Curr Protoc Microbiol [JOURNAL]
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Alexandre G
Curr Protoc Microbiol
· 2017 Nov · PMID 29120487
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Bacteria of the genus Azospirillum comprise 15 species to date, with A. brasilense the best studied species in the genus. Azospirillum are soil bacteria able to promote the growth of plants from 113 species spanning 35 b...
Bacteria of the genus Azospirillum comprise 15 species to date, with A. brasilense the best studied species in the genus. Azospirillum are soil bacteria able to promote the growth of plants from 113 species spanning 35 botanical families. These non-pathogenic and beneficial bacteria are ubiquitous in soils and inhabit the roots of diverse plants. These bacteria are microaerophilic, able to fix nitrogen under free-living conditions, motile, and able to navigate in gradients of various chemicals, including oxygen. These physiological traits are used to isolate these soil bacteria from soil and plant root samples, providing isolates that can be used for studying microbial physiology and plant growth promotion. © 2017 by John Wiley & Sons, Inc.
Miossec MJ, Valenzuela SL, Mendez KN
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, Castro-Nallar E
Curr Protoc Microbiol
· 2017 Nov · PMID 29120486
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As the field of microbiomics advances, the burden of computational work that scientists need to perform in order to extract biological insight has grown accordingly. Likewise, while human microbiome analyses are increasi...
As the field of microbiomics advances, the burden of computational work that scientists need to perform in order to extract biological insight has grown accordingly. Likewise, while human microbiome analyses are increasingly shifting toward a greater integration of various high-throughput data types, a core number of methods form the basis of nearly every study. In this unit, we present step-by-step protocols for five core stages of human microbiome research. The protocols presented in this unit provide a base case for human microbiome analysis, complete with sufficient detail for researchers to tailor certain aspects of the protocols to the specificities of their data. © 2017 by John Wiley & Sons, Inc.
Samanta D, Gilk SD
Curr Protoc Microbiol
· 2017 Nov · PMID 29120485
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Coxiella burnetii is the causative agent of human Q fever, a zoonotic disease that can cause a debilitating, flu-like illness in acute cases, or a life-threatening endocarditis in chronic patients. An obligate intracellu...
Coxiella burnetii is the causative agent of human Q fever, a zoonotic disease that can cause a debilitating, flu-like illness in acute cases, or a life-threatening endocarditis in chronic patients. An obligate intracellular bacterial pathogen, Coxiella survives and multiplies in a large lysosome-like vacuole known as the Coxiella parasitophorous vacuole (CPV). A unique characteristic of the CPV is the acidic environment (pH ∼5.0), which is required to activate Coxiella metabolism and the Coxiella type 4 secretion system (T4SS), a major virulence factor required for intracellular survival. Further, inhibiting or depleting vacuolar ATPase, a host cell protein that regulates lysosomal pH, inhibits intracellular Coxiella growth. Together, these data suggest that CPV pH is an important limiting factor for Coxiella growth and virulence. This unit describes a method to determine CPV pH using live cell microscopy of a pH-sensitive fluorophore conjugated to dextran. This technique is useful to measure changes in CPV pH during infection or in response to drug treatment. © 2017 by John Wiley & Sons, Inc.
Sherwani S, Chowdhury M, Bugert JJ
Curr Protoc Microbiol
· 2017 Nov · PMID 29120484
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Molluscum contagiosum virus (MCV) is a common skin pathogen of children and young adults. Infection with MCV causes benign skin tumors in children and young adults and is mostly self-limiting. In contrast to orthopoxviru...
Molluscum contagiosum virus (MCV) is a common skin pathogen of children and young adults. Infection with MCV causes benign skin tumors in children and young adults and is mostly self-limiting. In contrast to orthopoxviruses, MCV infections tend to take a subacute clinical course but may persist for up to 12 months. Current numbers for MCV seroprevalence in different geographical areas are based on a variety of historical serological methods from complement fixation assays to MCV ELISAs based on purified MCV virions and MC133 antigen expressed in a Semliki Forest Virus expression system. A standardized ELISA for the assessment of MCV seroprevalence would be useful to determine global MCV seroprevalence. The methods described show that polypeptides derived from MCV open reading frames MC084 (residues V123 to R230 and V33 to G117), mc133 (residues M1 to N370), and glutathione S-transferase (GST)-H3L (residues I142 to W251) expressed in E. coli RIL+ as GST fusion proteins can be used to assess antibody binding in a GST capture ELISA. We show how the ELISA can be used to screen a panel of patient sera previously characterized with the mc084 V123-R230 ELISA. © 2017 by John Wiley & Sons, Inc.
