: 10.1186/s13007-016-0137-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 07/19/2016] [Indexed: 05/20/2023]
Abstract
BACKGROUND Rust fungi are obligate pathogens with multiple life stages often including different spore types and multiple plant hosts. While individual rust pathogens are often associated with specific plants, a wide range of plant species are infected with rust fungi. To study the interactions between these important pathogenic fungi and their host plants, one must be able to differentiate fungal tissue from plant tissue. This can be accomplished using the In situ hybridization (ISH) protocol described here. RESULTS To validate reproducibility using the ISH protocol, samples of Chrysanthemum × morifolium infected with Puccinia horiana, Gladiolus × hortulanus infected with Uromyces transversalis and Glycine max infected with Phakopsora pachyrhizi were tested alongside uninfected leaf tissue samples. The results of these tests show that this technique clearly distinguishes between rust pathogens and their respective host plant tissues. CONCLUSIONS This ISH protocol is applicable to rust fungi and potentially other plant pathogenic fungi as well. It has been shown here that this protocol can be applied to pathogens from different genera of rust fungi with no background staining of plant tissue. We encourage the use of this protocol for the study of plant pathogenic fungi in paraffin embedded sections of host plant tissue.
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Affiliation(s)
- Mitchell A. Ellison
- Department of Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Michael B. McMahon
- USDA-ARS Foreign Disease-Weed Science Research Unit, Ft. Detrick, MD USA
| | - Morris R. Bonde
- USDA-ARS Foreign Disease-Weed Science Research Unit, Ft. Detrick, MD USA
| | | | - Douglas G. Luster
- USDA-ARS Foreign Disease-Weed Science Research Unit, Ft. Detrick, MD USA
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Hugenholtz P, Skarshewski A, Parks DH. Genome-Based Microbial Taxonomy Coming of Age. Cold Spring Harb Perspect Biol 2016; 8:cshperspect.a018085. [PMID: 26988968 DOI: 10.1101/cshperspect.a018085] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Reconstructing the complete evolutionary history of extant life on our planet will be one of the most fundamental accomplishments of scientific endeavor, akin to the completion of the periodic table, which revolutionized chemistry. The road to this goal is via comparative genomics because genomes are our most comprehensive and objective evolutionary documents. The genomes of plant and animal species have been systematically targeted over the past decade to provide coverage of the tree of life. However, multicellular organisms only emerged in the last 550 million years of more than three billion years of biological evolution and thus comprise a small fraction of total biological diversity. The bulk of biodiversity, both past and present, is microbial. We have only scratched the surface in our understanding of the microbial world, as most microorganisms cannot be readily grown in the laboratory and remain unknown to science. Ground-breaking, culture-independent molecular techniques developed over the past 30 years have opened the door to this so-called microbial dark matter with an accelerating momentum driven by exponential increases in sequencing capacity. We are on the verge of obtaining representative genomes across all life for the first time. However, historical use of morphology, biochemical properties, behavioral traits, and single-marker genes to infer organismal relationships mean that the existing highly incomplete tree is riddled with taxonomic errors. Concerted efforts are now needed to synthesize and integrate the burgeoning genomic data resources into a coherent universal tree of life and genome-based taxonomy.
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Affiliation(s)
- Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia QLD 4072, Australia
| | - Adam Skarshewski
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia QLD 4072, Australia
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia QLD 4072, Australia
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Stefanis C, Mantzourani I, Plessas S, Alexopoulos A, Galanis A, Bezirtzoglou E, Kandylis P, Varzakas T. Reviewing Classical and Molecular Techniques Regarding Profiling of Probiotic Character of Microorganisms. CURRENT RESEARCH IN NUTRITION AND FOOD SCIENCE 2016. [DOI: 10.12944/crnfsj.4.1.05] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
In recent years the roles of probiotics as functional ingredients in food has been highly adopted by the consumers and are under constant investigation by the scientific community. As a result, several probiotic-containing foods have been introduced in the market with an annual share of several billion dollars. Of particular interest in the probiotics research is the profiling of probiotic character of the microbes involving both in vitro and in vivo approaches. Initially traditional microbiological techniques were used; however they suffer by many limitations and therefore the development of new techniques, which are primarily based on the analysis of nucleic acids have been introduced. The scope of this review is to present current knowledge about the methodological approaches that are used to quantify and characterize the potential probiotic character of microorganisms. Moreover, it will focus on molecular and non-molecular tools and finally will report some new perspectives in the study of probiotics using omics techniques.
