Early Detection of Fungal Plant Pathogens by Real-Time Quantitative PCR: The Case of Diplodia sapinea on Pine

This chapter reports the use of real-time quantitative PCR to detect Diplodia sapinea, a fungal plant pathogen that causes shoot tip dieback and tree mortality on pine trees. This molecular approach represents a reliable and sensitive tool to detect fungal pathogens in DNA extracted from plant tissues and its use can be also recommended to study fungal behavior in host tissues by quantifying fungal growth in the latent phase, when symptoms in the host are not present yet.

qPCR Applications for the Determination of the Biological Age

Individual age is a phenotypic trait that provides useful information not only in forensic investigations but also in the aging research which is becoming an urgent call due to the dramatic growth of the aging population worldwide.TaqMan quantification PCR (qPCR) can be successfully applied to biological age estimation, using method defined in Zubakov et al. (Curr Biol 20:R970-R971, 2010). Since levels of signal joint T-cell receptor rearrangement excision circle (sjTREC) in human lymphocytes are known to decrease with age increasing, the qPCR of sjTREC represents a simple and relatively reproducible technique which offers highly accurate age estimation results.

Detection of Yellow Fever Virus by Quantitative Real-Time PCR (qPCR)

The recent resurgence of yellow fever virus (YFV) activity in the tropical regions of Africa and South America has sparked renewed interest in this infamous arboviral disease. Also, the development and production of viral vaccines involve several steps that need the monitoring of viral load throughout the process (antigen production, purification, and inactivation). Currently, these steps are followed by plaque lysis titration assay, whose results take about 7-10 days to come out and thus resulting in a laborious and time-consuming approach. With the advent of quantitative real-time PCR (qPCR), we have a faster method to be applied during vaccine production and also to be effectively used for the diagnosis of YFV infection. The technique herein standardized proved to be effective for determining YF viral load both in vivo and in vitro, thus becoming a very important tool for laboratory analysis to verify the vaccination status of individuals, beyond acting as a quality control for vaccine production and diagnosis.

Determination and Quantification of Bacterial Virulent Gene Expression Using Quantitative Real-Time PCR

Polymerase chain reaction (PCR) plays significant roles in modern molecular biology. However, it is relatively cumbersome and less accurate to use the traditional PCR method in quantifying gene expression because it requires first generating a standard curve with multiple input controls showing linearity with amplified control PCR products on a electrophoresis gel to compare with the abundance of the to-be-determined gene transcript PCR amplicons. Quantitative real-time PCR (qRT-PCR) is a time-efficient and reliable tool for accurate quantification and comparison of gene (RNA transcript) expression from various biological samples. Current technology has simplified and expedited the qPCR process significantly. However, proper techniques and standard protocols are required in eliminating potentially erroneous experimental outcome. Here, we provide an example from a drug-treated bacterial gene expression study with detailed protocols to demonstrate real-time qPCR with SYBR^™ Green and TaqMan^®, two of the most adapted and well-established qPCR technologies. Relative quantification of gene (RNA transcript) expression using qRT-PCR is demonstrated in detail from sample preparations to data analysis.

Impact of Atrazine Exposure on the Microbial Community Structure in a Brazilian Tropical Latosol Soil

Atrazine is a triazine herbicide that is widely used to control broadleaf weeds. Its widespread use over the last 50 years has led to the potential contamination of soils, groundwater, rivers, and lakes. Its main route of complete degradation is via biological means, which is carried out by soil microbiota using a 6-step pathway. The aim of the present study was to investigate whether application of atrazine to soil changes the soil bacterial community. We used 16S rRNA gene sequencing and qPCR to elucidate the microbial community structure and assess the abundance of the atrazine degradation genes atzA, atzD, and trzN in a Brazilian soil. The results obtained showed that the relative abundance of atzA and trzN, encoding triazine-initiating metabolism in Gram-negative and -positive bacteria, respectively, increased in soil during the first weeks following the application of atrazine. In contrast, the abundance of atzD, encoding cyanuric acid amidohydrolase-the fourth step in the pathway-was not related to the atrazine treatment. Moreover, the overall soil bacterial community showed no significant changes after the application of atrazine. Despite this, we observed increases in the relative abundance of bacterial families in the 4th and 8th weeks following the atrazine treatment, which may have been related to higher copy numbers of atzA and trzN, in part due to the release of nitrogen from the herbicide. The present results revealed that while the application of atrazine may temporarily increase the quantities of the atzA and trzN genes in a Brazilian Red Latosol soil, it does not lead to significant and long-term changes in the bacterial community structure.

Analysis of Metabolites and Gene Expression Changes Relative to Apricot (Prunus armeniaca L.) Fruit Quality During Development and Ripening

Apricot (Prunus armeniaca L.) is a valuable worldwide agronomical crop, with a delicious fruit highlighted as a functional food with both nutritional and bioactive properties, remarkably beneficial to human health. Apricot fruit ripening is a coordinated developmental process which requires change in the expression of hundreds to thousands of genes to modify many biochemical and physiological processes arising from quality characteristics in ripe fruit. In addition, enhancing fruit and nutraceutical quality is one of the central objectives to be improved in the new varieties developed by breeding programs. In this study we analyzed the contents of main metabolites linked to the nutraceutical value of apricot fruits, together with the most important pomological characteristics and biochemical contents of fruit during the ripening process in two contrasted apricot genotypes. Additionally, the gene expression changes were analyzed using RNA-Seq and real time qPCR. Results showed that genes with differential expression in the biosynthetic pathways, such as phenylpropanoids, flavonoids, starch and sucrose and carotenoid metabolism, could be possible candidates as molecular markers of fruit quality characteristics for fruit color and soluble solid content. The gene involves in carotenoid metabolism carotenoid cleavage dioxygenase 4, and the gene sucrose synthase in starch and sucrose metabolism were identified as candidate genes in the ripening process for white skin ground color and flesh color and high soluble sugar content. The application of these candidate genes on marker-assisted selection in apricot breeding programs may contribute to the early selection of high-quality fruit genotypes with suitable nutraceutical values.

Molecular Approaches for Low-Cost Point-of-Care Pathogen Detection in Agriculture and Forestry

Early detection of plant diseases is a crucial factor to prevent or limit the spread of a rising infection that could cause significant economic loss. Detection test on plant diseases in the laboratory can be laborious, time consuming, expensive, and normally requires specific technical expertise. Moreover, in the developing countries, it is often difficult to find laboratories equipped for this kind of analysis. Therefore, in the past years, a high effort has been made for the development of fast, specific, sensitive, and cost-effective tests that can be successfully used in plant pathology directly in the field by low-specialized personnel using minimal equipment. Nucleic acid-based methods have proven to be a good choice for the development of detection tools in several fields, such as human/animal health, food safety, and water analysis, and their application in plant pathogen detection is becoming more and more common. In the present review, the more recent nucleic acid-based protocols for point-of-care (POC) plant pathogen detection and identification are described and analyzed. All these methods have a high potential for early detection of destructive diseases in agriculture and forestry, they should help make molecular detection for plant pathogens accessible to anyone, anywhere, and at any time. We do not suggest that on-site methods should replace lab testing completely, which remains crucial for more complex researches, such as identification and classification of new pathogens or the study of plant defense mechanisms. Instead, POC analysis can provide a useful, fast, and efficient preliminary on-site screening that is crucial in the struggle against plant pathogens.

Analysis of Caveolin in Primary Cilia

Recent evidence has indicated that caveolins are localized at the base of primary cilia, which are microtubule-based sensory organelles present on the cell surface, and that Caveolin-1 (CAV1) plays important roles in regulating ciliary membrane composition and function. Here we describe methods to analyze the localization and function of CAV1 in primary cilia of cultured mammalian cells. These include methods for culturing and transfecting mammalian cells with a CAV1-encoding plasmid or small interfering RNA (siRNA), analysis of mammalian cells by immunofluorescence microscopy (IFM) with antibodies against ciliary markers and CAV1, as well as methods for analyzing ciliary CAV1 function in siRNA-treated cells by IFM and cell-based signaling assays.