Gullett J, O'Neal L, Mukherjee T
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, Alexandre G
Curr Protoc Microbiol
· 2017 Nov · PMID 29120483
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Bacteria of the genus Azospirillum, including the most comprehensively studied Azospirillum brasilense, are non-pathogenic soil bacteria that promote the growth of diverse plants, making them an attractive model to under...
Bacteria of the genus Azospirillum, including the most comprehensively studied Azospirillum brasilense, are non-pathogenic soil bacteria that promote the growth of diverse plants, making them an attractive model to understand non-symbiotic, beneficial plant-bacteria associations. Research into the physiology and genetics of these organisms spans decades and a range of molecular tools and protocols have been developed for allelic exchange mutagenesis, in trans expression of genes, and fusions to reporter genes. © 2017 by John Wiley & Sons, Inc.
Beigel B, Verma A
Curr Protoc Microbiol
· 2017 Nov · PMID 29120482
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This protocol describes a method for the rapid detection of leptospiral DNA in environmental water. In summary, the DNA is extracted from water samples and tested in a TaqMan-based real-time quantitative polymerase chain...
This protocol describes a method for the rapid detection of leptospiral DNA in environmental water. In summary, the DNA is extracted from water samples and tested in a TaqMan-based real-time quantitative polymerase chain reaction (qPCR) for the presence of lipl32, a gene that is present only in pathogenic Leptospira spp. The gene target used in this assay is important in that it only detects pathogenic leptospires and not the saprophytic leptospires that may be present in environmental samples. © 2017 by John Wiley & Sons, Inc.
Harris G, KuoLee R, Xu HH
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, Chen W
Curr Protoc Microbiol
· 2017 Aug · PMID 28800159
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This unit describes basic protocols for infecting mice through intranasal and intraperitoneal routes with Acinetobacter baumannii to induce associated pneumonia and sepsis, the two most common manifestations of clinical...
This unit describes basic protocols for infecting mice through intranasal and intraperitoneal routes with Acinetobacter baumannii to induce associated pneumonia and sepsis, the two most common manifestations of clinical infections with this pathogen. By selecting the appropriate protocols and bacterial strains of different virulence, these mouse models provide an opportunity to study the infection pathogenesis and host-immune responses, and to evaluate the efficacies of prophylactic and therapeutic anti-A. baumannii candidates. © 2017 by John Wiley & Sons, Inc.
Allen B, Drake M, Harris N
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, Sullivan T
Curr Protoc Microbiol
· 2017 Aug · PMID 28800158
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The DOE Systems Biology Knowledgebase (KBase, http://kbase.us/) is an open-access bioinformatics software and data platform for analyzing plants, microbes, and their communities. KBase enables scientists to create, execu...
The DOE Systems Biology Knowledgebase (KBase, http://kbase.us/) is an open-access bioinformatics software and data platform for analyzing plants, microbes, and their communities. KBase enables scientists to create, execute, collaborate on, and share reproducible analyses of their biological data in the context of public data and private collaborator data. For microbiologists researching prokaryotes, KBase offers analysis tools for performing quality control and assessment of Next-Generation Sequencing reads, de novo assembly, genome annotation, and tools for analyzing structural and functional features of genomes. This unit demonstrates an example workflow for taking a comparative and iterative approach to assembly and annotation of prokaryotic genomes using KBase that can be used by microbiologists seeking to perform isolate analysis in a rapid and reproducible fashion. © 2017 by John Wiley & Sons, Inc.
Pawlowic MC, Vinayak S, Sateriale A
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, Brooks CF, Striepen B
Curr Protoc Microbiol
· 2017 Aug · PMID 28800157
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The apicomplexan parasite Cryptosporidium is a leading cause of diarrheal disease and an important contributor to overall global child mortality. We currently lack effective treatment and immune prophylaxis. Recent advan...