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Affiliation(s)
- Christos Stefanis
- Democritus University of Thrace, Department of Agricultural Development, Laboratory of Microbiology, Biotechnology and Hygiene, Pandazidou 193, GR68200, Orestiada, Greece
| | - Ioanna Mantzourani
- Democritus University of Thrace, Department of Agricultural Development, Laboratory of Microbiology, Biotechnology and Hygiene, Pandazidou 193, GR68200, Orestiada, Greece
| | - Stavros Plessas
- Democritus University of Thrace, Department of Agricultural Development, Laboratory of Microbiology, Biotechnology and Hygiene, Pandazidou 193, GR68200, Orestiada, Greece
| | - Athanasios Alexopoulos
- Democritus University of Thrace, Department of Agricultural Development, Laboratory of Microbiology, Biotechnology and Hygiene, Pandazidou 193, GR68200, Orestiada, Greece
| | - Alexis Galanis
- Democritus University of Thrace, Department of Molecular Biology and Genetics, Dragana University Campus, GR68100, Alexandroupolis, Greece
| | - Eugenia Bezirtzoglou
- Democritus University of Thrace, Department of Agricultural Development, Laboratory of Microbiology, Biotechnology and Hygiene, Pandazidou 193, GR68200, Orestiada, Greece
| | - Panagiotis Kandylis
- Department of Food Technology, Technological and Educational Institution of Peloponnese, Antikalamos, Kalamata, Greece
| | - Theodoros Varzakas
- Department of Food Technology, Technological and Educational Institution of Peloponnese, Antikalamos, Kalamata, Greece
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Kliot A, Ghanim M. Fluorescent in situ hybridization for the localization of viruses, bacteria and other microorganisms in insect and plant tissues. Methods 2016; 98:74-81. [PMID: 26678796 DOI: 10.1016/j.ymeth.2015.12.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 12/03/2015] [Accepted: 12/06/2015] [Indexed: 12/21/2022] Open
Abstract
Methods for the localization of cellular components such as nucleic acids, proteins, cellular vesicles and more, and the localization of microorganisms including viruses, bacteria and fungi have become an important part of any research program in biological sciences that enable the visualization of these components in fixed and live tissues without the need for complex processing steps. The rapid development of microscopy tools and technologies as well as related fluorescent markers and fluorophores for many cellular components, and the ability to design DNA and RNA sequence-based molecular probes and antibodies which can be visualized fluorescently, have rapidly advanced this field. This review will focus on some of the localizations methods which have been used in plants and insect pests in agriculture, and other microorganisms, which are rapidly advancing the research in agriculture-related fields.
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Affiliation(s)
- Adi Kliot
- Department of Entomology, The Volcani Center, Bet Dagan 50250, Israel
| | - Murad Ghanim
- Department of Entomology, The Volcani Center, Bet Dagan 50250, Israel.
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Cortez-Pinto H, Borralho P, Machado J, Lopes MT, Gato IV, Santos AM, Guerreiro AS. Microbiota Modulation With Synbiotic Decreases Liver Fibrosis in a High Fat Choline Deficient Diet Mice Model of Non-Alcoholic Steatohepatitis (NASH). GE-PORTUGUESE JOURNAL OF GASTROENTEROLOGY 2016; 23:132-141. [PMID: 28868449 PMCID: PMC5580012 DOI: 10.1016/j.jpge.2016.01.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 01/18/2016] [Indexed: 02/07/2023]
Abstract
BACKGROUND Gut microbiota may play a role in non-alcoholic steatohepatitis (NASH). Previous studies showed that prebiotics and probiotics might halt the progression of steatohepatitis. AIM To clarify the potential effect of Synbiotic 2000®Forte (Synb) in preventing or ameliorating diet induced steatohepatitis, particularly in fibrosis progression and how this intervention correlates with gut microbiota composition and endotoxinemia. METHODS Twenty-seven C57BL/6 mice were divided into three groups: chow diet (CD, n = 7); high-fat choline deficient diet (HFCD, n = 10) and HFCD diet supplemented with Synbiotic 2000®Forte (four probiotic strains and four prebiotics mixture) (HFCD + Synb, n = 10). At 6 and 18 weeks, blood samples (lipopolysaccharides assay - LPS), cecal feaces (gut microbiota) and liver tissue (histology) were collected for analysis. RESULTS Both HCFD diet mice developed steatohepatitis with ballooning at 6 and 18 weeks, opposite to CD. Comparison of histological scores in HFCD and HFCD + Synb, at 6 and 18 weeks showed no significant difference regarding steatosis, inflammation, or ballooning. Evaluating fibrosis with Sirius Red, and degree of smooth-muscle cell activation, HFCD mice had significantly more fibrosis; addition of Synb significantly reduced fibrosis at 6 weeks and 18 weeks. Serum endotoxin levels were similarly increased in HFCD and HFCD + Synb at week 6; however at week 18 HFCD + Synb had significantly lower endotoxin levels than HFCD. Gut microbiota of HFCD vs CD, showed no significant differences regarding the phyla Firmicutes and Bacteroidetes, either at 6 or 18 weeks; Proteobacteria increased at 6 week (3.3) and 18 week (7.5), while the addition of Synb resulted in a decrease at week 18 (-3.90). Fusobacteria markedly increase at week 18 (10.0), but less so with the addition of Synb (5.2). CONCLUSION Synbiotic 2000®Forte is able to modulate the mouse gut microbiota reducing the degree of fibrosis while simultaneously decreasing endotoxemia.
