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Kao YT, Calabrese S, Borst N, Lehnert M, Lai YK, Schlenker F, Juelg P, Zengerle R, Garstecki P, von Stetten F. Microfluidic One-Pot Digital Droplet FISH Using LNA/DNA Molecular Beacons for Bacteria Detection and Absolute Quantification. BIOSENSORS 2022; 12:bios12040237. [PMID: 35448297 PMCID: PMC9032532 DOI: 10.3390/bios12040237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/06/2022] [Accepted: 04/10/2022] [Indexed: 02/06/2023]
Abstract
We demonstrate detection and quantification of bacterial load with a novel microfluidic one-pot wash-free fluorescence in situ hybridization (FISH) assay in droplets. The method offers minimal manual workload by only requiring mixing of the sample with reagents and loading it into a microfluidic cartridge. By centrifugal microfluidic step emulsification, our method partitioned the sample into 210 pL (73 µm in diameter) droplets for bacterial encapsulation followed by in situ permeabilization, hybridization, and signal detection. Employing locked nucleic acid (LNA)/DNA molecular beacons (LNA/DNA MBs) and NaCl-urea based hybridization buffer, the assay was characterized with Escherichia coli, Klebsiella pneumonia, and Proteus mirabilis. The assay performed with single-cell sensitivity, a 4-log dynamic range from a lower limit of quantification (LLOQ) at ~3 × 103 bacteria/mL to an upper limit of quantification (ULOQ) at ~3 × 107 bacteria/mL, anda linearity R2 = 0.976. The total time-to-results for detection and quantification was around 1.5 hours.
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Affiliation(s)
- Yu-Ting Kao
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (Y.-T.K.); (N.B.); (Y.-K.L.); (R.Z.)
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland;
| | - Silvia Calabrese
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (S.C.); (M.L.); (F.S.); (P.J.)
| | - Nadine Borst
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (Y.-T.K.); (N.B.); (Y.-K.L.); (R.Z.)
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (S.C.); (M.L.); (F.S.); (P.J.)
| | - Michael Lehnert
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (S.C.); (M.L.); (F.S.); (P.J.)
| | - Yu-Kai Lai
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (Y.-T.K.); (N.B.); (Y.-K.L.); (R.Z.)
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland;
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (S.C.); (M.L.); (F.S.); (P.J.)
| | - Franziska Schlenker
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (S.C.); (M.L.); (F.S.); (P.J.)
| | - Peter Juelg
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (S.C.); (M.L.); (F.S.); (P.J.)
| | - Roland Zengerle
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (Y.-T.K.); (N.B.); (Y.-K.L.); (R.Z.)
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (S.C.); (M.L.); (F.S.); (P.J.)
| | - Piotr Garstecki
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland;
| | - Felix von Stetten
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (Y.-T.K.); (N.B.); (Y.-K.L.); (R.Z.)
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (S.C.); (M.L.); (F.S.); (P.J.)
- Correspondence: ; Tel.: +49-761-203-73243
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Uncovering the hidden bacterial ghost communities of yeast and experimental evidences demonstrates yeast as thriving hub for bacteria. Sci Rep 2021; 11:9394. [PMID: 33931672 PMCID: PMC8087679 DOI: 10.1038/s41598-021-88658-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 04/15/2021] [Indexed: 11/09/2022] Open
Abstract
Our major concern was to address “yeast endobacteria” which was based on a few reports in the recent past where bacteria may find yeast as a niche for survival. In this study, we report the microbiota of twenty-nine axenic yeast cultures recovered from different habitats based on their 16S rRNA gene-amplicon metagenomes. Yeasts were identified based on D1/D2 or ITS gene sequences. Bacterial diversity was widespread, varied and rich among all yeasts except for four strains. Taxa belonging to the phylum Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes and the genera; Streptococcus, Propionibacterium were common to all the yeasts. Candida tropicalis was used as a model organism to confirm bacteria through fluorescence in situ hybridization (FISH), isolating and re-introducing the isolated bacteria into the yeast. FISH analysis confirmed the endobacteria of C. tropicalis and we have successfully isolated four bacteria only after lysis and disruption of yeast cells. These bacteria were identified as species of Pseudomonas, Chryseobacterium, Lysinibacillus and Propionibacterium. Guestimates indicate 95% of bacterial species of C. tropicalis are yet-to-be-cultivated. We have successfully reintroduced mCherry tagged Pseudomonas into C. tropicalis. Also, auto-fluorescent Prochlorococcus and Rhodopseudomonas could be introduced into C. tropicalis while mCherry tagged E. coli or Salmonella could not be introduced. FISH analysis confirmed the presence of both native and infected bacterial cells present in C. tropicalis. Our findings unveil the insights into the ghost microbiota associated with yeast, which otherwise are considered to be axenic cultures. Their inherent occurrence, together with co-cultivation experiments under laboratory conditions suggests that yeasts are a thriving hub for bacterial communities.
