Dataset Information

The Level of Selected Bacterial Phyla on the Skin Surface of Small Ruminants According to the Breed and Species.

ABSTRACT: For decades, skin has been assigned the main role of an insulator of the inside of the body from the external environment, but it also plays a role in maintaining homeostasis. In this study, the level of selected bacterial phyla (Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria) was assessed in three sheep breeds (Świniarka sheep, Uhruska sheep and BCP line (synthetic sheep breed; n = 6) and in two breeds of goats (Boer, Saenian; n = 6) living in the same environment and fed on the same feed, where the aim was to identify differences in terms of race, species and individual differences. Significant differences were found in Firmicute, Actinobacteria and Proteobacteria phyla (p ≤ 0.05). Statistically significant and positive correlations were demonstrated between Actinobacteria and Proteobacteria, Proteobacteria and Bacteroidetes or Firmicutes and Bacteroidetes. The obtained results suggest that the species and racial differences in the level of the studied bacterial phyla may also result from the physicochemical differences of the skin surface, as they could exacerbate the variations in humidity, temperature, composition of antimicrobial peptides (AMP) and lipid content. In addition, individual differences were observed, which indicate a similar effect of an individual on the microbiological composition of its organism.

SUBMITTER: Cholewinska P

PROVIDER: S-EPMC8472796 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:Protein function prediction has been the most worked upon and the most challenging problem for computational biologists. The vast majority of known proteins have yet not been characterised experimentally, and there is significant gap between their structures and functions. New un-annotated sequences are being added to the public protein databases (e.g. UniprotKB) at an enormous pace [1]. Such proteins with unknown functions might play key role in the metabolism, growth and development regulation. Thus, if functions of unknown proteins left undiscovered, researchers may skip important information(s). Based on their sequence, structure, evolutionary history, and their association with other proteins, tools of computational biology can provide insights into the function of proteins [2]. For proteins with well characterised close relatives, it is trivial to infer function. Orphan proteins without discernible sequence relatives present a greater challenge [3]. Here the task of experimental characterisation is blind and becomes unwieldy. It is highly unlikely that all known proteins will ever be completely experimentally characterised [4]. Thus, there is an emergent need to develop fast and accurate computational approaches to fulfil this requirement. Towards this end, we prepared a dataset for protein function prediction by extracting protein sequences and annotations of reviewed prokaryotic proteins (total count 323,719 as accessed on date March 10, 2019) belonging to 9 bacterial phyla Actinobacteria, Bacteroidetes, Chlamydiae, Cyanobacteria, Firmicutes, Fusobacteria, Proteobacteria, Spirochaetes and Tenericutes. Corresponding to the most frequent 1739 Gene Ontology (Molecular Function) terms, samples were filtered, and 171,212 proteins were retrieved for feature generation. The Dataset was generated by calculating the sequence, sub-sequence, physiochemical, annotation-based features for each 171,212 reviewed proteins using method in [10]. These features constitute a total of 9890 attributes for each sequence of protein along with 1739 Gene Ontology terms. Each protein sequence is assigned one or more of 1739 Gene Ontology (Molecular Function) term as its target label. The Dataset contains the Entry and Entry name of each sequence corresponding to UniprotKB Database. This dataset being huge in size (171,212 samples X 9890 features, 1739 classes with multiple values) and equipped with enough number of positive and negative samples of each 1739 class, is good for testing efficiency of any upcoming deep learning models [5]. We divided the full dataset of 171,212 reviewed proteins in the ratio 3:1 to form Train/Test dataset 1; train dataset with 128,409 samples and test dataset with 42,803 samples to facilitate training of a deep learning model. The train and test datasets are stratified to contain good proportion of each 1739 classes. We then prepared a dataset 2 of pathogenic unreviewed proteins of the 9 bacterial phyla each with 9890 features same as train/train dataset of reviewed proteins but without target labels in order to predict their functions using deep learning model proposed in [5].

Dataset Information

The Level of Selected Bacterial Phyla on the Skin Surface of Small Ruminants According to the Breed and Species.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets