EMDS-5: Environmental Microorganism image dataset Fifth Version for multiple image analysis tasks

Environmental Microorganism Data Set Fifth Version (EMDS-5) is a microscopic image dataset including original Environmental Microorganism (EM) images and two sets of Ground Truth (GT) images. The GT image sets include a single-object GT image set and a multi-object GT image set. EMDS-5 has 21 types of EMs, each of which contains 20 original EM images, 20 single-object GT images and 20 multi-object GT images. EMDS-5 can realize to evaluate image preprocessing, image segmentation, feature extraction, image classification and image retrieval functions. In order to prove the effectiveness of EMDS-5, for each function, we select the most representative algorithms and price indicators for testing and evaluation. The image preprocessing functions contain two parts: image denoising and image edge detection. Image denoising uses nine kinds of filters to denoise 13 kinds of noises, respectively. In the aspect of edge detection, six edge detection operators are used to detect the edges of the images, and two evaluation indicators, peak-signal to noise ratio and mean structural similarity, are used for evaluation. Image segmentation includes single-object image segmentation and multi-object image segmentation. Six methods are used for single-object image segmentation, while k-means and U-net are used for multi-object segmentation. We extract nine features from the images in EMDS-5 and use the Support Vector Machine (SVM) classifier for testing. In terms of image classification, we select the VGG16 feature to test SVM, k-Nearest Neighbors, Random Forests. We test two types of retrieval approaches: texture feature retrieval and deep learning feature retrieval. We select the last layer of features of VGG16 network and ResNet50 network as feature vectors. We use mean average precision as the evaluation index for retrieval. EMDS-5 is available at the URL:https://github.com/NEUZihan/EMDS-5.git.

A reported Antarctic environmental microorganism isolated from the blood of sheep on the Mongolian Plateau

Herein, we report a novel Carnobacterium-like organism, CS13T, isolated from the blood of sheep with persistent diarrhea from a grassland pasturing area in Xilingol League, Inner Mongolia Municipality, China. Homology analysis indicated that CS13T belongs to the genus Carnobacterium and is 100% related to the reported environmental microorganism Carnobacterium antarticum sp. CP1 (C. CP1), which was isolated from sandy soil near Davis Station, Antarctica; the following strains are closely related: Carnobacterium mobile DSM 4848 (97%) and Carnobacterium funditum DSM 5970 (96%). Similar to those of the C. CP1, the short rod-shaped cells of CS13T are 0.4-0.8 μm wide and 1.0-1.5 μm long; exist singly, paired or catenoid; are gram positive, non-spore forming, and facultatively anaerobic; and produce hemolysin. CS13T cannot produce gas or H2S but can ferment sucrose, galactose, salicin, and esculin to produce acid. However, in contrast to C. CP1, CS13T can produce acid from cellobiose and maltose and is weakly positive for D-mannose fermentation; the growth temperatures range from 20-37°C, the pH range is 5.0-9.0, and the G+C content is 37.84% (4-36°C, pH 6.0-9.5, and 38.1% for C. CP1). Furthermore, based on gene annotation analysis, we found that CS13T has 31 more specific genes than C. CP1 (133 to 102) and that the nonredundant protein similarity to C. CP1 is only 84.2%. Based on the physiological-biochemical and genetic analysis results, we infer that the organisms isolated from the Mongolian Plateau and sandy soil in Antarctica belong to the same novel species of the genus Carnobacterium; therefore, this novel species probably has distributed globally and should not be called species antarticum.