Detection and Characterization of Circulating Tumor Cells by Quantitative Real-Time PCR

We propose two different approaches involving the use of quantitative real-time PCR for the detection or analysis of circulating tumor cells. In one case cells are indirectly identified through the expression of a marker mRNA, while in the other one cells are enriched by size prior to be submitted to mutational analysis for a specific target. Both methods have been successfully applied to the study of circulating melanoma cells.

Effects of applying inorganic fertilizer and organic manure for 35 years on the structure and diversity of ammonia-oxidizing archaea communities in a Chinese Mollisols field

In this study, we investigated the physicochemical properties of soil, and the diversity and structure of the soil ammonia-oxidizing archaea (AOA) community, when subjected to fertilizer treatments for over 35 years. We collected soil samples from a black soil fertilization trial in northeast China. Four treatments were tested: no fertilization (CK); manure (M); nitrogen (N), phosphorus (P), and potassium (K) chemical fertilizer (NPK); and N, P, and K plus M (MNPK). We employed 454 high-throughput pyrosequencing to measure the response of the soil AOA community to the long-term fertilization. The fertilization treatments had different impacts on the shifts in the soil properties and AOA community. The utilization of manure alleviated soil acidification and enhanced the soybean yield. The soil AOA abundance was increased greatly by inorganic and organic fertilizers. In addition, the community Chao1 and ACE were highest in the MNPK treatment. In terms of the AOA community composition, Thaumarchaeota and Crenarchaeota were the main AOA phyla in all samples. Compared with CK and M, the abundances of Thaumarchaeota were remarkably lower in the MNPK and NPK treatments. There were distinct shifts in the compositions of the AOA operational taxonomic units (OTUs) under different fertilization management practices. OTU51 was the dominant OTU in all treatments, except for NPK. OTU79 and OTU11 were relatively abundant OTUs in NPK. Only Nitrososphaera AOA were tracked from the black soil. Redundancy analysis indicated that the soil pH and soil available P were the two main factors that affected the AOA community structure. The abundances of AOA were positively correlated with the total N and available P concentrations, and negatively correlated with the soil pH.

Real-time PCR to differentiate among Leishmania (Viannia) subgenus, Leishmania (Leishmania) infantum and Leishmania (Leishmania) amazonensis: Application on Brazilian clinical samples

Leishmaniasis is a complex disease caused by Leishmania species belonging to subgenera Leishmania and Viannia. In South America, L. (L.) infantum is considered the most important causative agent of visceral leishmaniasis, while L. (L.) amazonensis and Viannia subgenus species are responsible for the different cutaneous or mucocutaneous forms. In our previous work, we developed a diagnostic approach for Leishmania species discrimination based on two qPCRs (qPCR-ML and qPCR-ama) targeting the minicircle kDNA followed by melting analysis. This approach allowed to (i) differentiate the subgenera Leishmania and Viannia, and (ii) distinguish between L. (L.) infantum and L. (L.) amazonensis. The aim of this work was to demonstrate the applicability of the approach previously described, using human and canine clinical samples and strains from a Brazilian region, where L. (L.) infantum, L. (L.) amazonensis and Viannia subgenus species coexist. After validation on New World strains, the diagnostic approach was applied blindly to 36 canine clinical samples (peripheral blood and bone marrow) and 11 human clinical samples (peripheral blood and bone marrow). The sensitivity was 95.6% (95% confidence interval 77.3-100%) and 100% (95% confidence interval 76.9-100%) in the canine bone marrow samples and human (peripheral blood and bone marrow) samples, respectively, compared to conventional PCR assays. Concerning the Leishmania species identification, the conventional and qPCR-based methods showed kappa value of 0.876 (95% confidence interval 0.638-1.000), indicating good agreement. Therefore, this approach proved to be useful in both veterinary and human clinical context in regions co-endemic for L. (L.) infantum, L. (L.) amazonensis, and Viannia subgenus, helping to provide rapid diagnosis and to allow studies of species distribution.

