Reorganizing heterogeneous information from host-microbe interaction reveals innate associations among samples

The information on host-microbe interactions contained in the operational taxonomic unit(OTU)abundance table can serve as a clue to understanding the biological traits of OTUs and samples.Some studies have inferred the taxonomies or functions of OTUs by constructing co-occurrence networks,but co-occurrence networks can only encompass a small fraction of all OTUs due to the high sparsity of the OTU table.There is a lack of studies that intensively explore and use the information on sample-OTU interactions.This study constructed a sample-OTU heterogeneous information network and represented the nodes in the network through the heterogeneous graph embedding method to form the OTU space and sample space.Taking advantage of the represented OTU and sample vectors combined with the original OTU abundance information,an Integrated Model of Embedded Taxonomies and Abundance(IMETA)was proposed for predicting sample attributes,such as phenotypes and individual diet habits.Both the OTU space and sample space contain reasonable biological or medical semantic information,and the IMETA using embedded OTU and sample vectors can have stable and good performance in the sample classification tasks.This suggests that the embedding representation based on the sample-OTU heterogeneous information network can provide more useful information for understanding microbiome samples.This study conducted quantified representations of the biological characteristics within the OTUs and samples,which is a good attempt to increase the utilization rate of information in the OTU abundance table,and it promotes a deeper understanding of the underlying knowledge of human microbiome.

Persistent Nocardia beijingensis infection in a patient with postoperative abscess and misuse of antibiotics in China

Here we describe the first case of abscess infection caused by Nocardia beijingensis in China.The patient was immunocompetent but suffered from postoperative abscess for 6 years.This study highlights the necessity of long-term infected foci to be thoroughly examined to identify the pathogen,as well as the importance of accurate Nocardia identification and antimicrobial susceptibility tests for understanding the pathogen’s epidemiology,clinical significance,and treatment strategy.

Tongue coating microbiome as a potential biomarker for gastritis including precancerous cascade

The development of gastritis is associated with an increased risk of gastric cancer. Current invasive gastritis diagnostic methods are not suitable for monitoring progressIn this work based on 78 gastritis patients and 50 healthy individuals, we observed that the variation of tongue-coating microbiota was associated with the occurrenee and development of gastritis. Twenty-one microbial species were identified for differentiating tongue-coating microbiomes of gastritis and healthy individuals. Pathways such as microbial metabolism in diverse environments, biosynthesis of antibiotics and bacterial chemotaxis were up-regulated in gastritis patients. The abundance of Campylobacter concisus was found associated with the gastric precancerous cascade. Furthermore, Campylobacter concisus could be detected in tongue coating and gastric fluid in a validation cohort containing 38 gastritis patients. These observations provided biological evidence of tongue diagnosis in traditional Chinese medicine, and indicated that tongue-coating microbiome could be a potential non-invasive biomarker, which might be suitable for long-term monitoring of gastritis.

EpiFIT: functional interpretation of transcription factors based on combination of sequence and epigenetic information

Backgrounds Transcription factor is one of the most important regulators in the transcriptional process.Nevertheless,the functional interpretation of transcription factors is still a main challenge due to the poor performance of methods relating to regulatory regions to genes.Epigenetic information,such as chromatin accessibility,contains genome-wide knowledge about transcription regulation and thus may shed light on the functional interpretation of transcription factors.Methods:We propose EpiFIT(Epigenetic based Functional Interpretation of Transcription factors),a tool to infer functions of transcription factors from ChlP-seq data.Briefly,we adopt a variable distance rule to establish associations between regulatory regions and nearby genes.The associations are then filtered to ensure that the remaining regions and associated genes are co-open.Finally,GO enrichment is applied to all related genes and a ranking list of GO terms is provided as functional interpretation.Results:We first examined the chromatin openness correlation between regulatory regions and associated genes.The correlation can help EpiFIT purify regulatory region-gene associations.By evaluating EpiFIT on a set of real data,we demonstrated that EpiFIT outperforms other existing methods for precisely interpreting transcription factor functions.We further verify the efficiency of openness in interpretation and the ability of EpiFIT to build distal region-gene associations.Conclusion:EpiFIT is a powerful tool for interpreting the transcription factor functions.We believe EpiFIT will facilitate the functional interpretation of other regulatory elements,and thus open a new door to understanding the regulatory mechanism.Availability:The application is freely accessible at website:bioinfo.au.tsinghua.edu.cn/openness/EpiFIT/.