The apicomplexan parasite Cryptosporidium is a leading cause of diarrheal disease and an important contributor to overall global child mortality. We currently lack effective treatment and immune prophylaxis. Recent advances now permit genetic modification of this important pathogen. We expect this to produce rapid advances in fundamental as well as translational research on cryptosporidiosis. Here we outline genetic engineering for Cryptosporidium in sufficient detail to establish transfection in any laboratory that requires access to this key technology. This chapter details the conceptual design consideration, as well as the experimental steps required to transfect, select, and isolate transgenic parasites. We also provide detail on key in vitro and in vivo assays to detect, validate, and quantify genetically modified Cryptosporidium parasites. © 2017 by John Wiley & Sons, Inc.
Winfree S, Gilk SD
Curr Protoc Microbiol
· 2017 Aug · PMID 28800156
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The gram-negative bacterium Coxiella burnetii causes human Q fever, a disease characterized by a debilitating flu-like illness in acute cases and endocarditis in chronic patients. An obligate intracellular pathogen, Coxi...
The gram-negative bacterium Coxiella burnetii causes human Q fever, a disease characterized by a debilitating flu-like illness in acute cases and endocarditis in chronic patients. An obligate intracellular pathogen, Coxiella burnetii survives within a large, lysosome-like vacuole inside the host cell. A unique feature of the Coxiella parasitophorous vacuole (PV) is high levels of fusion with the host endocytic pathway, with PV-endosome fusion critical for Coxiella survival within the host cell. This unit describes quantitating PV-endosome fusion by measuring delivery of the fluid phase endosome marker dextran to the PV using live cell imaging. To study the effect of host cell proteins involved in PV-endosome fusion, details are provided for using siRNA knockdown host cells. This method is a powerful tool for understanding mechanisms underlying Coxiella's ability to manipulate host cell trafficking pathways. © 2017 by John Wiley & Sons, Inc.
Balakrishnan L, Milavetz B
Curr Protoc Microbiol
· 2017 Aug · PMID 28800155
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Simian virus 40 (SV40) is one of the best-characterized members of the polyomavirus family of small DNA tumor viruses. It has a small genome of 5243 bp and utilizes cellular proteins for its molecular biology, with the e...
Simian virus 40 (SV40) is one of the best-characterized members of the polyomavirus family of small DNA tumor viruses. It has a small genome of 5243 bp and utilizes cellular proteins for its molecular biology, with the exception of the T-antigen protein, which is coded by the virus and is involved in regulating transcription and directing replication. Importantly, SV40 exists as chromatin in both the virus particle and intracellular minichromosomes. These facts, combined with high yields of virus and minichromosomes following infection and ease of manipulation, have made SV40 an extremely useful model to study all aspects of eukaryotic molecular biology. This unit describes procedures for working with SV40 and preparing SV40 chromatin from infected cells and virus particles, as well as procedures for using SV40 chromatin to study epigenetic regulation. © 2017 by John Wiley & Sons, Inc.
Boileau MJ, Mani R, Clinkenbeard KD
Curr Protoc Microbiol
· 2017 May · PMID 28510364
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Bdellovibrio bacteriovorus 109J is a Gram-negative predatory bacterium with obligate host dependency on other Gram-negative bacteria. This bacteriolytic predator collides with, enters, and establishes growth within the p...
Bdellovibrio bacteriovorus 109J is a Gram-negative predatory bacterium with obligate host dependency on other Gram-negative bacteria. This bacteriolytic predator collides with, enters, and establishes growth within the prey (host) periplasm, eventually lysing the prey cell wall to release fresh, motile B. bacteriovorus progeny. Laboratory maintenance of B. bacteriovorus has been previously described by other investigators. The protocols included in this unit deal with the technique required to lyophilize or freeze dry host-dependent B. bacteriovorus. This is an alternative means to frozen glycerol stocks for the long-term storage of B. bacteriovorus. It includes the cultivation process and methods to lyophilize B. bacteriovorus as well as recommended storage conditions. In addition, this unit provides insight on the formulation's shelf-life including the time to active culture after reviving lyophilized stocks of B. bacteriovorus following short-, medium-, and long-term storage. © 2017 by John Wiley & Sons, Inc.
