ABSTRACT
Introduction: Single microbial pathogens or host-microbiome dysbiosis are the causes of lung diseases with suspected infectious etiology. Metagenome sequencing provides an overview of the microbiome content. Due to the rarity of most granulomatous lung diseases collecting large systematic datasets is challenging. Thus, single-patient data often can only be summarized visually. Objective: To increase the information gain from a single-case metagenome analysis we suggest a quantitative and qualitative approach. Results: The 16S metagenomic results of 7 patients with pulmonary sarcoidosis were compared with those of 22 healthy individuals. From lysed blood, total microbial DNA was extracted and sequenced. Cleaned data reads were identified taxonomically using Kraken 2 software. Individual metagenomic data were visualized with a Sankey diagram, Krona chart, and a heat-map. We identified five genera that were exclusively present or significantly enhanced in patients with sarcoidosis - Veillonella, Prevotella, Cutibacterium, Corynebacterium, and Streptococcus. Conclusions: Our approach can characterize the blood microbiome composition and diversity in rare diseases at an individual level. Investigation of the blood microbiome in patients with granulomatous lung diseases of unknown etiology, such as sarcoidosis could enhance our comprehension of their origin and pathogenesis and potentially uncover novel personalized therapeutics.
ABSTRACT
The degree of developmental stability of individuals and populations is most often estimated by their level of fluctuating asymmetry (FA) - the random deviations from perfect symmetry. In our previous work, we recorded high levels of FA (FAMI index: frequency of asymmetric manifestation of an individual) in Pelophylax ridibundus populations that inhabit biotopes at Sazliyka River, south Bulgaria with high levels of anthropogenic pollution (domestic sewage pollution). At the same time, in the biotopes located in the upper reaches of the river (less disrupted habitats), the populations showed low levels of FA. Currently, we present the results of the study of the values of several morphological parameters: snout-vent length (SVL), body weight (BW), and body condition factor (CF) in the same populations of P. ridibundus. In addition, we evaluate the correlation between the values of these morphological parameters and the values of fluctuating asymmetry (the FAMI index), using the Kendall rank correlation analysis. The analysis of the relationships between the parameters characterizing the physical fitness of frogs and the indicator of developmental stability - the FAMI index - did not establish statistically significant correlations in the analyses in the whole groups of P. ridibundus from each site and in the correlations between sexes. We believe that the approaches to the study of developmental stability (analysis of fluctuating asymmetry levels) and those related to the assessment of physical fitness (health status) of frogs should be applied independently of each other.
Subject(s)
Ranidae , Rivers , Animals , Environmental Pollution , Health Status , Humans , Physical FitnessABSTRACT
The steady elaboration of the Metagenomic and Metadesign of Subways and Urban Biomes (MetaSUB) international consortium project raises important new questions about the origin, variation, and antimicrobial resistance of the collected samples. CAMDA (Critical Assessment of Massive Data Analysis, http://camda.info/) forum organizes annual challenges where different bioinformatics and statistical approaches are tested on samples collected around the world for bacterial classification and prediction of geographical origin. This work proposes a method which not only predicts the locations of unknown samples, but also estimates the relative risk of antimicrobial resistance through spatial modeling. We introduce a new component in the standard analysis as we apply a Bayesian spatial convolution model which accounts for spatial structure of the data as defined by the longitude and latitude of the samples and assess the relative risk of antimicrobial resistance taxa across regions which is relevant to public health. We can then use the estimated relative risk as a new measure for antimicrobial resistance. We also compare the performance of several machine learning methods, such as Gradient Boosting Machine, Random Forest, and Neural Network to predict the geographical origin of the mystery samples. All three methods show consistent results with some superiority of Random Forest classifier. In our future work we can consider a broader class of spatial models and incorporate covariates related to the environment and climate profiles of the samples to achieve more reliable estimation of the relative risk related to antimicrobial resistance.
ABSTRACT
Pollution effects on haematological parameters in Pelophylax ridibundus individuals were investigated; animals were collected from two sites in Southern Bulgaria: the Tsalapitsa rice fields (RF) and the Vacha river (reference site, RS). Blood analysis showed significant differences between the haematological parameters of RBC, WBC, Hb, packed cell volume (PCV) and frogs' leucogram from RF and those from RS. These findings provide information on long-term background pollution of the habitat (RF) under investigation. In our view, the erythropenia, leucopenia, hypоchromia, lower values of PCV, St-neutrophilia, Sg-neutropenia, basopenia, eosinophilia, monocytosis and lymphopenia that were found in Pelophylax ridibundus individuals inhabiting the Tsalapitsa rice fields were probably caused by the pesticides and fertilizers that enter the paddy cages during the rice production process. The present study proves the practical usefulness of haematological parameters of Pelophylax ridibundus individuals in bioindication analyses for environmental assessment of agroecosystems.