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Adebowale O, Good L. Development of a fixation-free fluorescence in situ hybridization for the detection of Salmonella species. Biol Methods Protoc 2020; 5:bpaa024. [PMID: 33381652 PMCID: PMC7756007 DOI: 10.1093/biomethods/bpaa024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/28/2020] [Accepted: 11/03/2020] [Indexed: 11/13/2022] Open
Abstract
Salmonella is one of the most important infectious bacteria causing severe gastroenteritis and deaths in humans and animals, and the prompt diagnosis is crucial for effective control and treatment. The detection of Salmonella still depends principally on culture-based methods, which is time-consuming and laborious. Recently, polyhexamethylene biguanide (PHMB) was discovered to have cellular delivery properties and its combination with the fluorescence in situ hybridization (FISH) method was exploited for oligomer delivery and the rapid detection of Salmonella spps in this study. Cell-associated fluorescence was quantified using Volocity® 3-D image analysis software (Volocity 6.3, PerkinElmer, Inc.). PHMB complexed with fluorophore-labelled species-specific oligomers permeabilized freshly grown viable strains of Salmonella cells and mediated strong cell-associated fluorescence signals. This strategy further enabled a fixation-free protocol and hybridization in a single reaction. Using the modified FISH method, monoculture Salmonella strains were validated as well as detected in artificially contaminated water and milk within a turnaround period of 5 h. The method was observed to be comparable with the standard FISH technique (sFISH; P > 0.05). The findings suggest that fixation-free delivery and hybridization of oligomers using PHMB can provide a simplified and prompt strategy for Salmonella detection at the species level, and promote early management responses to the disease and appropriate antimicrobial therapy.
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Affiliation(s)
- Oluwawemimo Adebowale
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London NW1 0TU, UK
| | - Liam Good
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London NW1 0TU, UK
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Kumar G, Radha V, Jagadeeshwari U, Sasikala C, Venkata Ramana C. Bacterial communities of sponges from the wetland ecosystem of Little Rann of Kutch, India with particular reference to Planctomycetes. 3 Biotech 2020; 10:478. [PMID: 33094088 PMCID: PMC7568738 DOI: 10.1007/s13205-020-02449-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 09/21/2020] [Indexed: 10/23/2022] Open
Abstract
Five sponge specimens belonging to the genera Spongilla and Ciocalypta were collected from Little Rann of Kutch (in Gujarat, India) and analysed for associated microbiomes. Critical analysis was done with respect to members of the phylum Planctomycetes, using two different strategies; 1. Culture-independent metagenomic approach and 2. culture-dependent anaerobic enrichment for anammox-planctomycetes. The 16S rRNA gene (V1-V3 region) amplicon metagenome analysis revealed significant divergence in bacterial diversity, including Planctomycetes among the sponges analysed. Community metagenomics revealed a total of 376 Operational Taxonomic Units (OTUs) belonging to 41 different phyla. OTUs belonging to Proteobacteria was the most abundant (38%) among the sponge analysed. The KEGG annotation predicted a total of 6909 KEGG orthologs (KOs); most of the KOs are associated with membrane transport, xenobiotic degradation, production of secondary metabolites, amino acid metabolism and carbohydrate metabolism. In the culture-dependent study, FISH analysis confirmed the association of anammox-planctomycetes with sponges. Partial 16S rRNA gene sequences of two planctomycetes (JC545, JC543) were cladding with those of uncultured Phycisphaerae class. The other three putative anammox bacteria (JC541, JC542, JC544) formed a different clade with "Candidatus Brocadia anammoxidans". These three putative bacteria believably represent new species/genus related to "Candidatus Brocadia".
