Challenges and Perspective in Integrated Multi-Omics in Gut Microbiota Studies

Daliri, Eric Banan‐Mwine; Ofosu, Fred Kwame; Chelliah, Ramachandran; Lee, Byong H.; Oh, Deog‐Hwan

doi:10.3390/biom11020300

Cited by 44 publications

(37 citation statements)

References 81 publications

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“…It has been studied in more than 300 clinical and over 1000 scientific studies. Lactobacillus reuteri (Daliri, Ofosu, Xiuqin, Chelliah, & Oh, 2021) and Lactobacillus johnsonii (Davoren et al., 2019) are two novel LAB probiotics that have potential for the development of functional dairy products.…”

Section: Probioticsmentioning

confidence: 99%

Probiotics in the dairy industry—Advances and opportunities

Gao

Zhang

et al. 2021

Comp Rev Food Sci Food Safe

116

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The past two decades have witnessed a global surge in the application of probiotics as functional ingredients in food, animal feed, and pharmaceutical products. Among food industries, the dairy industry is the largest sector where probiotics are employed in a number of dairy products including sour/fermented milk, yogurt, cheese, butter/cream, ice cream, and infant formula. These probiotics are either used as starter culture alone or in combination with traditional starters, or incorporated into dairy products following fermentation, where their presence imparts many functional characteristics to the product (for instance, improved aroma, taste, and textural characteristics), in addition to conferring many health‐promoting properties. However, there are still many challenges related to the stability and functionality of probiotics in dairy products. This review highlights the advances, opportunities, and challenges of application of probiotics in dairy industries. Benefits imparted by probiotics to dairy products including their role in physicochemical characteristics and nutritional properties (clinical and functional perspective) are also discussed. We transcend the traditional concept of the application of probiotics in dairy products and discuss paraprobiotics and postbiotics as a newly emerged concept in the field of probiotics in a particular relation to the dairy industry. Some potential applications of paraprobiotics and postbiotics in dairy products as functional ingredients for the development of functional dairy products with health‐promoting properties are briefly elucidated.

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Section: Probioticsmentioning

confidence: 99%

Probiotics in the dairy industry—Advances and opportunities

Gao

Zhang

et al. 2021

Comp Rev Food Sci Food Safe

116

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“…Shotgun metatranscriptomics can answer the question of what microbes are doing “right then” in an ecosystem ( Franzosa et al., 2014 ). Analyzing their RNA provides clues to determining their metabolic activities in response to stress and how such alteration in metabolic activity influences host phenotypes in healthy or diseased conditions ( Daliri et al., 2021 ).…”

Section: Influences Of the Gut Microbiome And Analysis Approachesmentioning

confidence: 99%

“…Metabolomics involves the study of metabolites in a biological sample as well as the exploration of microbe-derived therapeutic products. A targeted or untargeted approach can be used ( Daliri et al., 2021 ). The former is used to study metabolites in specific pathways associated with a particular disease, while the latter measures as many metabolites in the sample as possible ( Commisso et al., 2013 ; Vignoli et al., 2019 ).…”

Section: Influences Of the Gut Microbiome And Analysis Approachesmentioning

confidence: 99%

Microbiota and Ocular Diseases

Xue

Zou

et al. 2021

Front. Cell. Infect. Microbiol.

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Recent advances have identified significant associations between the composition and function of the gut microbiota and various disorders in organ systems other than the digestive tract. Utilizing next-generation sequencing and multiomics approaches, the microbial community that possibly impacts ocular disease has been identified. This review provides an overview of the literature on approaches to microbiota analysis and the roles of commensal microbes in ophthalmic diseases, including autoimmune uveitis, age-related macular degeneration, glaucoma, and other ocular disorders. In addition, this review discusses the hypothesis of the “gut-eye axis” and evaluates the therapeutic potential of targeting commensal microbiota to alleviate ocular inflammation.

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“…Several studies have reported on manufacturing foods with increased riboflavin, such as bread, pasta, and soy milk, using LAB that overproduces riboflavin [18][19][20], and reports on improving riboflavin deficiency using fermented soy milk rich in riboflavin are also available [16]. There have also been studies on the treatment of gastrointestinal diseases using riboflavin overproducing LAB [25][26][27]. However, there is not enough evidence on whether consuming these foods can resolve riboflavin deficiency, and there is no research on whether riboflavin is absorbed in vivo by directly ingesting riboflavinoverproducing LAB.…”

Section: Introductionmentioning

confidence: 99%

Probiotic Potential of a Novel Vitamin B2-Overproducing Lactobacillus plantarum Strain, HY7715, Isolated from Kimchi

Kim¹,

Choi²,

Lee³

et al. 2021

Applied Sciences

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Vitamin B2, also known as riboflavin, is essential for maintaining human health. The purpose of this study was to isolate novel lactic acid bacteria that overproduce vitamin B2 and to validate their potential as probiotics. In this study, Lactobacillus plantarum HY7715 (HY7715) was selected among lactic acid bacteria isolated from Kimchi. HY7715 showed a very high riboflavin-producing ability compared to the control strain due to the high expression of ribA, ribB, ribC, ribH, and ribG genes. HY7715 produced 34.5 ± 2.41 mg/L of riboflavin for 24 h without consuming riboflavin in the medium under optimal growth conditions. It was able to produce riboflavin in an in vitro model of the intestinal environment. In addition, when riboflavin deficiency was induced in mice through nutritional restriction, higher levels of riboflavin were detected in plasma and urine in the HY7715 administration group than in the control group. HY7715 showed high survival rate in simulated gastrointestinal conditions and had antibiotic resistance below the cutoff MIC value suggested by the European Food Safety Authority; moreover, it did not cause hemolysis. In conclusion, HY7715 could be considered a beneficial probiotic strain for human and animal applications, suggesting that it could be a new alternative to address riboflavin deficiency.

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Challenges and Perspective in Integrated Multi-Omics in Gut Microbiota Studies

Cited by 44 publications

References 81 publications

Probiotics in the dairy industry—Advances and opportunities

Probiotics in the dairy industry—Advances and opportunities

Microbiota and Ocular Diseases

Probiotic Potential of a Novel Vitamin B2-Overproducing Lactobacillus plantarum Strain, HY7715, Isolated from Kimchi

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