A rich meconium metabolome in human infants is associated with early-life gut microbiota composition and reduced allergic sensitization

Petersen, Charisse; Dai, Darlene; Boutin, Rozlyn C.T.; Sbihi, Hind; Sears, Malcolm R.; Moraes, Theo J.; Becker, Allan B.; Azad, Meghan B.; Mandhane, Piush J.; Subbarao, Padmaja; Turvey, Stuart E.; Finlay, B. Brett

doi:10.1016/j.xcrm.2021.100260

Cited by 25 publications

(25 citation statements)

References 43 publications

(61 reference statements)

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“…WGCNA was originally applied to transcriptomics data, but it has also been recently employed for network generation using metabolomics data from human and human microbiome ( Osterhoff et al, 2014 ; Pedersen and Sofia, 2018 ; Vernocchi et al, 2020 ; Murga-Garrido et al, 2021 ; Petersen et al, 2021 ), animal ( Wu et al, 2021 ), and plants ( DiLeo et al, 2011 ). ( Samal and Martin, 2011 ).…”

Section: Experimental Networkmentioning

confidence: 99%

Networks and Graphs Discovery in Metabolomics Data Analysis and Interpretation

Amara

Frainay

Jourdan

et al. 2022

Front. Mol. Biosci.

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Both targeted and untargeted mass spectrometry-based metabolomics approaches are used to understand the metabolic processes taking place in various organisms, from prokaryotes, plants, fungi to animals and humans. Untargeted approaches allow to detect as many metabolites as possible at once, identify unexpected metabolic changes, and characterize novel metabolites in biological samples. However, the identification of metabolites and the biological interpretation of such large and complex datasets remain challenging. One approach to address these challenges is considering that metabolites are connected through informative relationships. Such relationships can be formalized as networks, where the nodes correspond to the metabolites or features (when there is no or only partial identification), and edges connect nodes if the corresponding metabolites are related. Several networks can be built from a single dataset (or a list of metabolites), where each network represents different relationships, such as statistical (correlated metabolites), biochemical (known or putative substrates and products of reactions), or chemical (structural similarities, ontological relations). Once these networks are built, they can subsequently be mined using algorithms from network (or graph) theory to gain insights into metabolism. For instance, we can connect metabolites based on prior knowledge on enzymatic reactions, then provide suggestions for potential metabolite identifications, or detect clusters of co-regulated metabolites. In this review, we first aim at settling a nomenclature and formalism to avoid confusion when referring to different networks used in the field of metabolomics. Then, we present the state of the art of network-based methods for mass spectrometry-based metabolomics data analysis, as well as future developments expected in this area. We cover the use of networks applications using biochemical reactions, mass spectrometry features, chemical structural similarities, and correlations between metabolites. We also describe the application of knowledge networks such as metabolic reaction networks. Finally, we discuss the possibility of combining different networks to analyze and interpret them simultaneously.

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Section: Experimental Networkmentioning

confidence: 99%

Networks and Graphs Discovery in Metabolomics Data Analysis and Interpretation

Amara

Frainay

Jourdan

et al. 2022

Front. Mol. Biosci.

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“… 111 , 112 Lower relative abundances of certain bacteria (for example, Bifidobacterium, Akkermansia and Faecalibacterium), higher relative abundance of particular fungi (Candida and Rhodotorula) and a distinct fecal metabolome enriched for pro-inflammatory metabolites is a risk factor for the development of allergy. 113 Neonatal gut microbiome dysbiosis might promote the CD4+ T cell dysfunction associated with childhood atopy. 114 The onset of this mechanism might well be before birth.…”

Section: The Gastrointestinal Microbiomementioning

confidence: 99%

“… 114 The onset of this mechanism might well be before birth. 113 A greater relative abundance of Bacteroidaceae, Clostridiaceae, and Enterobacteriaceae and a lower relative concentration of Bifidobacteriaceae and Lactobacillaceae is associated with the development of allergic sensitization, eczema, or asthma. 115 In light of this, modulation of the GI microbiome is a potential preventive and therapeutic target in infants with CMA.…”