Watts EA, Dhara A, Sinai AP
Curr Protoc Microbiol
· 2017 May · PMID 28510363
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The protozoan parasite Toxoplasma gondii is capable of infecting all warm-blooded animals and humans. Infectious, transmissible forms of the parasite include oocysts produced by the sexual cycle within the definitive fel...
The protozoan parasite Toxoplasma gondii is capable of infecting all warm-blooded animals and humans. Infectious, transmissible forms of the parasite include oocysts produced by the sexual cycle within the definitive feline host and tissue cysts that form Toxoplasma in the central nervous system and muscle during the asexual cycle within all chronically infected warm-blooded hosts. These tissue cysts are populated with slow-growing bradyzoites, which until recently have been thought to be dormant entities in the context of immune sufficiency. Reactivation to active growth during immune suppression is of critical clinical importance. However, little is known about tissue cysts or the bradyzoites they house, as the diversity of tissue cysts cannot be replicated in cell culture systems. This protocol for optimization of tissue cyst purification from the brains of infected mice using Percoll gradients provides an efficient means to recover in vivo-derived tissue cysts that can be applied to imaging, cell biological, biochemical, transcriptomic, and proteomic analyses. © 2017 by John Wiley & Sons, Inc.
Garcia EC
Curr Protoc Microbiol
· 2017 May · PMID 28510362
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Burkholderia thailandensis is a Gram-negative bacterium endemic to Southeast Asian and northern Australian soils. It is non-pathogenic; therefore, it is commonly used as a model organism for the related human pathogens B...
Burkholderia thailandensis is a Gram-negative bacterium endemic to Southeast Asian and northern Australian soils. It is non-pathogenic; therefore, it is commonly used as a model organism for the related human pathogens Burkholderia mallei and Burkholderia pseudomallei. B. thailandensis is relatively easily genetically manipulated and a variety of robust genetic tools can be used in this organism. This unit describes protocols for conjugation, natural transformation, mini-Tn7 insertion, and allelic exchange in B. thailandensis. © 2017 by John Wiley & Sons, Inc.
Mueller KE, Wolf K, Fields KA
Curr Protoc Microbiol
· 2017 May · PMID 28510361
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Gene inactivation is essential for forward and reverse genetic approaches to establish protein function. Techniques such as insertion or chemical mutagenesis have been developed to mutagenize chlamydiae via targeted or r...
Gene inactivation is essential for forward and reverse genetic approaches to establish protein function. Techniques such as insertion or chemical mutagenesis have been developed to mutagenize chlamydiae via targeted or random mutagenesis, respectively. Both of these approaches require transformation of chlamydiae to either introduce insertion elements or complement mutants. We have recently developed a targeted mutagenesis strategy, fluorescence-reported allelic exchange mutagenesis (FRAEM), to delete Chlamydia trachomatis L2 genes. This approach overcomes several barriers for genetically manipulating intracellular bacteria. Perhaps most significantly, FRAEM employs fluorescence reporting to indicate successful transformation and subsequent recombination events. Three protocols are provided that detail methods to construct gene-specific suicide vectors, transform C. trachomatis L2 to select for recombinants, and isolate clonal populations via limiting dilution. In aggregate, these protocols will allow investigators to engineer C. trachomatis L2 strains carrying complete deletions of desired gene(s). © 2017 by John Wiley & Sons, Inc.
Henno L, Tombak EM, Geimanen J
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, Orav M, Ustav E, Ustav M
Curr Protoc Microbiol
· 2017 May · PMID 28510360
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This unit includes the necessary information to conduct neutral/neutral and neutral/alkaline two-dimensional and neutral/neutral/alkaline three-dimensional agarose gel electrophoresis. The methodology has been optimized...
This unit includes the necessary information to conduct neutral/neutral and neutral/alkaline two-dimensional and neutral/neutral/alkaline three-dimensional agarose gel electrophoresis. The methodology has been optimized over the years to gain a better outcome from the hard-to-interpret signals of human papilloma virus replication intermediates obtained from two- and three-dimensional agarose gels. Examples of typical results and interpretation of replication intermediate patterns are included, and the outcomes of multiple-dimension assays are assessed using previously published experimental data. © 2017 by John Wiley & Sons, Inc.
