Multi-omics reveals microbiome, host gene expression, and immune landscape in gastric carcinogenesis

Park, Chan Hyuk; Hong, Changjin; Lee, Areum; Sung, Jaeyun; Hwang, Tae Hyun

doi:10.1016/j.isci.2022.103956

Cited by 23 publications

(15 citation statements)

References 63 publications

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“…Effective international cooperation could promote academic exchanges. It may be a solution to the research of gut microbiome in disease by conducting well-designed large-scale cohort studies and randomized clinical trials, meanwhile combining multi-omics techniques and integrating microbiome data ( Heintz-Buschart et al, 2016 ; Park et al, 2022 ). Due to confounding factors, it is necessary to establish standardized experimental procedures and subsequent data analysis pipelines ( Szóstak et al, 2022 ).…”

Section: Discussionmentioning

confidence: 99%

The gut microbiome in human health and disease—Where are we and where are we going? A bibliometric analysis

Huang

Liu

et al. 2022

Front. Microbiol.

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BackgroundThere are trillions of microbiota in our intestinal tract, and they play a significant role in health and disease via interacting with the host in metabolic, immune, neural, and endocrine pathways. Over the past decades, numerous studies have been published in the field of gut microbiome and disease. Although there are narrative reviews of gut microbiome and certain diseases, the whole field is lack of systematic and quantitative analysis. Therefore, we outline research status of the gut microbiome and disease, and present insights into developments and characteristics of this field to provide a holistic grasp and future research directions.MethodsAn advanced search was carried out in the Web of Science Core Collection (WoSCC), basing on the term “gut microbiome” and its synonyms. The current status and developing trends of this scientific domain were evaluated by bibliometric methodology. CiteSpace was used to perform collaboration network analysis, co-citation analysis and citation burst detection.ResultsA total of 29,870 articles and 13,311 reviews were retrieved from the database, which involve 42,900 keywords, 176 countries/regions, 19,065 institutions, 147,225 authors and 4,251 journals. The gut microbiome and disease research is active and has received increasing attention. Co-cited reference analysis revealed the landmark articles in the field. The United States had the largest number of publications and close cooperation with other countries. The current research mainly focuses on gastrointestinal diseases, such as inflammatory bowel disease (IBD), ulcerative colitis (UC) and Crohn’s disease (CD), while extra-intestinal diseases are also rising, such as obesity, diabetes, cardiovascular disease, Alzheimer’s disease, Parkinson’s disease. Omics technologies, fecal microbiota transplantation (FMT) and metabolites linked to mechanism would be more concerned in the future.ConclusionThe gut microbiome and disease has been a booming field of research, and the trend is expected to continue. Overall, this research field shows a multitude of challenges and great opportunities.

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Section: Discussionmentioning

confidence: 99%

The gut microbiome in human health and disease—Where are we and where are we going? A bibliometric analysis

Huang

Liu

et al. 2022

Front. Microbiol.

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“…Metagenomics can be used to detect known species as well as unknown microbes (Ko et al, 2022). In addition, multiomics approaches that can help identify connections between the microbiome of an antimicrobial surface and human gene expression can be beneficial for studies on AMC health risks (Lobanov et al, 2022;Park et al, 2022) The microbial metabolomics-based approach can provide an additional methodological repertoire for surface hygiene studies, complementing metagenomic, metatranscriptomic, and proteomic analyses (Tang, 2011;Vernocchi et al, 2016;Ahn and Hayes, 2021). Although metagenomic mappings of interior surfaces have been carried out for a decade, genetic real-life studies of AMCs are scarce.…”

Section: High Throughput Metagenomic Sequencing and Other Omics Studiesmentioning

confidence: 99%

Microbiota shaping and bioburden monitoring of indoor antimicrobial surfaces

Mäki

Salonen²,

Kivisaari³

et al. 2023

Front. Built Environ.

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Indoor residents are constantly exposed to dynamic microbiota that have significant health effects. In addition to hand hygiene, cleaning, and disinfection, antimicrobial coatings (AMCs) can prevent the spread of infectious diseases in public areas. The sustainable use of antimicrobial-coated products requires an assessment of their pros and cons for human health and the environment. The toxicity and resistance risks of AMCs have been considered, but large-scale genetic studies on the microbial community compositions and resistomes of AMCs are scarce. The use of an AMC can reduce the total number of microbes on a surface but poses the risk of dysbiosis, microbial imbalance, such as the polarized growth of metallophilic, metal- and antimicrobial-resistant, and other survivor bacteria, and the overall reduction of microbial diversity. Loss of diversity may lead to the enrichment of harmful bacteria and an increased risk of communicable or immunological non-communicable inflammatory diseases (NCDs). In public buildings, such as kindergartens and nursing homes for the elderly, the use of AMCs is likely to increase due to epidemics and pandemics in recent years. Therefore, comprehensive metagenomic research is needed to monitor the effects of AMCs on indoor microbial community compositions and functions. Although the determination of good indoor microbiota and homeostasis is difficult, microbial communities that have health-protective or harmful effects can and should be identified using a metagenomic sequencing approach before the large-scale implementation of AMCs.

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“…Nyholm et al recently coined the term ‘holo-omics’ to describe experiments that aim to obtain multiple omics data from both host and microbiota domains. This holistic approach has been recently applied to study the plant microbiome (Zolti et al 2020 ; for a review, see Xu et al 2021b ), the human microbiome (Heintz-Buschart et al 2016 , Lloyd-Price et al 2019 , Park et al 2022 ) [for a review, see Zhang et al ( 2019 )]. For example, Lloyd-Price et al ( 2019 ) provided a comprehensive multiomics data during the functional dysbiosis in the human gut microbiome upon the progression of the inflammatory bowel disease.…”

Section: Introductionmentioning

confidence: 99%

The coral microbiome: towards an understanding of the molecular mechanisms of coral–microbiota interactions

Mohamed

Ochsenkühn

Moustafa

et al. 2023

FEMS Microbiology Reviews

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Corals live in a complex, multi-partite symbiosis with diverse microbes across kingdoms, some of which are implicated in vital functions, such as those related to resilience against climate change. However, knowledge gaps and technical challenges limit our understanding of the nature and functional significance of complex symbiotic relationships within corals. Here, we provide an overview of the complexity of the coral microbiome focusing on taxonomic diversity and functions of well-studied and cryptic microbes. Mining the coral literature indicate that while corals collectively harbor a third of all marine bacterial phyla, known bacterial symbionts and antagonists of corals represent a minute fraction of this diversity and that these taxa cluster into select genera, suggesting selective evolutionary mechanisms enabled these bacteria to gain a niche within the holobiont. Recent advances in coral microbiome research aimed at leveraging microbiome manipulation to increase coral's fitness to help mitigate heat stress-related mortality are discussed. Then, insights into the potential mechanisms through which microbiota can communicate with and modify host responses are examined by describing known recognition patterns, potential microbially-derived coral epigenome effector proteins and coral gene regulation. Finally, the power of omics tools used to study corals are highlighted with emphasis on an integrated host-microbiota multiomics framework to understand the underlying mechanisms during symbiosis and climate change-driven dysbiosis.

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Multi-omics reveals microbiome, host gene expression, and immune landscape in gastric carcinogenesis

Cited by 23 publications

References 63 publications

The gut microbiome in human health and disease—Where are we and where are we going? A bibliometric analysis

The gut microbiome in human health and disease—Where are we and where are we going? A bibliometric analysis

Microbiota shaping and bioburden monitoring of indoor antimicrobial surfaces

The coral microbiome: towards an understanding of the molecular mechanisms of coral–microbiota interactions

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