Human gut metatranscriptome changes induced by a fermented milk product are associated with improved tolerance to a flatulogenic diet

Oyarzun, Iñigo; Nevé, Boris Le; Yáñez, Francisca; Xie, Zhenrong; Pichaud, Matthieu; Serrano-Gómez, Gerard; Roca, Joaquím; Veiga, Patrick; Azpiroz, Fernando; Tap, Julien; Manichanh, Chaysavanh

doi:10.1016/j.csbj.2022.04.001

Cited by 2 publications

(4 citation statements)

References 42 publications

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Section: Resultsmentioning

confidence: 96%

“…Identification of overlapping proteins between the two catalogues provides support that these proteins are not spurious. Expression was quantified in 862 metatranscriptomic samples from three studies ( Figure 2c ) 7,72,73 . We identified transcriptional evidence for 13,756,670 MiProGut proteins (47.1%), compared to 7,689,106 UHGP proteins.…”

Section: Resultsmentioning

confidence: 99%

“…DIAMOND (v2.1.8.162) 64 mapped metatranscriptomic reads 7,72,73 against the MiProGut-90 and UHGP-90 protein catalogues using the ‘blastx’ command with options ‘--id 90 --evalue 1e-6 -k 1 --max-hsps 1’. The aligned fraction was calculated per-sample as: (aligned reads / total reads) × 100.…”

Section: Methodsmentioning

confidence: 99%

“…Across all samples, MiProGut covered an additional 22.9 ± 9.9% reads compared to UHGP. The largest increase occurred in a Spanish cohort where MiProGut increased read coverage by an additional 41.6 ± 8.6% 72 . Small proteins have been understudied in the human gut as many gene prediction tools exclude them by default 80 .…”

Section: Enhanced Coverage Of the Protein Landscape From The Human Gutmentioning

confidence: 96%

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Lineage-specific microbial protein prediction enables large-scale exploration of protein ecology within the human gut

Schmitz,

Dimonaco,

Clavel

et al. 2024

Preprint

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Microbes use a range of genetic codes and gene structures, yet these are ignored during metagenomic analysis. This causes spurious protein predictions, preventing functional assignment which limits our understanding of ecosystems. To resolve this, we developed a lineage-specific gene prediction approach that uses the correct genetic code based on the taxonomic assignment of genetic fragments, removes partial predictions, and optimises prediction of small proteins. Applied to 9,634 metagenomes and 3,594 genomes from the human gut, this approach increased the landscape of captured expressed microbial proteins by 78.9%, including previously hidden functional groups. Optimised small protein prediction captured 3,772,658 small protein clusters, many with antimicrobial activity. Integration of the protein sequences and sample metadata into a tool, InvestiGUT, enables association of protein prevalence with host parameters. Accurate prediction of proteins is critical for understanding the functionality of microbiomes, hence this work will enhance understanding mechanistic interactions between microbes and hosts.

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Section: Resultsmentioning

confidence: 96%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Enhanced Coverage Of the Protein Landscape From The Human Gutmentioning

confidence: 96%

See 2 more Smart Citations

Lineage-specific microbial protein prediction enables large-scale exploration of protein ecology within the human gut

Schmitz,

Dimonaco,

Clavel

et al. 2024

Preprint

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Methodological Guidelines of the Scientific Community for Human Microbiome Research (CHMR) and the Russian Gastroenterology Association (RGA) on the Use of Probiotics, Prebiotics, Synbiotics, Metabiotics and Functional Foods Enriched with Them for the Treatment and Prevention of Gastrointestinal Diseases in Adults and Children

Ivashkin,

Gorelov,

Abdulganieva

et al. 2024

Rossijskij žurnal gastroènterologii, gepatologii, koloproktolog

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Aim: to optimize outcomes of the treatment and prevention of gastrointestinal diseases in adults and children. Key points. The Methodological Guidelines contain sections on the terminology, classification, mechanisms of action, requirements for sale in the Russian Federation, requirements for proving the efficacy and safety of probiotics, prebiotics, synbiotics and metabiotics, as well as functional foods enriched with them. An overview of relevant data allowing to include these drugs and products in the treatment an d prevention of gastrointestinal diseases in adults and children is presented. Conclusion. The clinical efficacy of probiotics, prebiotics, synbiotics and metabiotics depends on the specificity and quantity of their components, the dosage form, the regimen and duration of treatment. Products and functional foods with proven efficacy and safety are recommended for the treatment and prevention of gastrointestinal diseases in adults and children.

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Human gut metatranscriptome changes induced by a fermented milk product are associated with improved tolerance to a flatulogenic diet

Cited by 2 publications

References 42 publications

Lineage-specific microbial protein prediction enables large-scale exploration of protein ecology within the human gut

Lineage-specific microbial protein prediction enables large-scale exploration of protein ecology within the human gut

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