Section: The Gastrointestinal Microbiomementioning

confidence: 99%

Current Guidelines and Future Strategies for the Management of Cow’s Milk Allergy

Vandenplas¹,

Brough²,

Fiocchi³

et al. 2021

JAA

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Exclusive breast feeding is recommended in all guidelines as the first choice feeding. Cow milk allergy (CMA) can be diagnosed by a diagnostic elimination diet for 2 to 4 weeks with a hypo-allergenic formula, followed by a challenge test with intact cow milk protein. The most often used hypo-allergenic formula for the diagnostic elimination diet and the therapeutic diet is a CM based extensive hydrolysate. CM-based partial hydrolysates cannot be recommended in the management of CMA because of insufficient efficacy and possible reactions, but about half of the infants with CMA may tolerate a partial hydrolysate. The pros and cons of other dietary options are discussed in this paper. The use of an amino acid-based formula and/or rice based hydrolysate formula during the diagnostic elimination and therapeutic diet is debated. When available, there is sufficient evidence to consider rice hydrolysates as an adequate alternative to CM-based hydrolysates, since some infants will still react to the CM hydrolysate. The pros and cons of dietary options such as soy formula, buckwheat, almond, pea or other plant based dietary products are discussed. Although the majority of the plant-based beverages are nutritionally inadequate, some are nutritionally adapted for toddlers. However, accessibility and content vary by country and, thus far there is insufficient evidence on the efficacy and tolerance of these plant-based drinks (except for soy formula and rice hydrolysates) to provide an opinion on them. Conclusion: A diagnostic elimination diet, followed by a challenge remains the diagnostic standard. The use of an awareness tool may result in a decrease of delayed diagnosis. Breastmilk remains the ideal source of nutrition and when not available a CM extensively hydrolyzed formula, rice hydrolysate or amino acid formula should be recommended. More evidence is needed regarding plant-based drinks.

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“…The composition of gut microbiota at the age of 3-6 months was found to be associated with milk allergy by the age of 8 years with the enrichment of class Clostridia and phylum Firmicutes in the infant's gut microbiota (Bunyavanich et al, 2016). Moreover, a recent study has shown that the newborns, who developed IgE-mediated allergic sensitization by 1 year of their age, exhibited less diverse gut metabolic activities at their birth, and the specific metabolic clusters were associated with the abundance of key taxa, driving the maturation of gut microbiota (Petersen et al, 2021).…”

Section: Gut Microbiota In Early Childhoodmentioning

confidence: 99%

Advances in the Relationships Between Cow’s Milk Protein Allergy and Gut Microbiota in Infants

Yang

Ying

et al. 2021

Front. Microbiol.

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Cow’s milk protein allergy (CMPA) is an immune response to cow’s milk proteins, which is one of the most common food allergies in infants and young children. It is estimated that 2–3% of infants and young children have CMPA. The diet, gut microbiota, and their interactions are believed to be involved in the alterations of mucosal immune tolerance, which might lead to the development of CMPA and other food allergies. In this review, the potential molecular mechanisms of CMPA, including omics technologies used for analyzing microbiota, impacts of early microbial exposures on CMPA development, and microbiota–host interactions, are summarized. The probiotics, prebiotics, synbiotics, fecal microbiota transplantation, and other modulation strategies for gut microbiota and the potential application of microbiota-based design of diets for the CMPA treatment are also discussed. This review not only summarizes the current studies about the interactions of CMPA with gut microbiota but also gives insights into the possible CMPA treatment strategies by modulating gut microbiota, which might help in improving the life quality of CMPA patients in the future.

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A rich meconium metabolome in human infants is associated with early-life gut microbiota composition and reduced allergic sensitization

Cited by 25 publications

References 43 publications

Networks and Graphs Discovery in Metabolomics Data Analysis and Interpretation

Networks and Graphs Discovery in Metabolomics Data Analysis and Interpretation

Current Guidelines and Future Strategies for the Management of Cow’s Milk Allergy

Advances in the Relationships Between Cow’s Milk Protein Allergy and Gut Microbiota in Infants

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