Verma SK, Lindsay DS, Grigg ME
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, Dubey JP
Curr Protoc Microbiol
· 2017 May · PMID 28510359
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More than 200 valid Sarcocystis species have been described in the parasitological literature. The developmental life cycle in the intermediate host and definitive host has only been described for a few species. Sarcocys...
More than 200 valid Sarcocystis species have been described in the parasitological literature. The developmental life cycle in the intermediate host and definitive host has only been described for a few species. Sarcocystis parasites are common pathogens infecting a wide range of animals, including humans, and this unit reviews the methods used for isolating infective stages of the parasite from both definitive and intermediate host(s), as well as methods used to initiate cultures from sporocysts and merozoites and for cryopreservation of various Sarcocystis spp. These methods are based on published reports and our experience with Sarcocystis species in cell culture over many years. The information presented is suitable for the efficient culture of many Sarcocystis species; however, some minor modifications may be needed based on the unique developmental patterns of some species. © 2017 by John Wiley & Sons, Inc.
Khan A, Grigg ME
Curr Protoc Microbiol
· 2017 Feb · PMID 28166387
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Toxoplasma gondii is a highly successful apicomplexan protozoan capable of infecting any warm-blooded animal worldwide. In humans, Toxoplasma infections are life-long, with approximately one-third of the world's populati...
Toxoplasma gondii is a highly successful apicomplexan protozoan capable of infecting any warm-blooded animal worldwide. In humans, Toxoplasma infections are life-long, with approximately one-third of the world's population chronically infected. Although normally controlled by the host immune system, T. gondii infection can lead to a variety of clinical outcomes in individuals with immature or suppressed immune systems. After penetrating the intestine, parasites rapidly disseminate throughout the body and stimulate production of the cytokines interleukin (IL)-12, IL-18, and interferon (IFN)-γ by immune cells. These cytokines play a key role in host resistance to T. gondii by promoting a strong Th1 response. Recent reports show that gut commensal bacteria can act as molecular adjuvants during T. gondii infection. Thus, T. gondii is an excellent model system to study host-pathogen interactions. This unit outlines the protocols for in vitro and in vivo maintenance and growth of T. gondii. © 2017 by John Wiley & Sons, Inc.
Dhakal D, Chung NT, Rayamajhi V
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, Sohng JK
Curr Protoc Microbiol
· 2017 Feb · PMID 28166386
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Actinomadura spp. are aerobic, Gram-positive, catalase-positive, non-acid fast, non-motile actinomycetes. Some species of Actinomadura are associated with opportunistic infections in humans. However, many bioactive compo...
Actinomadura spp. are aerobic, Gram-positive, catalase-positive, non-acid fast, non-motile actinomycetes. Some species of Actinomadura are associated with opportunistic infections in humans. However, many bioactive compounds with pharmaceutical applications can be isolated from various Actinomadura spp. This unit includes general protocols for the laboratory maintenance of Actinomadura spp., including growth in liquid medium, growth on solid agar, long-term storage, and generation of a higher producing strain by ribosome engineering. Actinomadura hibisca P157-2 is used as a prototype for explaining the considerations for efficient laboratory maintenance of Actinomadura spp. © 2017 by John Wiley & Sons, Inc.
Vanmechelen B, Rector A, Maes P
Curr Protoc Microbiol
· 2017 Feb · PMID 28166385
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Many methods for the discovery of novel viruses are based on amplification of the virus using consensus or degenerate PCR primers. A downside of this approach is that it requires prior knowledge of the viral nucleotide s...
Many methods for the discovery of novel viruses are based on amplification of the virus using consensus or degenerate PCR primers. A downside of this approach is that it requires prior knowledge of the viral nucleotide sequence to be applicable. Presented in this unit is a method for the sequence-independent amplification of circular viral genomes that is based on the rolling-circle mechanism used by certain viruses in their natural replication cycle. The amplification of the virus of interest is coupled to the isolation of the viral genome by gel extraction following a restriction digestion. Once isolated, the sequence of the viral genome can be determined by nanopore sequencing, a rapid and inexpensive next-generation sequencing technology that generates long reads in real time. The method described in this unit was originally developed for the discovery of papillomaviruses, but can be used for the identification of all types of circular DNA viruses. © 2017 by John Wiley & Sons, Inc.