Fluorescent Oligonucleotide Probes for the Quantification of RNA by Real-Time qPCR

Quantitative real-time PCR (qPCR) is a widely adopted technique used for scientific, clinical, diagnostic, or quality control purposes. One of the main applications of qPCR is gene expression analysis, although mutation detection, genotyping, DNA detection, and quantification (from pathogens or genetically modified organisms) are also investigated using this technique.Although nonspecific detection based on DNA-binding dyes (including SYBR Green I) offers versatility in qPCR assays, detection of the PCR product using fluorescent probes confers higher specificity and sensitivity to assays, justifying the use of fluorescent probes as a detection method.This chapter seeks to propose a procedure for the design of qPCR assays using fluorescent hydrolysis probe technology. Particular attention will be paid to explaining the steps necessary to ensure the specificity of the oligonucleotides used as primers or fluorescent probes.

The effect of APTR, Fn14 and CD133 expressions on liver fibrosis in biliary atresia patients

PURPOSE

Although some biomarkers of hepatic progenitor cells have been reported to be involved in the liver fibrosis in patients with biliary atresia (BA), however, research still shows conflicting results. Therefore, we investigated the effect of Alu-mediated p21 transcriptional regulator (APTR), fibroblast growth factor-inducible 14 (Fn14) and CD133 expressions on liver fibrosis in Indonesian BA patients.

METHODS

Nineteen liver samples from BA patients and 9 liver specimens from non-BA controls were obtained. The expressions of APTR, Fn14 and CD133 were analyzed by quantitative real-time polymerase chain reaction (qPCR).

RESULTS

APTR expression was strongly up-regulated (1.5-fold) in liver BA specimens compared to liver controls (ΔC_T 3.2 ± 0.6 vs 3.8 ± 0.51; p = 0.028). Moreover, Fn14 and CD133 expressions were similar in the BA and control groups (ΔC_T 2.7 ± 1.3 vs. 1.4 ± 1.6, p = 0.07; and 12.0 ± 3.7 vs. 11.78 ± 2.30, p = 0.88, respectively). Intriguingly, CD133 expression was strongly related with the survival of BA patients (p = 0.0061), but not with age at Kasai procedure (p = 0.36) and the presence of cirrhosis (p = 0.77).

CONCLUSION

We present the first study of aberrant APTR expressions in the liver of BA infants which might contribute to liver fibrogenesis in BA infants.

Detection of MicroRNAs Released from Argonautes

The Argonaute (AGO) family of proteins plays an essential role in the process of microRNA (miRNA)-mediated gene silencing. More specifically, they are the only known proteins to associate directly with miRNAs within the RNA-induced silencing complex (RISC). Given the importance of miRNA regulation of the transcriptome and its vast implications for human disease, it is essential to understand the molecular underpinnings of miRNA-AGO interactions. Although there are methods available to investigate mature miRNA decay and loading onto AGO2, no feasible method exists to detail the opposite process: release of miRNA from associated AGO proteins. In this chapter, we describe in detail a methodology derived from biochemical approaches, which can be used to quantify the release of any given miRNA from AGOs.

Assessment of the diversity and abundance of the total and active fungal population and its correlation with humification during two-phase olive mill waste (''alperujo") composting

Metagenomic and transcriptomic techniques applied to composting could increase our understanding of the overall microbial ecology and could help us to optimise operational conditions which are directly related with economic interest. In this study, the fungal diversity and abundance of two-phase olive mill waste ("alperujo") composting was studied using Illumina MiSeq sequencing and quantitative PCR, respectively. The results showed an increase of the fungal diversity during the process, with Ascomycota being the predominant phylum. Penicillium was the main genera identified at the mesophilic and maturation phases, with Debaryomyces and Sarocladium at the thermophilic phase, respectively. The fungal abundance was increased during composting, which confirms their important role during thermophilic and maturation phases. Some Basidiomycota showed an increased during the process, which showed a positive correlation with the humification parameters. According to that, the genus Cystofilobasidium could be used as a potential fungal biomarker to assess alperujo compost maturation.

