A Review of the Oesophageal Microbiome in Health and Disease
Publication date: Available online 9 October 2017 Source:Methods in Microbiology Author(s): Dervla Kelly, Liying Yang, Zhiheng Pei Microbial members of the gastrointestinal tract, known as the GTI microbiome, are beneficial for host metabolism and digestion, thereby creating a symbiotic relationship with their host (Petersen & Round, 2014). The microbiome has recently emerged as contributing to many intestinal disease states such as gastrointestinal reflux disease, Barrett's oesophagus and oesophageal cancers. Given that the local bacterial population influences individuals’ disease susceptibility, the micro...
Source: Methods in Microbiology - October 10, 2017 Category: Microbiology Source Type: research
Chapter 4 Electron cryotomography
Publication date: 2016 Source:Methods in Microbiology, Volume 43 Author(s): C.M. Oikonomou, M.T. Swulius, A. Briegel, M. Beeby, Q. Yao, G.J. Jensen Electron cryotomography (ECT) delivers 3D images of native structures inside intact cells with resolution on the scale of large macromolecular complexes (~4nm). It has proven to be an invaluable tool for interrogating the organization of bacterial cells and the structures of the nanomachines inside them. Here we present a brief introduction to the technique, a few examples of what we have learned by imaging bacterial cells with ECT over the last 15 years and a frank dis...
Source: Methods in Microbiology - November 24, 2016 Category: Microbiology Source Type: research
Chapter 3 Microfluidics for bacterial imaging
Publication date: 2016 Source:Methods in Microbiology, Volume 43 Author(s): L.E. Eland, A. Wipat, S. Lee, S. Park, L.J. Wu Microfluidics offers the technology for creating and maintaining microenvironments that is much needed for the microscopic study of bacteria. Over the past decade, microfluidics has been used in an increasingly large number of research studies, resulting in many important insights and discoveries. This chapter highlights some recent applications of microfluidic microscopy for bacteria, ranging from research in the engineering of bacterial systems, multispecies biofilm and microbial ecology, bact...
Source: Methods in Microbiology - November 24, 2016 Category: Microbiology Source Type: research
Chapter 2 Time-lapse microscopy and image analysis of Escherichia coli cells in mother machines
Publication date: 2016 Source:Methods in Microbiology, Volume 43 Author(s): Y. Yang, X. Song, A.B. Lindner High-throughput longitudinal measurements of single cells by automated time-lapse microscopy, combined with dynamic system modelling, have in recent decades advanced our understanding of microbial physiology, such as cell size control, gene expression and regulation, subcellular organisation and organelle dynamics, development and cell fate decision. However, the sheer large numbers of cells resulting from exponential growth often limit both the experimental duration and numbers of single cells quantified. To add...
Source: Methods in Microbiology - November 24, 2016 Category: Microbiology Source Type: research
Chapter 1 Methods for visualization of peptidoglycan biosynthesis
Publication date: 2016 Source:Methods in Microbiology, Volume 43 Author(s): Y.-P. Hsu, X. Meng, M.S. VanNieuwenhze Peptidoglycan is a rigid envelope surrounding the cytoplasmic membrane of most bacterial species. It helps protect bacterial cells from environmental stress and helps preserve cell morphology throughout their life cycle. Peptidoglycan biosynthesis is also an important regulator of bacterial cell division. Since the discovery of penicillin, it has also been an important drug target for antibacterial discovery and development. As a result, a significant effort has been directed at expanding our knowledge of...
Source: Methods in Microbiology - November 24, 2016 Category: Microbiology Source Type: research
Time-lapse microscopy and image analysis of Escherichia coli cells in mother machines
Publication date: Available online 8 November 2016 Source:Methods in Microbiology Author(s): Y. Yang, X. Song, A.B. Lindner High-throughput longitudinal measurements of single cells by automated time-lapse microscopy, combined with dynamic system modelling, have in recent decades advanced our understanding of microbial physiology, such as cell size control, gene expression and regulation, subcellular organisation and organelle dynamics, development and cell fate decision. However, the sheer large numbers of cells resulting from exponential growth often limit both the experimental duration and numbers of single cells q...
Source: Methods in Microbiology - November 8, 2016 Category: Microbiology Source Type: research
Methods for visualization of peptidoglycan biosynthesis
Publication date: Available online 4 November 2016 Source:Methods in Microbiology Author(s): Y.-P. Hsu, X. Meng, M.S. VanNieuwenhze Peptidoglycan is a rigid envelope surrounding the cytoplasmic membrane of most bacterial species. It helps protect bacterial cells from environmental stress and helps preserve cell morphology throughout their life cycle. Peptidoglycan biosynthesis is also an important regulator of bacterial cell division. Since the discovery of penicillin, it has also been an important drug target for antibacterial discovery and development. As a result, a significant effort has been directed at expanding...
Source: Methods in Microbiology - November 4, 2016 Category: Microbiology Source Type: research
Microfluidics for bacterial imaging
Publication date: Available online 27 October 2016 Source:Methods in Microbiology Author(s): L.E. Eland, A. Wipat, S. Lee, S. Park, L.J. Wu Microfluidics offers the technology for creating and maintaining microenvironments that is much needed for the microscopic study of bacteria. Over the past decade, microfluidics has been used in an increasingly large number of research studies, resulting in many important insights and discoveries. This chapter highlights some recent applications of microfluidic microscopy for bacteria, ranging from research in the engineering of bacterial systems, multispecies biofilm and microb...
