Dysfunctional gut microbiota and relative co-abundance network in infantile eczema

Wang, Heping; Li, Yinhu; Feng, Xin; Li, Yufeng; Wang, Wenjian; Qiu, Chuangzhao; Xu, Jianqiang; Yang, Zhenyu; Li, Zhichuan; Zhou, Qian; Yao, Kaihu; Wang, Hongmei; Li, Yuzheng; Li, Dongfang; Dai, Wenkui; Zheng, Yuejie

doi:10.1186/s13099-016-0118-0

Cited by 37 publications

(35 citation statements)

References 23 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The last decades have witnessed the advent and widespread application of viral metagenomics to study viral diversity and to describe novel viruses from many animal hosts, including non-human primates (NHPs) [1][2][3][4]. Such virological surveillance of viruses circulating in wildlife can serve as baseline exploratory dataset that can be further explored to identify the presence of unusual viruses in hosts showing symptoms of diseases.…”

Section: Introductionmentioning

confidence: 99%

“…For instance, several novel circular ssDNA viruses were identified, while their pathological role remains to be determined [2,17,18]. Recently, a novel astrovirus strain, close to the human MLB2 strain, has been identified from stool of a diarrheic captive chimpanzee in China [3]. In order to expand our knowledge on the viral repertory associated with free-living NHPs, stool samples were collected from wild gorillas in the Republic of the Congo, Central Africa in 2015.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Detection of novel RNA viruses from free-living gorillas, Republic of the Congo: genetic diversity of picobirnaviruses

et al. 2018

View full text Add to dashboard Cite

Most of the emerging infectious diseases reported so far originated in wildlife. Therefore, virological surveillance of animals and particularly great apes is of great interest to establish the repertory of viruses associated with healthy hosts. This will further help to identify the emergence of new viruses and predict the possibility of interspecies transmission. In this study, we performed shotgun viral metagenomics on stool samples collected from seventeen free-living wild gorillas from the Republic of the Congo. The analysis revealed the presence of novel RNA viruses (picobirnaviruses, partitivirus, and Picornavirales (posa-like and dicistrovirus-like viruses)). Among these, picobirnavirus-related sequences were abundantly covered in the stools. Based on genetic variations both in capsid and RdRp proteins of picobirnaviruses, at least 96 variants were identified and most of them were novel. Among the 96, 22 variants had a nearly complete genome or segment. A comprehensive sequence analysis identified a potential new genogroup/genetic cluster and the presence of a short linear amino acid motif (ExxRxNxxxE) in a hypothetical protein. The sequence analysis of posa-like virus and dicistrovirus showed that these two viruses were novel members in the respective viral families. In conclusion, the identification of novel RNA viruses and their genetic diversity increases our knowledge about viruses that are associated with stools of wild gorillas and contributes to the initiatives in the search for potential emerging zoonotic viruses.

show abstract

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Detection of novel RNA viruses from free-living gorillas, Republic of the Congo: genetic diversity of picobirnaviruses

et al. 2018

View full text Add to dashboard Cite

show abstract

“…To obtain high quality data, the raw reads were removed when they contained more than 10 low-quality (< Q20) bases or 15 bases of adapter sequences (Wang et al, 2016 ). Based on at least 50 overlapping bases, the filtered reads were connected into tags, and using USEARCH (v7.0.1090; Edgar, 2013 ), the tags clustered into operational taxonomic units (OTUs) with 97% similarity.…”

Section: Methodsmentioning

confidence: 99%

Distinct Skin Microbiota Imbalance and Responses to Clinical Treatment in Children With Atopic Dermatitis

Liu

Wang

Dai

et al. 2020

Front. Cell. Infect. Microbiol.

Self Cite

View full text Add to dashboard Cite

Background: Atopic dermatitis (AD) is a common cutaneous disease, associated with imbalances in the skin microbiota. Objective: To explore the characteristics of the cutaneous microbiota and its dynamic changes during clinical treatment. Methods: Cutaneous swab samples were collected from 51 AD patients before treatment, and 40 AD patients remained after a 2-week treatment with mometasone and mupirocin. Results: AD patients exhibited significant enrichments of Prevotella and Desulfovibrio as well as obvious reductions of Corynebacterium, Streptococcus and Parabacteroides. Based on the proportion of Staphylococcus aureus, the AD patients were further classified into S. aureus-predominant group (AD.S) and S. aureus-non-dominant (AD.ND) group. The AD.S group exhibited lower skin microbial diversity and higher atopic dermatitis (SCORAD) index. In the AD.S group, the cutaneous microbial diversity significantly increased from 2.9 ± 0.8 to 3.7 ± 1.0, while the relative abundance of S. aureus decreased from 42.5 ± 20.7 to 10.3 ± 28.4 after treatment. In contrast, no significant skin microbiota changes were detected in the AD.ND group. Conclusions: AD patients with predominant S. aureus had higher disease severity and lower microbiota diversity compared to patients in the AD.ND group. Mometasone and mupirocin therapy had significant effects on skin microbiota in AD.S patients, but had a paradoxical response in the AD.ND patients.

show abstract

“…Considering the absence of background network for microbial communities, we selected edges (i.e., one edge represented the association between two microbiota, represented by a pair of OTUs here) from a direct rank cut-off for correlations because the distribution of the new PCC values is not the normal distribution. Then, the top-ranked edges with strong relations were finally selected, which consisted of conventional node-network or microbiota community (Wang et al, 2016; Sung et al, 2017), and were used as the background “nodes” for constructing the following edge-network (e.g., a network of OTU-pairs).…”

Section: Methodsmentioning

confidence: 99%

Characterizing the Personalized Microbiota Dynamics for Disease Classification by Individual-Specific Edge-Network Analysis

Chen

Wang

2019

Front. Genet.

View full text Add to dashboard Cite

Environmental factors such as the gut microbiome are thought to play an important role in the development and treatment of many diseases. But our understanding of microbiota compositional dynamics is still unclear and incomplete because the intestinal microbial community is an easily-changed ecosystem. It is urgently required to understand the large variations among individuals. These variations, however, will be an asset rather than a limitation to personalized medicine. For a proof-of-concept study on individual-specific disease classification based on microbiota compositional dynamics, we implemented an adjusted individual-specific edge-network analysis (iENA) method to address a limited number of samples from one individual, and compared it to the temporal 16S rRNA (ribosomal RNA) gene sequencing data from individuals in a challenge study. Our identified individual-specific OTU markers or their combined markers are consistent with previously reported markers, and the predictive score based on them can perform a better AUROC than the previous 0.83 and achieve about 90% accuracy on predicting whether an individual developed diarrhea [i.e., were symptomatic (Sx)] or not. In addition, iENA also showed satisfactory efficiency on another dataset about bacterial vaginosis (BV). All these results suggest that the combination of high-throughput microbiome experiments and computational systems biology approaches can efficiently recommend potential candidate species in the defense against various pathogens for precision medicine.

show abstract

Dysfunctional gut microbiota and relative co-abundance network in infantile eczema

Cited by 37 publications

References 23 publications

Detection of novel RNA viruses from free-living gorillas, Republic of the Congo: genetic diversity of picobirnaviruses

Detection of novel RNA viruses from free-living gorillas, Republic of the Congo: genetic diversity of picobirnaviruses

Distinct Skin Microbiota Imbalance and Responses to Clinical Treatment in Children With Atopic Dermatitis

Characterizing the Personalized Microbiota Dynamics for Disease Classification by Individual-Specific Edge-Network Analysis

Contact Info

Product

Resources

About