Food Omics Validation: Towards Understanding Key Features for Gut Microbiota, Probiotics and Human Health

Jiménez-Pranteda, María Luján; Pérez-Davó, Azahara; Monteoliva‐Sánchez, Mercedes; Ramos‐Cormenzana, A.; Aguilera, Margarita

doi:10.1007/s12161-014-9923-6

Cited by 14 publications

(7 citation statements)

References 164 publications

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“…Moreover, despite their numerous benefits, inadequate consumption of probiotics can even have undesirable effects, such as harmful metabolic activities, alterations of the integrity of the intestinal barrier, an inappropriate immune response, and the generation of antibiotic resistance genes and systemic infections [ 5 , 6 ]. Currently, the evaluation process of health claims determines the benefit of probiotics through clinical trials, which verify and demonstrate, in the last phase, the modulating capacities for the control of dysbiosis in patients with certain pathological disorders or phenotypes using omics complementary technologies [ 7 ]. It is also important to harmonize the knowledge on what specific probiotics should be recommended for dysbiosis, in what doses, and for how long.…”

Section: Introductionmentioning

confidence: 99%

“…In that direction, more research about bacteria components of the intestinal microbiota that could become new candidates for next-generation probiotics with specific biotherapeutic and detoxifying role could be developed [ 30 ]. Moreover, this area of research is now evolving in parallel with omics methodologies [ 7 ], improved identification, culturing, and next-generation sequencing technologies [ 31 ].…”

Section: Introductionmentioning

confidence: 99%

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Probiotic Strains and Intervention Total Doses for Modulating Obesity-Related Microbiota Dysbiosis: A Systematic Review and Meta-analysis

et al. 2020

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Obesity is a growing health threat worldwide. Administration of probiotics in obesity has also parallelly increased but without any protocolization. We conducted a systematic review exploring the administration pattern of probiotic strains and effective doses for obesity-related disorders according to their capacity of positively modulating key biomarkers and microbiota dysbiosis. Manuscripts targeting probiotic strains and doses administered for obesity-related disorders in clinical studies were sought. MEDLINE, Scopus, Web of Science, and Cochrane Library databases were searched using keywords during the last fifteen years up to April 2020. Two independent reviewers screened titles, abstracts, and then full-text papers against inclusion criteria according to PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines. From 549 interventional reports identified, we filtered 171 eligible studies, from which 24 full-text assays were used for calculating intervention total doses (ITD) of specific species and strains administered. Nine of these reports were excluded in the second-step because no specific data on gut microbiota modulation was found. Six clinical trials (CT) and 9 animal clinical studies were retained for analysis of complete outcome prioritized (body mass index (BMI), adiposity parameters, glucose, and plasma lipid biomarkers, and gut hormones). Lactobacillus spp. administered were double compared to Bifidobacterium spp.; Lactobacillus as single or multispecies formulations whereas most Bifidobacteria only through multispecies supplementations. Differential factors were estimated from obese populations’ vs. obesity-induced animals: ITD ratio of 2 × 106 CFU and patterns of administrations of 11.3 weeks to 5.5 weeks, respectively. Estimation of overall probiotics impact from selected CT was performed through a random-effects model to pool effect sizes. Comparisons showed a positive association between the probiotics group vs. placebo on the reduction of BMI, total cholesterol, leptin, and adiponectin. Moreover, negative estimation appeared for glucose (FPG) and CRP. While clinical trials including data for positive modulatory microbiota capacities suggested that high doses of common single and multispecies of Lactobacillus and Bifidobacterium ameliorated key obesity-related parameters, the major limitation was the high variability between studies and lack of standardized protocols. Efforts in solving this problem and searching for next-generation probiotics for obesity-related diseases would highly improve the rational use of probiotics.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Probiotic Strains and Intervention Total Doses for Modulating Obesity-Related Microbiota Dysbiosis: A Systematic Review and Meta-analysis

et al. 2020

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“…Integrating multi-omics datasets is an innovative assignment, due to the increased complexity and diversity of the collected data [ 136 ]. This integration is increasingly reliant on efficient bioinformatics tools and advanced statistical methods [ 137 , 138 , 139 ].…”

