Functional genomic analysis of Hawaii marine metagenomes

Wang, Xiaoqi; Wang, Qi; Guo, Xiao; Liu, Luying; Guo, Jiangtao; Yao, Jianming; Zhu, Huaiqiu

doi:10.1007/s11434-014-0658-y

Cited by 7 publications

(5 citation statements)

References 40 publications

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“…3,4 They can subsequently act as pathogens or triggers to induce various diseases such as cardiovascular diseases, 5 respiratory diseases, 6 and even lung cancers. 7 As a result of their free mobility, airborne bacteria are important in microbial exchange among the biosphere and other environments, such as soil and marine environments, 8 thereby facilitating the transfer of antibiotic resistance genes (ARGs), virulence factors, and functional genes. 9 Considering the potential importance of airborne bacteria in public health, numerous studies have devoted considerable efforts to investigate factors influencing airborne bacterial composition and biodiversity, including meteorological parameters 10,11 and anthropogenic activities.…”

Section: ■ Introductionmentioning

confidence: 99%

“…Additionally, extensive studies have shown that airborne bacteria have profound implications for public health by colonizing the skin, mucous membranes, digestive system, and respiratory tracts. , They can subsequently act as pathogens or triggers to induce various diseases such as cardiovascular diseases, respiratory diseases, and even lung cancers . As a result of their free mobility, airborne bacteria are important in microbial exchange among the biosphere and other environments, such as soil and marine environments, thereby facilitating the transfer of antibiotic resistance genes (ARGs), virulence factors, and functional genes …”

Section: Introductionmentioning

confidence: 99%

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Global Meta-analysis of Airborne Bacterial Communities and Associations with Anthropogenic Activities

Jiang

Wang

Guo

et al. 2022

Environ. Sci. Technol.

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Airborne microbiome alterations, an emerging global health concern, have been linked to anthropogenic activities in numerous studies. However, these studies have not reached a consensus. To reveal general trends, we conducted a meta-analysis using 3226 air samples from 42 studies, including 29 samples of our own. We found that samples in anthropogenic activity-related categories showed increased microbial diversity, increased relative abundance of pathogens, increased co-occurrence network complexity, and decreased positive edge proportions in the network compared with the natural environment category. Most of the above conclusions were confirmed using the samples we collected in a particular period with restricted anthropogenic activities. Additionally, unlike most previous studies, we used 15 human-production process factors to quantitatively describe anthropogenic activities. We found that microbial richness was positively correlated with fine particulate matter concentration, NH 3 emissions, and agricultural land proportion and negatively correlated with the gross domestic product per capita. Airborne pathogens showed preferences for different factors, indicating potential health implications. SourceTracker analysis showed that the human body surface was a more likely source of airborne pathogens than other environments. Our results advance the understanding of relationships between anthropogenic activities and airborne bacteria and highlight the role of airborne pathogens in public health.

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Section: ■ Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Global Meta-analysis of Airborne Bacterial Communities and Associations with Anthropogenic Activities

Jiang

Wang

Guo

et al. 2022

Environ. Sci. Technol.

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“…We first annotated all genes of the microbiome with the KEGG database and the ALCME database separately ( Leplae et al., 2010 ; Wang et al., 2015 ; Kanehisa et al., 2016 ). Since the KEGG functional annotation rate for viral genes was low (overall annotation rate: 46.8%), we used annotation of ALCME in later analyses (overall annotation rate: 80.1%).…”

Section: Methodsmentioning

confidence: 99%

More Positive or More Negative? Metagenomic Analysis Reveals Roles of Virome in Human Disease-Related Gut Microbiome

Wang

Guo

et al. 2022

Front. Cell. Infect. Microbiol.

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Viruses are increasingly viewed as vital components of the human gut microbiota, while their roles in health and diseases remain incompletely understood. Here, we first sequenced and analyzed the 37 metagenomic and 18 host metabolomic samples related to irritable bowel syndrome (IBS) and found that some shifted viruses between IBS and controls covaried with shifted bacteria and metabolites. Especially, phages that infect beneficial lactic acid bacteria depleted in IBS covaried with their hosts. We also retrieved public whole-genome metagenomic datasets of another four diseases (type 2 diabetes, Crohn’s disease, colorectal cancer, and liver cirrhosis), totaling 438 samples including IBS, and performed uniform analysis of the gut viruses in diseases. By constructing disease-specific co-occurrence networks, we found viruses actively interacting with bacteria, negatively correlated with possible dysbiosis-related and inflammation-mediating bacteria, increasing the connectivity between bacteria modules, and contributing to the robustness of the networks. Functional enrichment analysis showed that phages interact with bacteria through predation or expressing genes involved in the transporter and secretion system, metabolic enzymes, etc. We further built a viral database to facilitate systematic functional classification and explored the functions of viral genes on interacting with bacteria. Our analyses provided a systematic view of the gut virome in the disease-related microbial community and suggested possible positive roles of viruses concerning gut health.

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“…Genome analysis revealed the secrets of sex and lifestyle in caterpillar fungus [92], and uncovered disease resistance mechanisms in Medicago truncatula [93]. Recently, a study using functional genomic analysis afforded a clue to reveal the special living strategies of microbial community from sea surface to deep sea in Hawaii [94]. In plant science, as WRKY transcription factors are important molecules in regulating plant development and resistance.…”

Section: Genomicsmentioning

confidence: 99%

From Chinese Science Bulletin to Science Bulletin: celebrate the coming 50th birthday

Jia

Chen

2015

Science Bulletin

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Functional genomic analysis of Hawaii marine metagenomes

Cited by 7 publications

References 40 publications

Global Meta-analysis of Airborne Bacterial Communities and Associations with Anthropogenic Activities

Global Meta-analysis of Airborne Bacterial Communities and Associations with Anthropogenic Activities

More Positive or More Negative? Metagenomic Analysis Reveals Roles of Virome in Human Disease-Related Gut Microbiome

From Chinese Science Bulletin to Science Bulletin: celebrate the coming 50th birthday

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