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Affiliation(s)
- Helena Cortez-Pinto
- Gastroenterology and Hepatology Department, Centro Hospitalar Lisboa Norte, Lisbon, Portugal.,Nutrition Laboratory, Faculdade de Medicina de Lisboa, Lisbon, Portugal
| | - Paula Borralho
- Pathology Institut, Faculdade de Medicina de Lisboa, Lisbon, Portugal
| | - Jorge Machado
- Infectious Diseases Department, Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisbon, Portugal
| | - Maria T Lopes
- CEDOC - Chronic Diseases Research Center, NOVA Medical School, Faculdade de Ciências Médicas de Lisboa, Lisbon, Portugal
| | - Inês V Gato
- Infectious Diseases Department, Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisbon, Portugal
| | - António M Santos
- CEDOC - Chronic Diseases Research Center, NOVA Medical School, Faculdade de Ciências Médicas de Lisboa, Lisbon, Portugal
| | - António S Guerreiro
- CEDOC - Chronic Diseases Research Center, NOVA Medical School, Faculdade de Ciências Médicas de Lisboa, Lisbon, Portugal
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Icgen B, Yilmaz F. Design a cadA-targeted DNA probe for screening of potential bacterial cadmium biosorbents. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:5743-5752. [PMID: 26585451 DOI: 10.1007/s11356-015-5810-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 11/13/2015] [Indexed: 06/05/2023]
Abstract
Due to their metal removal ability, bacterial biosorbents can be effectively used for the treatment of wastewaters containing heavy metals. Searching for bacterial biosorbents for hazardous heavy metals like cadmium is a pivotal for remediation efforts. The gene cadA, that mediates resistance to cadmium over an ATP-dependent efflux mechanism, provides a good target for the selection of potential cadmium biosorbents. For this reason, in this study, a 36-mer-oligonucleotide DNA probe based on the entire 3.5-kb BglII-XbaI fragment of cadA operon from staphylococcal plasmid pI258 was prepared by using Vector NTI Express software. Under the hybridization conditions of 46 °C, 50 % formamide, and 0.028 M NaCl, the designed cadA probe appeared to be highly specific to the cadA-positive Staphylococcus warneri and Delftia acidovorans isolates tested. The results indicated that the newly designed cadA-targeted DNA probe has potential as a specific, sensitive, and quantitative tool in selecting and in situ screening of potential cadmium biosorbents.
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Affiliation(s)
- Bulent Icgen
- Department of Environmental Engineering, Middle East Technical University, 06800, Ankara, Turkey.
| | - Fadime Yilmaz
- Department of Environmental Engineering, Middle East Technical University, 06800, Ankara, Turkey
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Hovasse A, Bruneel O, Casiot C, Desoeuvre A, Farasin J, Hery M, Van Dorsselaer A, Carapito C, Arsène-Ploetze F. Spatio-Temporal Detection of the Thiomonas Population and the Thiomonas Arsenite Oxidase Involved in Natural Arsenite Attenuation Processes in the Carnoulès Acid Mine Drainage. Front Cell Dev Biol 2016; 4:3. [PMID: 26870729 PMCID: PMC4734075 DOI: 10.3389/fcell.2016.00003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 01/11/2016] [Indexed: 11/19/2022] Open
Abstract
The acid mine drainage (AMD) impacted creek of the Carnoulès mine (Southern France) is characterized by acid waters with a high heavy metal content. The microbial community inhabiting this AMD was extensively studied using isolation, metagenomic and metaproteomic methods, and the results showed that a natural arsenic (and iron) attenuation process involving the arsenite oxidase activity of several Thiomonas strains occurs at this site. A sensitive quantitative Selected Reaction Monitoring (SRM)-based proteomic approach was developed for detecting and quantifying the two subunits of the arsenite oxidase and RpoA of two different Thiomonas groups. Using this approach combined with FISH and pyrosequencing-based 16S rRNA gene sequence analysis, it was established here for the first time that these Thiomonas strains are ubiquitously present in minor proportions in this AMD and that they express the key enzymes involved in natural remediation processes at various locations and time points. In addition to these findings, this study also confirms that targeted proteomics applied at the community level can be used to detect weakly abundant proteins in situ.
