Microbiology

Creating a robust and controlled infection model is imperative for studying the innate immune response. Leveraging the particular strengths of the zebrafish model system, such as optical transparency, ex utero development, and large clutch size, allows for the development of methods that yield consistent and reproducible results. We created a robust model for activation of innate immunity by microinjecting bacterial particles or live bacteria into larval zebrafish, unlike previous studies which largely restricted such manipulations to embryonic stages of zebrafish. The ability to introduce stimuli locally or systemically at larval stages provides significant advantages to examine host response in more mature tissues as well as the possibility to interrogate adaptive immunity at older larval stages. This protocol describes two distinct modes of microinjection to introduce lipopolysaccharide (LPS) or bacteria into the living larval zebrafish: one localized to the brain, and another into the bloodstream via the caudal vein plexus.

Graphic abstract:


Schematic shows the two distinct modes of larval zebrafish microinjection, either in the brain parenchyma or in the blood stream intravenously. Reagents introduced into the zebrafish to assess immune response are depicted in the “injection components” as described in the protocol.

Ralstonia solanacearum is a bacterial phytopathogen able to cause bacterial wilt disease in more than 200 plant species. Plant disease biocontrol strategies are used for controlling this disease and tomato is used as a model plant to conduct R. solanacearum associated studies. Conventional screening methods such as seed bacterization, soil drenching and root bacterization (in grown plants) to assess the ability of biocontrol bacteria to antagonize R. solanacearum under in planta conditions in different hosts are time-consuming and costly. A fast, cost effective method is a key requirement to advance the research on R. solanacearum biocontrol. In this protocol, we have inoculated the roots of tomato seedlings with bacterial isolates showing antagonistic activity against R. solanacearum under in vitro conditions. After 16 h of treatment with the antagonizing bacteria, seedlings were inoculated with R. solanacearum by a well-established root-dip method. Then the seedlings were maintained at controlled conditions and the number of wilted/dead seedlings were recorded up to 10^th day post R. solanacearum inoculation. Biocontrol efficacy was calculated from the records for each tested isolate. This protocol is advantageous than already available protocols in the sense that it can be completed within a very short duration (~18 days for tomato) and there is no requirement of culture media to maintain the seedlings. This method can be used for quickly screening large number of bacterial isolates and different host genotypes within a short period of time and at a minimum cost.

Investigation of bacterial gene regulation upon environmental changes is still a challenging task. For example, Vibrio cholerae, a pathogen of the human gastrointestinal tract, faces diverse transient conditions in different compartments upon oral ingestion. Genetic reporter systems have been demonstrated to be extremely powerful tools to unravel gene regulation events in complex conditions, but so far focused mainly on gene induction. Herein, we describe the TetR-controlled recombination-based in vivo expression technology TRIVET, which allows detection of gene silencing events. TRIVET resembles a modified variant of the in vivo expression technology (IVET) as well as recombination-based in vivo expression technology (RIVET), which were used to identify conditional gene induction in several bacteria during host colonization. Like its predecessors, TRIVET is a single cell based reporter system, which allows the analysis of bacterial gene repression in a spatiotemporal manner via phenotypical changes in the resistance profile. Briefly, a promoterless tetR (encoding the transcriptional repressor TetR) can be integrated randomly into the bacterial genome via transposon mutagenesis or site-specific downstream of a promoter of interest via homologous recombination. Reduction of transcriptional expression of TetR results in a de-repression of the TetR-controlled resolvase TnpR, which in turn leads to excision of an antibiotic resistance cassette (also known as res-cassette) and altered resistance profile observable via streaking on ampicillin and kanamycin plates. This alteration can then be quantified as the ratio between resistant and non-resistant isolates. Furthermore, the newly introduced second reporter gene, a promoterless phoA (encoding the alkaline phosphatase PhoA) offers an additional validation step of the results via an independent colorimetric assay to measure enzyme activity. The protocol presented herein also offers an approach to identify the gene locus in case of the random screen for gene repression as well as a quantification of the conditional repression of a gene of interest. Although the current protocol is established for gene repression during host colonization, it can likely be adapted to study gene silencing under various conditions faced by a bacterium.

Parasites of the genus Leishmania infect the mammalian hosts, including mice and humans and cause cutaneous or visceral leishmaniasis depending upon the parasite species transmitted by the vector sandfly. Leishmania amazonensis is one of the Leishmania species responsible for the cutaneous form of the disease. We have inoculated with these parasites the ear dermis of mice. RNA preparations were performed from fragmented tissues using a buffer containing guanidin isothiocynate (RLT buffer, RNeasy Mini Kit, Qiagen, SAS, France) and β-mercaptoethanol. Both reagents facilitate the isolation of intact RNA from tissues and the use of the RNeasy Kits present with several advantages that facilitate the isolation of pure non-degraded total RNA: i) This method allows to avoid the presence of phenol in the RNA extraction buffer, commonly used in alternative protocols; ii) Moreover Diethylpyrocarbonate (DEPC) treatment of glassware, to avoid RNAses contamination of the samples, is not required with this protocol; iii) Finally, it is a fast procedure and the isolated total RNA may be concentrated in a small volume thus facilitating its use for downstream experimental procedures.