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Affiliation(s)
- Gaurav Kumar
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500046 India
| | - Vaddavalli Radha
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500046 India
| | - Uppadda Jagadeeshwari
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University Hyderabad, Kukatpally, Hyderabad, 500085 India
| | - Chintalapati Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University Hyderabad, Kukatpally, Hyderabad, 500085 India
| | - Chintalapati Venkata Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500046 India
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Fessler M, Gummesson B, Charbon G, Svenningsen SL, Sørensen MA. Short‐term kinetics of rRNA degradation inEscherichia coliupon starvation for carbon, amino acid or phosphate. Mol Microbiol 2020; 113:951-963. [DOI: 10.1111/mmi.14462] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 01/13/2020] [Accepted: 01/14/2020] [Indexed: 11/27/2022]
Affiliation(s)
- Mathias Fessler
- Department of Biology University of Copenhagen Copenhagen N Denmark
- DTU Environment Technical University of Denmark Kongens Lyngby Denmark
| | - Bertil Gummesson
- Department of Biology University of Copenhagen Copenhagen N Denmark
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Ma Q, Bücking H, Gonzalez Hernandez JL, Subramanian S. Single-Cell RNA Sequencing of Plant-Associated Bacterial Communities. Front Microbiol 2019; 10:2452. [PMID: 31736899 PMCID: PMC6828647 DOI: 10.3389/fmicb.2019.02452] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 10/11/2019] [Indexed: 11/29/2022] Open
Abstract
Plants in soil are not solitary, hence continually interact with and obtain benefits from a community of microbes ("microbiome"). The meta-functional output from the microbiome results from complex interactions among the different community members with distinct taxonomic identities and metabolic capacities. Particularly, the bacterial communities of the root surface are spatially organized structures composed of root-attached biofilms and planktonic cells arranged in complex layers. With the distinct but coordinated roles among the different member cells, bacterial communities resemble properties of a multicellular organism. High throughput sequencing technologies have allowed rapid and large-scale analysis of taxonomic composition and metabolic capacities of bacterial communities. However, these methods are generally unable to reconstruct the assembly of these communities, or how the gene expression patterns in individual cells/species are coordinated within these communities. Single-cell transcriptomes of community members can identify how gene expression patterns vary among members of the community, including differences among different cells of the same species. This information can be used to classify cells based on functional gene expression patterns, and predict the spatial organization of the community. Here we discuss strategies for the isolation of single bacterial cells, mRNA enrichment, library construction, and analysis and interpretation of the resulting single-cell RNA-Seq datasets. Unraveling regulatory and metabolic processes at the single cell level is expected to yield an unprecedented discovery of mechanisms involved in bacterial recruitment, attachment, assembly, organization of the community, or in the specific interactions among the different members of these communities.
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Affiliation(s)
- Qin Ma
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Heike Bücking
- Biology and Microbiology Department, South Dakota State University, Brookings, SD, United States
| | - Jose L. Gonzalez Hernandez
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD, United States
- Biology and Microbiology Department, South Dakota State University, Brookings, SD, United States
| | - Senthil Subramanian
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD, United States
- Biology and Microbiology Department, South Dakota State University, Brookings, SD, United States
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Lee WS, Lee S, Kang T, Ryu CM, Jeong J. Detection of Ampicillin-Resistant E. coli Using Novel Nanoprobe-Combined Fluorescence In Situ Hybridization. NANOMATERIALS 2019; 9:nano9050750. [PMID: 31100845 PMCID: PMC6567190 DOI: 10.3390/nano9050750] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 05/04/2019] [Accepted: 05/12/2019] [Indexed: 12/11/2022]
Abstract
Antibiotic-resistant bacteria present a global threat because the infections they cause are difficult to treat. Therefore, it is highly important to develop advanced methods for the identification of antibiotic resistance gene in the virulent bacteria. Here, we report the development of novel nanoprobes for fluorescence in situ hybridization (FISH) and the application of the nanoprobe to the detection of ampicillin-resistant Escherichia coli. The nanoprobe for FISH was synthesized by the modified sol-gel chemistry and the synthesized nanoprobe provided strong fluorescent signals and pH stability even under natural light condition. For the double-identification of bacteria species and ampicillin-resistance with a single probe in situ, the nanoprobes were conjugated to the two kinds of biotinylated probe DNAs; one for E. coli-species specific gene and the other for a drug-resistant gene. By using the nanoprobe-DNA conjugants, we successfully detected the ampicillin-resistant E. coli through the FISH technique. This result suggests the new insight into light stable FISH application of the nanoprobe for a pathogenic antibiotic-resistance bacterium.