Source: Methods in Microbiology - October 28, 2016 Category: Microbiology Source Type: research
Electron cryotomography
Publication date: Available online 27 October 2016 Source:Methods in Microbiology Author(s): C.M. Oikonomou, M.T. Swulius, A. Briegel, M. Beeby, Q. Yao, G.J. Jensen Electron cryotomography (ECT) delivers 3D images of native structures inside intact cells with resolution on the scale of large macromolecular complexes (~4nm). It has proven to be an invaluable tool for interrogating the organization of bacterial cells and the structures of the nanomachines inside them. Here we present a brief introduction to the technique, a few examples of what we have learned by imaging bacterial cells with ECT over the last 15 year...
Source: Methods in Microbiology - October 26, 2016 Category: Microbiology Source Type: research
Chapter 12 Bacterial Typing and Identification By Genomic Analysis of 16S –23S rRNA Intergenic Transcribed Spacer (ITS) Sequences
Publication date: 2014 Source:Methods in Microbiology, Volume 41 Author(s): Volker Gürtler, Gangavarapu Subrahmanyam, Malathi Shekar, Biswajit Maiti, Indrani Karunasagar The rrn operon is the basic building block of all bacteria found in 1–15 copies per bacterial genome in all bacteria. All bacterial genomes contain rrn operons that contain four basic components: (i) 16S rRNA gene; (ii) 16S–23S intergenic transcribed spacer (ITS); (iii) 23S rRNA gene; (iv) 5S rRNA gene. The chapter “Bacterial Typing and Identification By Genomic Analysis of 16S–23S rRNA Intergenic Transcribed Spacer (ITS) Sequencesâ€...
Source: Methods in Microbiology - July 20, 2016 Category: Microbiology Source Type: research
Chapter 6 Low-Density TaqMan ® Array Cards for the Detection of Pathogens
Publication date: 2015 Source:Methods in Microbiology, Volume 42 Author(s): Jude Heaney, Kathryn Rolfe, Nicholas S. Gleadall, Jane S. Greatorex, Martin D. Curran Real-time PCR assays have revolutionised diagnostic microbiology over the past 15 years or more. Adaptations and improvements over that time frame have led to the development of multiplex assays. However, limitations in terms of available fluorophores has meant the number of assays which can be combined has remained in single figures. This latter limitation has led to the focus tending to be on individual pathogens and their detection. This chapter d...
Source: Methods in Microbiology - July 20, 2016 Category: Microbiology Source Type: research
Chapter 17 Artificial Nucleic Acid Probes and Their Applications in Clinical Microbiology
Publication date: 2015 Source:Methods in Microbiology, Volume 42 Author(s): Alon Singer, Yi-Wei Tang Nucleic acid probes are ubiquitous in molecular diagnostics as their inherent attributes lend themselves extremely well for those purposes. With the aim of developing ever more capable diagnostics, the emphasis has been on designing smarter assays or improving the sensors themselves, enabling the development of more accurate and more sensitive molecular diagnostics. Recently, however, a number of groups have begun designing and utilising artificial nucleic acid probes which have been specifically engineered to overc...
Source: Methods in Microbiology - November 28, 2015 Category: Microbiology Source Type: research
Chapter 16 Virology
Publication date: 2015 Source:Methods in Microbiology, Volume 42 Author(s): Richard Allen White, Jessica N. Brazelton de Cárdenas, Randall T. Hayden In the past 25 years, virology has had major technology breakthroughs stemming first from the introduction of nucleic acid amplification testing, but more recently from the use of next-generation sequencing, digital PCR, and the possibility of single virion genomics. These technologies have and will improve diagnosis and disease state monitoring in clinical settings, aid in environmental monitoring, and reveal the vast genetic potential of viruses. Using the princip...
Source: Methods in Microbiology - November 28, 2015 Category: Microbiology Source Type: research
Chapter 15 Next-Generation Sequencing for Pathogen Detection and Identification
Publication date: 2015 Source:Methods in Microbiology, Volume 42 Author(s): Kenneth G. Frey, Kimberly A. Bishop-Lilly Over the past decade, the field of genomics has seen such drastic improvements in sequencing chemistries that high-throughput sequencing, or next-generation sequencing (NGS), is being applied to generate data across many disciplines. NGS instruments are becoming less expensive, faster, and smaller, and therefore are being adopted in an increasing number of laboratories, including clinical laboratories. Thus far, clinical use of NGS has been mostly focused on the human genome, for purposes such as ch...
Source: Methods in Microbiology - November 28, 2015 Category: Microbiology Source Type: research
Chapter 14 MALDI-TOF Mass Spectrometry in the Clinical Microbiology Laboratory; Beyond Identification
Publication date: 2015 Source:Methods in Microbiology, Volume 42 Author(s): Sören Schubert, Markus Kostrzewa Within less than a decade, matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) has become a gold standard for microbial identification in clinical microbiology laboratories. Besides identification of microorganisms, the typing of single strains as well as antibiotic and antimycotic resistance testing has come into focus in order to speed up the diagnostic process. Similarly to microbial identification, the main drivers are the reduction of cost per test and the more r...
Source: Methods in Microbiology - November 28, 2015 Category: Microbiology Source Type: research