Molecular Monitoring of Chronic Myeloid Leukemia

Molecular diagnosis and measurement of minimal residual disease (MRD) in patients with chronic myeloid leukemia (CML) is essential for clinical management. In the era of tyrosine kinase inhibitor therapy molecular tests including BCR-ABL1 transcript monitoring and kinase domain mutation analysis are the main tools used to inform choice of treatment, appropriate dosage and even whether therapy can be safely withdrawn. Quantitation of BCR-ABL1 oncogene transcript by real-time quantitative PCR (qPCR) is currently the gold-standard method for monitoring as it provides superior sensitivity over karyotyping and fluorescent in situ hybridization (FISH). Here we describe step-by-step methods of RNA conversion to cDNA along with the qPCR protocol which is used in one of the main reference laboratories for this test.

A Gene Expression Analysis of M1 and M2 Polarized Macrophages

Macrophages are professional innate immune cells that are broadly disseminated throughout the body, shape various innate and adaptive immune responses, and play crucial roles in inflammation, homeostasis, wound healing, and tissue remodelling. According to their surrounding microenvironments, macrophages can differentiate themselves in different phenotypes. Over the last two decades, gene expression profiling has been used to decipher new transcripts associated with macrophage phenotypes. This chapter outlines protocols used to isolate and culture murine macrophages and how they can be "polarized" to obtain a specific phenotype. Furthermore, we describe a protocol for gene expression profiling using a quantitative real-time polymerase chain reaction (qPCR), a high-standard technology in the field of gene expression.

Expression profiles of types 2 and 3 iodothyronine deiodinase genes in relation to vitellogenesis in a tropical damselfish, Chrysiptera cyanea

Thyroid hormone (TH) is involved in regulating the reproduction of vertebrates. Its physiological action in the target tissues is due to the conversion of TH by iodothyronine deiodinases. In this study, we aimed to clone and characterize type 2 (sdDio2) and type 3 (sdDio3) of the sapphire devil Chrysiptera cyanea, a tropical damselfish that undergoes active reproduction under long-day conditions, and to study the involvement of THs in the ovarian development of this species. When the cDNAs of sdDio2 and sdDio3 were partially cloned, they had deduced amino acid sequences of lengths 271 and 267, respectively, both of which were characterized by one selenocysteine residue. Real-time quantitative PCR (qPCR) revealed that both genes are highly expressed in the whole brain, and sdDio2 and sdDio3 are highly transcribed in the liver and ovary, respectively. In situ hybridization analyses showed positive signals of sdDio2 and sdDio3 transcripts in the hypothalamic area of the brain. Little change in mRNA abundance of sdDio2 and sdDio3 in the brain was observed during the vitellogenic phases. It is assumed that simultaneous activation and inactivation of THs occur in this area because oral administration of triiodothyronine (T3), but not of thyroxine (T4), upregulated mRNA abundance of both genes in the brain. The transcript levels of sdDio2 in the liver and sdDio3 in the ovary increased as vitellogenesis progressed, suggesting that, through the metabolism of THs, sdDio2 and sdDio3 play a role in vitellogenin synthesis in the liver and yolk accumulation/E2 synthesis in the ovary. Taken together, these results suggest that iodothyronine deiodinases act as a driver for vitellogenesis in tropical damselfish by conversion of THs in certain peripheral tissues.

Human rDNA copy number is unstable in metastatic breast cancers

Chromatin-mediated silencing, including the formation of heterochromatin, silent chromosome territories, and repressed gene promoters, acts to stabilize patterns of gene regulation and the physical structure of the genome. Reduction of chromatin-mediated silencing can result in genome rearrangements, particularly at intrinsically unstable regions of the genome such as transposons, satellite repeats, and repetitive gene clusters including the rRNA gene clusters (rDNA). It is thus expected that mutational or environmental conditions that compromise heterochromatin function might cause genome instability, and diseases associated with decreased epigenetic stability might exhibit genome changes as part of their aetiology. We find the support of this hypothesis in invasive ductal breast carcinoma, in which reduced epigenetic silencing has been previously described, by using a facile method to quantify rDNA copy number in biopsied breast tumours and pair-matched healthy tissue. We found that rDNA and satellite DNA sequences had significant copy number variation - both losses and gains of copies - compared to healthy tissue, arguing that these genome rearrangements are common in developing breast cancer. Thus, any proposed aetiology onset or progression of breast cancer should consider alterations to the epigenome, but must also accommodate concomitant changes to genome sequence at heterochromatic loci.