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Affiliation(s)
- Agnès Hovasse
- Laboratoire de Spectrométrie de Masse BioOrganique, Institut Pluridisciplinaire Hubert Curien, UMR7178, Centre National de la Recherche Scientifique, Université de Strasbourg Strasbourg, France
| | - Odile Bruneel
- Laboratoire HydroSciences Montpellier, UMR HSM 5569, Centre National de la Recherche Scientifique, Institut de Recherche pour le Développement, Université Montpellier Montpellier, France
| | - Corinne Casiot
- Laboratoire HydroSciences Montpellier, UMR HSM 5569, Centre National de la Recherche Scientifique, Institut de Recherche pour le Développement, Université Montpellier Montpellier, France
| | - Angélique Desoeuvre
- Laboratoire HydroSciences Montpellier, UMR HSM 5569, Centre National de la Recherche Scientifique, Institut de Recherche pour le Développement, Université Montpellier Montpellier, France
| | - Julien Farasin
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, Centre National de la Recherche Scientifique-Université de Strasbourg, Département Microorganismes, Génomes, Environnement, Equipe Ecophysiologie Moléculaire des Microorganismes Strasbourg, France
| | - Marina Hery
- Laboratoire HydroSciences Montpellier, UMR HSM 5569, Centre National de la Recherche Scientifique, Institut de Recherche pour le Développement, Université Montpellier Montpellier, France
| | - Alain Van Dorsselaer
- Laboratoire de Spectrométrie de Masse BioOrganique, Institut Pluridisciplinaire Hubert Curien, UMR7178, Centre National de la Recherche Scientifique, Université de Strasbourg Strasbourg, France
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse BioOrganique, Institut Pluridisciplinaire Hubert Curien, UMR7178, Centre National de la Recherche Scientifique, Université de Strasbourg Strasbourg, France
| | - Florence Arsène-Ploetze
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, Centre National de la Recherche Scientifique-Université de Strasbourg, Département Microorganismes, Génomes, Environnement, Equipe Ecophysiologie Moléculaire des Microorganismes Strasbourg, France
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Roberfroid S, Vanderleyden J, Steenackers H. Gene expression variability in clonal populations: Causes and consequences. Crit Rev Microbiol 2016; 42:969-84. [PMID: 26731119 DOI: 10.3109/1040841x.2015.1122571] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
During the last decade it has been shown that among cell variation in gene expression plays an important role within clonal populations. Here, we provide an overview of the different mechanisms contributing to gene expression variability in clonal populations. These are ranging from inherent variations in the biochemical process of gene expression itself, such as intrinsic noise, extrinsic noise and bistability to individual responses to variations in the local micro-environment, a phenomenon called phenotypic plasticity. Also genotypic variations caused by clonal evolution and phase variation can contribute to gene expression variability. Consequently, gene expression studies need to take these fluctuations in expression into account. However, frequently used techniques for expression quantification, such as microarrays, RNA sequencing, quantitative PCR and gene reporter fusions classically determine the population average of gene expression. Here, we discuss how these techniques can be adapted towards single cell analysis by integration with single cell isolation, RNA amplification and microscopy. Alternatively more qualitative selection-based techniques, such as mutant screenings, in vivo expression technology (IVET) and recombination-based IVET (RIVET) can be applied for detection of genes expressed only within a subpopulation. Finally, differential fluorescence induction (DFI), a protocol specially designed for single cell expression is discussed.
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Affiliation(s)
- Stefanie Roberfroid
- a Department of Microbial and Molecular Systems , Centre of Microbial and Plant Genetics, KU Leuven , Leuven , Belgium
| | - Jos Vanderleyden
- a Department of Microbial and Molecular Systems , Centre of Microbial and Plant Genetics, KU Leuven , Leuven , Belgium
| | - Hans Steenackers
- a Department of Microbial and Molecular Systems , Centre of Microbial and Plant Genetics, KU Leuven , Leuven , Belgium
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50
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Mikelsaar M, Sepp E, Štšepetova J, Songisepp E, Mändar R. Biodiversity of Intestinal Lactic Acid Bacteria in the Healthy Population. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 932:1-64. [DOI: 10.1007/5584_2016_3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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