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Affiliation(s)
- Wang Sik Lee
- Environmental Disease Research Center, Korea Research Institute of Bioscience Biotechnology (KRIBB), Daejeon 34141, Korea.
- Department of Nanobiotechnology, KRIBB School of Biotechnology, UST, Daejeon 34113, Korea.
| | - Soohyun Lee
- Infectious Disease Research Center, KRIBB, Daejeon 34141, Korea.
| | - Taejoon Kang
- Department of Nanobiotechnology, KRIBB School of Biotechnology, UST, Daejeon 34113, Korea.
- Bionanotechnology Research Center, KRIBB, Daejeon 34141, Korea.
| | - Choong-Min Ryu
- Infectious Disease Research Center, KRIBB, Daejeon 34141, Korea.
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, UST, Daejeon 34113, Korea.
| | - Jinyoung Jeong
- Environmental Disease Research Center, Korea Research Institute of Bioscience Biotechnology (KRIBB), Daejeon 34141, Korea.
- Department of Nanobiotechnology, KRIBB School of Biotechnology, UST, Daejeon 34113, Korea.
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Hughes RA, Jin X, Zhang Y, Zhang R, Tran S, Williams PG, Lindsey JS, Miller ES. Genome sequence, metabolic properties and cyanobacterial attachment of Porphyrobacter sp. HT-58-2 isolated from a filamentous cyanobacterium–microbial consortium. Microbiology (Reading) 2018; 164:1229-1239. [DOI: 10.1099/mic.0.000706] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Rebecca-Ayme Hughes
- 1Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, USA
- 2Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695-7615, USA
| | - Xiaohe Jin
- 1Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, USA
| | - Yunlong Zhang
- 1Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, USA
| | - Ran Zhang
- 1Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, USA
| | - Sabrina Tran
- 1Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, USA
- 3Enloe Magnet High School, Raleigh, North Carolina 27610, USA
| | - Philip G. Williams
- 4Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii 96822-2275, USA
| | - Jonathan S. Lindsey
- 1Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, USA
| | - Eric S. Miller
- 2Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695-7615, USA
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Differential detection of pathogenic Yersinia spp. by fluorescence in situ hybridization. Food Microbiol 2016; 62:39-45. [PMID: 27889163 DOI: 10.1016/j.fm.2016.09.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 09/16/2016] [Accepted: 09/18/2016] [Indexed: 12/12/2022]
Abstract
Yersinia enterocolitica, Y. pseudotuberculosis and Y. pestis are pathogens of major medical importance, which are responsible for a considerable number of infections every year. The detection of these species still relies on cultural methods, which are slow, labour intensive and often hampered by the presence of high amounts of accompanying flora. In this study, fluorescence in situ hybridization (FISH) was used to develop a fast, sensitive and reliable alternative to detect viable bacteria in food. For this purpose, highly specific probes targeting the 16S and 23S ribosomal RNA were employed to differentially detect each of the three species. In order to enable the differentiation of single nucleotide polymorphisms (SNPs), suitable competitor oligonucleotides and locked nucleic acids (LNAs) were used. Starved cells still showed a strong signal and a direct viable count (DVC) approach combined with FISH optimized live/dead discrimination. Sensitivity of the FISH test was high and even a single cell per gram of spiked minced pork meat could be detected within a day, demonstrating the applicability to identify foodborne hazards at an early stage. In conclusion, the established FISH tests proved to be promising tools to compensate existing drawbacks of the conventional cultural detection of these important zoonotic agents.
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