Data on the differentiation among Leishmania (Viannia) spp., Leishmania (Leishmania) infantum and Leishmania (Leishmania) amazonensis in Brazilian clinical samples using real-time PCR

This article contains the data regarding Leishmania species identification in human and canine clinical samples from a Brazilian region endemic for Leishmania (Viannia) spp., Leishmania (Leishmania) infantum and Leishmania (Leishmania) amazonensis, using a previously developed approach involving two qPCR assays (qPCR-ML and qPCR-ama). The data are related to the article "Real-time PCR to differentiate among Leishmania (Viannia) subgenus, Leishmania (Leishmania) infantum and Leishmania (Leishmania) amazonensis: application on Brazilian clinical samples" [1], and include also details of clinical evaluation/diagnosis of human patients and primer sequences used in the qPCR assays. The Leishmania species has been determined in 27 canine samples and 11 human samples, exploiting HRM analysis of qPCR-ML and Cq values of qPCR-ML and qPCR-ama, as reported previously [2]. The qPCR data were in agreement with the species characterization obtained with other methods such as conventional species-specific PCR, ITS1 PCR-RFLP or DNA sequencing. Despite the limited number of clinical samples, these data are encouraging for a potential application in regions where L. (Viannia) spp., L. (L.) infantum and L. (L.) amazonensis are co-endemic.

GABAa receptor subunits expression in silver catfish (Rhamdia quelen) brain and its modulation by Nectandra grandiflora Nees essential oil and isolated compounds

Studies using silver catfish (Rhamdia quelen) as experimental models are often applied to screen essential oils (EO) with GABAergic-mediated effects. However, the expression of GABAa receptors in the silver catfish brain remains unknown. Thus, we assessed whether silver catfish express GABAa receptor subunits associated with sedation/anesthetic process and/or neurological diseases. Additionally, we evaluated the brain expression of GABAa receptor subunits in fish sedated with Nectandra grandiflora EO and its isolated compounds, the fish anesthetic (+)-dehydrofukinone (DHF), and dehydrofukinone epoxide (DFX), eremophil-11-en-10-ol (ERM) and selin-11-en-4-α-ol (SEL), which have GABAa-mediated anxiolytic-like effects in mice. The expression of the subunits gabra1, gabra2, gabra3, gabrb1, gabrd and gabrg2 in the silver catfish brain were assessed after a 24h-sedation bath by real time PCR. Since qPCR data rarely describes mechanisms of action, which are usually found through interactions with receptors, we also performed an antagonist-driven experiment using flumazenil (FMZ). Real-time PCR detected the mRNA expression of all targeted genes in R. quelen brain. The expression of gabra1 was decreased in fish sedated with ERM; EO increased gabra2, gabra3, gabrb1 and gabrg2 expression; SEL increased gabrb1, gabrd and gabrg2 expression. EO and compounds DFX, SEL and ERM induced sustained sedation in fish and FMZ-bath prompted the recovery from ERM- and DFX-induced sedation. Our results suggest that the EO, SEL, ERM and DFX sedative effects involve interaction with the GABAergic system. Our findings support the use of the silver catfish as robust and reliable experimental model to evaluate the efficacy of drugs with putative GABAergic-mediated effects.

Quantification of Pneumocystis jirovecii: Cross-Platform Comparison of One qPCR Assay with Leading Platforms and Six Master Mixes