Asthma is a global problem that affects millions of individuals. An increased risk of respiratory viral and bacterial infections is one of the complications of asthma. We recently reported that mice with ovalbumin-induced allergic airway disease (AAD) are protected against influenza-Streptococcus pneumoniae co-infection. Here, we describe in detail a protocol on how to induce AAD and influenza-S. pneumoniae co-infection in mice and to evaluate the specific roles of asthma on immunity to viral and bacterial pathogens in the hope of translating findings to benefit asthmatic individuals.

Red palm weevil (RPW), Rhynchophorus ferrugineus Olivier, is a devastating pest of palm trees worldwide. RPW gut is colonized by diverse bacterial species which profoundly influence host development and nutritional metabolism. However, the molecular mechanisms behind the interactions between RPW and its gut microbiota remain mostly unknown. Antibiotics are usually employed to remove gut bacteria to investigate the impact of gut bacteria on insect fitness. However, administration of antibiotics cannot thoroughly remove gut bacteria for most insect species. Therefore, establishing germfree (GF) organisms is a powerful way to reveal the mutual interactions between gut bacteria and their insect hosts. Here, we describe a protocol to generate and maintain RPW GF larvae, being completely devoid of gut bacteria in laboratory. RPW GF larvae were established from the dechorionated fresh eggs which were reared on the sterilized artificial food under axenic conditions. The establishment of GF larvae set a solid foundation to deeply elucidate the molecular mechanisms behind the interactions between RPW and its gut microbiota.

Reagents such as Amplex^® Red have been developed for detecting hydrogen peroxide (H₂O₂) and are used to measure the release of H₂O₂ from biological samples such as mammalian leukocytes undergoing the oxidative burst. Caenorhabditis elegans is commonly used as a model host in the study of interactions with microbial pathogens and releases reactive oxygen species (ROS) as a component of its defense response. We adapted the Amplex^® Red Hydrogen Peroxide/Peroxidase Assay Kit to measure H₂O₂ output from live Caenorhabditis elegans exposed to microbial pathogens. The assay differs from other forms of ROS detection in the worm, like dihydrofluorescein dyes and genetically encoded probes such as HyPer, in that it generally detects released, extracellular ROS rather than intracellular ROS, though the distinction between the two is blurred by the fact that certain species of ROS, including H₂O₂, can cross membranes. The protocol involves feeding C. elegans on a lawn of the pathogen of interest for a period of time. The animals are then rinsed off the plates in buffer and washed to remove any microbes on their cuticle. Finally, the animals in buffer are distributed into 96-well plates and Amplex^® Red and horseradish peroxidase (HRP) are added. Any H₂O₂ released into the buffer by the worms will react with the Amplex^® Red reagent in a 1:1 ratio in the presence of HRP to produce the red fluorescent excitation product resorufin that can be measured fluorometrically or spectrophotometrically, and the amount of H₂O₂ released can be calculated by comparison to a standard curve. The assay is most appropriate for studies focused on released ROS, and its advantages include ease of use, the ability to use small numbers of animals in a plate reader assay in which measurements can be taken either fluorometrically or spectrophotometrically.

Candida albicans is a leading human fungal pathogen that uses several metabolic adaptations to escape immune cells and causes systemic disease. Here, we describe a protocol for measuring one of these adaptations, the ability to thrive in hypoxic niches. Hypoxia was generated after successful subdermal infection with C. albicans in a murine infection model. Hypoxia was measured using a fluorescent dye for carbonic anhydrase 9, a host enzyme active under hypoxic conditions. Emitted fluorescence was subsequently quantified using an IVIS system. This protocol was optimized for the use in subdermal infection in mice but has the potential to be adapted to other models of fungal infection.

Soil organisms are diverse taxonomically and functionally. This ecosystem experiences highly complex networks of interactions, but may also present functionally independent entities. Plant roots, a metabolically active hotspot in the soil, take an essential part in shaping the rhizosphere. Tracking the dynamics of root-microbe interactions at high spatial resolution is currently limited due to methodological intricacy. In this study, we developed a novel microfluidics-based device enabling direct imaging of root-bacteria interactions in real time.

Short-Chain Fatty Acids (SCFAs) are a product of the fermentation of resistant starches and dietary fibers by the gut microbiota. The most important SCFA are acetate (C2), propionate (C3) and butyrate (C4). These metabolites are formed and absorbed in the colon and then transported through the hepatic vein to the liver. SCFAs are more concentrated in the intestinal lumen than in the serum. Butyrate is largely consumed in the gut epithelium, propionate in the liver and acetate in the periphery. SCFAs act on many cells including components of the immune system and epithelial cells by two main mechanisms: activation of G-protein coupled receptors (GPCRs) and inhibition of histone deacetylase. Considering the association between changes in SCFA concentrations and the development of diseases, methods to quantify these acids in different biological samples are important. In this study, we describe a protocol using gas chromatography to quantify SCFAs in the serum, feces and colonic luminal content. Separation of compounds was performed using a DB-23 column (60 m x 0.25 mm internal diameter [i.d.]) coated with a 0.15 µm thick layer of 80.2% 1-methylnaphatalene. This method has a good linear range (15-10,000 µg/ml). The precision (relative standard deviation [RSD]) is less than 15.0% and the accuracy (error relative [ER]) is within ± 15.0%. The extraction efficiency was higher than 97.0%. Therefore, this is cost effective and reproducible method for SCFA measurement in feces and serum.