Section: Information and Criteria For Searching And Culturing Next-generation Probioticsmentioning

confidence: 99%

Next Generation Probiotics for Neutralizing Obesogenic Effects: Taxa Culturing Searching Strategies

et al. 2021

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The combination of diet, lifestyle, and the exposure to food obesogens categorized into “microbiota disrupting chemicals” (MDC) could determine obesogenic-related dysbiosis and modify the microbiota diversity that impacts on individual health–disease balances, inducing altered pathogenesis phenotypes. Specific, complementary, and combined treatments are needed to face these altered microbial patterns and the specific misbalances triggered. In this sense, searching for next-generation beneficial microbes or next-generation probiotics (NGP) by microbiota culturing, and focusing on their demonstrated, extensive scope and well-defined functions could contribute to counteracting and repairing the effects of obesogens. Therefore, this review presents a perspective through compiling information and key strategies for directed searching and culturing of NGP that could be administered for obesity and endocrine-related dysbiosis by (i) observing the differential abundance of specific microbiota taxa in obesity-related patients and analyzing their functional roles, (ii) developing microbiota-directed strategies for culturing these taxa groups, and (iii) applying the successful compiled criteria from recent NGP clinical studies. New isolated or cultivable microorganisms from healthy gut microbiota specifically related to obesogens’ neutralization effects might be used as an NGP single strain or in consortia, both presenting functions and the ability to palliate metabolic-related disorders. Identification of holistic approaches for searching and using potential NGP, key aspects, the bias, gaps, and proposals of solutions are also considered in this review.

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“…Although promising, integrative omics currently presents great challenges such as a need to development and employ bioinformatics pipelines and algorithms to associate and harmonize large amounts of data generated by the different high-throughput platforms (Jiménez-Pranteda et al, 2015). Recently, feature-annotation enrichment analysis has been extensively used to identify biological processes by comparing de novo data with accumulated biological data deposited in public databases.…”

Section: Integrative Omics and Enrichment Approachesmentioning

confidence: 99%

Research Article Omics of probiotic bacteria: which features to seek?

Castro-Oliveira¹,

Silva²,

Carvalho³

et al. 2020

Genet. Mol. Res.

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Probiotics are live nonpathogenic microorganisms extensively used in food, pharmaceutical and medicinal industries. Recently, attention has focused on specific features of probiotics and on the abilities of some long known and recently described species of this group. In general, desired features of probiotics include resistance to acid and bile salts to avoid dysbiosis and induction of immune system development. The advent of next-generation sequencing technology has propelled the genomic area, allowing a search for probiotic features in a wide range of probiotic species, especially bacteria. In this context, functional genomics analyses can help interpret big data, correlating the findings with comparative genomics analyses, in a search for direct applications. To select the articles in this review, we used the following indexing terms: (probiotics OR probiosis) AND (genomics OR transcriptomics OR ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 19 (2): gmr18599 L. Castro-Oliveira et al. 2 proteomics OR metabolomics OR culturomics) AND bacteria. Proteomics and transcriptomics methodologies reveal important information about proteins and transcripts differentially expressed under specific conditions that mimic host environments in health and disease. In addition, new research approaches have been developed for probiotics, such as metabiotic and metagenomic analyses of host microbiota. Also, we examined probiotic related features, including bacterial safety aspects; tolerance towards digestive constraints, such as gastric juice and bile salts; bacterial pathogen exclusion mechanisms; adhesion-related genes; antimicrobial peptides; immune development and function; omics; metagenomics; culturomics; functional genomics; transcriptomics; proteomics; metabiotics and metabolomics. In summary, currently there is considerable interest in probiotic bacteria, and structural and functional genomics analyses have potential to help research in this area.

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Food Omics Validation: Towards Understanding Key Features for Gut Microbiota, Probiotics and Human Health

Cited by 14 publications

References 164 publications

Probiotic Strains and Intervention Total Doses for Modulating Obesity-Related Microbiota Dysbiosis: A Systematic Review and Meta-analysis

Probiotic Strains and Intervention Total Doses for Modulating Obesity-Related Microbiota Dysbiosis: A Systematic Review and Meta-analysis

Next Generation Probiotics for Neutralizing Obesogenic Effects: Taxa Culturing Searching Strategies

Research Article Omics of probiotic bacteria: which features to seek?

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