Diagnosis of Pneumocystis jirovecii pneumonia relies on nucleic acid quantification in respiratory samples. Lack of standardization among molecular assays results in significant differences among assays/centers. To further promote standardization, we compared four thermocyclers and six master mixes for the detection of P. jirovecii. Whole nucleic acid (WNA) was extracted from broncho-alveolar lavages. Positive and negative sample extracts were pooled to get enough homogeneous materials. Three master mixes were tested to detect DNA by qPCR (D1, D2, and D3), and three to detect WNA by reverse transcriptase qPCR (W1, W2, and W3) manufactured by Roche, Eurogentec, Applied Biosystem, Invitrogen and Thermofischer Scientific. Experiments were performed on four thermocyclers (Roche LightCycler 480, Qiagen Rotor-Gene Q, Applied Biosystem ABI7500, and QuantStudio). Comparison of quantitative cycle (Cq) values between the methods targeting WNA versus DNA showed lower Cq values for WNA, independently of thermocycler and master mix. For high and low fungal loads, ∆Cq values between DNA and WNA amplification were 6.97 (±2.95) and 5.81 (±3.30), respectively (p < 0.0001). Regarding DNA detection, lower Cqs were obtained with D1 compared to D2 and D3, with median ∆Cq values of 2.6 (p = 0.015) and 2.9 (p = 0.039) respectively. Regarding WNA detection, no mix was superior to the others. PCR efficiency was not significantly different according to the qPCR platform (p = 0.14). This study confirmed the superiority of WNA over DNA detection. A calibration method (e.g., an international standard) for accurate comparative assessment of fungal load seems necessary.

Setup of Quantitative PCR for Oral Neisseria spp. Evaluation in Celiac Disease Diagnosis

Coeliac disease (CD) is a multifactorial autoimmune disorder and gut dysbiosis contributes to its pathogenesis. We previously profiled by 16S rRNA sequencing duodenal and oropharyngeal microbiomes in active CD (a-CD), gluten-free diet (GFD) patients, and controls (CO) and found significantly higher levels of Neisseria spp., with pro-inflammatory activities, in a-CD patients than in the other two groups. In this study, we developed a fast and simple qPCR-based method to evaluate the abundance of the oral Neisseria spp. and the diagnostic performances of the test in CD diagnosis. The Neisseria spp. abundances detected by quantitative PCR (qPCR) were: CO = 0.14, GFD = 0.15, a-CD = 2.08, showing a similar trend to those previously measured by next generation sequencing (NGS). In particular, Neisseria spp. values obtained by both methods were significantly higher (p < 0.001) in a-CD than in the other two groups GFD and CO—the latter almost overlapping. We calculated by ROC curve analysis the threshold of 1.12 ng/μL of Neisseria spp. to discriminate between CO+GFD and a-CD patients with 100% and 96.7% of diagnostic sensitivity and specificity, respectively. In conclusion, our data, if confirmed in other cohorts, suggest the q-PCR evaluation of oral Neisseria spp. could be a fast and simple method to assess CD-associated dysbiosis for diagnostic purposes.

Urinary TMAO Levels Are Associated with the Taxonomic Composition of the Gut Microbiota and with the Choline TMA-Lyase Gene (cutC) Harbored by Enterobacteriaceae

Gut microbiota metabolization of dietary choline may promote atherosclerosis through trimethylamine (TMA), which is rapidly absorbed and converted in the liver to proatherogenic trimethylamine-N-oxide (TMAO). The aim of this study was to verify whether TMAO urinary levels may be associated with the fecal relative abundance of specific bacterial taxa and the bacterial choline TMA-lyase gene cutC. The analysis of sequences available in GenBank grouped the cutC gene into two main clusters, cut-Dd and cut-Kp. A quantitative real-time polymerase chain reaction (qPCR) protocol was developed to quantify cutC and was used with DNA isolated from three fecal samples collected weekly over the course of three consecutive weeks from 16 healthy adults. The same DNA was used for 16S rRNA gene profiling. Concomitantly, urine was used to quantify TMAO by ultra-performance liquid chromatography coupled with tandem mass spectrometry (UPLC-MS/MS). All samples were positive for cutC and TMAO. Correlation analysis showed that the cut-Kp gene cluster was significantly associated with Enterobacteriaceae. Linear mixed models revealed that urinary TMAO levels may be predicted by fecal cut-Kp and by 23 operational taxonomic units (OTUs). Most of the OTUs significantly associated with TMAO were also significantly associated with cut-Kp, confirming the possible relationship between these two factors. In conclusion, this preliminary method-development study suggests the existence of a relationship between TMAO excreted in urine, specific fecal bacterial OTUs, and a cutC subgroup ascribable to the choline-TMA conversion enzymes of Enterobacteriaceae.