Gut metabolites and bacterial community networks during a pilot intervention study with flaxseeds in healthy adult men

Lagkouvardos, Ilias; Kläring, Karoline; Heinzmann, Silke S.; Platz, Stefanie; Scholz, Birgit; Engel, Karl‐Heinz; Schmitt‐Kopplin, Philippe; Haller, Dirk; Rohn, Sascha; Skurk, Thomas; Clavel, Thomas

doi:10.1002/mnfr.201500125

Cited by 106 publications

(106 citation statements)

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“…Raw sequence reads were processed using IMNGS (www.imngs.org) with a pipeline developed in-house based on UPARSE 54 . Details about the analysis have already been described elsewhere 55 . OTUs clustered at 97% sequence identity and occurring at a relative abundance of ≥0.1% total reads in at least one sample were analysed further.…”

Section: Methodsmentioning

confidence: 99%

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

et al. 2016

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Intestinal bacteria influence mammalian physiology, but many types of bacteria are still uncharacterized. Moreover, reference strains of mouse gut bacteria are not easily available, although mouse models are extensively used in medical research. These are major limitations for the investigation of intestinal microbiomes and their interactions with diet and host. It is thus important to study in detail the diversity and functions of gut microbiota members, including those colonizing the mouse intestine. To address these issues, we aimed at establishing the Mouse Intestinal Bacterial Collection (miBC), a public repository of bacterial strains and associated genomes from the mouse gut, and studied host-specificity of colonization and sequence-based relevance of the resource. The collection includes several strains representing novel species, genera and even one family. Genomic analyses showed that certain species are specific to the mouse intestine and that a minimal consortium of 18 strains covered 50-75% of the known functional potential of metagenomes. The present work will sustain future research on microbiota-host interactions in health and disease, as it will facilitate targeted colonization and molecular studies. The resource is available at www.dsmz.de/miBC.

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Section: Methodsmentioning

confidence: 99%

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

et al. 2016

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“…Library preparation and sequencing were performed as described in detail previously 50 . Samples were processed in a semiautomated manner using a Biomek-4000 robot (Beckman-Coulter, Brea, CA).…”

Section: Methodsmentioning

confidence: 99%

Increased Pancreatic Protease Activity in Response to Antibiotics Impairs Gut Barrier and Triggers Colitis

Yoon

Schaubeck

Lagkouvardos

et al. 2018

Cellular and Molecular Gastroenterology and Hepatology

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Background & AimsAntibiotic (ABx) therapy is associated with increased risk for Crohn’s disease but underlying mechanisms are unknown. We observed high fecal serine protease activity (PA) to be a frequent side effect of ABx therapy. The aim of the present study was to unravel whether this rise in large intestinal PA may promote colitis development via detrimental effects on the large intestinal barrier.MethodsTranswell experiments were used to assess the impact of high PA in ABx-treated patients or vancomycin/metronidazole-treated mice on the epithelial barrier. Serine protease profiling was performed using liquid chromatography–mass spectrometry/mass spectrometry analysis. The impact of high large intestinal PA on the intestinal barrier in wild-type and interleukin (IL)10-/- mice and on colitis development in IL10-/- mice was investigated using vancomycin/metronidazole with or without oral serine protease inhibitor (AEBSF) treatment.ResultsThe ABx-induced, high large intestinal PA was caused by significantly increased levels of pancreatic proteases and impaired epithelial barrier integrity. In wild-type mice, the rise in PA caused a transient increase in intestinal permeability but did not affect susceptibility to chemically induced acute colitis. In IL10-/- mice, increased PA caused a consistent impairment of the intestinal barrier associated with inflammatory activation in the large intestinal tissue. In the long term, the vancomycin/metronidazole-induced lasting increase in PA aggravated colitis development in IL10-/- mice.ConclusionsHigh large intestinal PA is a frequent adverse effect of ABx therapy, which is detrimental to the large intestinal barrier and may contribute to the development of chronic intestinal inflammation in susceptible individuals.

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“…If not processed immediately, samples were stored at 2208C. Preparation of amplicon libraries (V3-V4 region) and sequencing was performed as described in detail previously (14). After purification with the AMPure XP system (Beckmann), sequencing was carried out in paired-end mode (PE275) with pooled samples containing 25% (vol:vol) PhiX standard library in a MiSeq system (Illumina Inc.) prepared according to the manufacturer's instructions.…”

Section: High-throughput Sequencing Of 16s Rrna Gene Ampliconsmentioning

confidence: 99%

“…16S rRNA amplicon data processing and statistics Data were analyzed as described previously (14). Raw reads were processed with the in-house-developed pipeline Integrated Microbial Next Generation Sequencing (15) based on the UPARSE approach (16).…”

Section: High-throughput Sequencing Of 16s Rrna Gene Ampliconsmentioning

confidence: 99%

Randomized controlled trial on the impact of early-life intervention with bifidobacteria on the healthy infant fecal microbiota and metabolome

Bazanella

Maier²,

Clavel

et al. 2017

The American Journal of Clinical Nutrition

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Background: Early-life colonization of the intestinal tract is a dynamic process influenced by numerous factors. The impact of probioticsupplemented infant formula on the composition and function of the infant gut microbiota is not well defined. Objective: We sought to determine the effects of a bifidobacteriacontaining formula on the healthy human intestinal microbiome during the first year of life. Design: A double-blind, randomized, placebo-controlled study of newborn infants assigned to a standard whey-based formula containing a total of 10 7 colony-forming units (CFU)/g of Bifidobacterium bifidum, Bifidobacterium breve, Bifidobacterium longum, B. longum subspecies infantis (intervention), or to a control formula without bifidobacteria (placebo). Breastfed controls were included. Diversity and composition of fecal microbiota were determined by 16S ribosomal RNA gene amplicon sequencing, and metabolite profiles were analyzed by ultrahigh-performance liquid chromatography-mass spectrometry over a period of 2 y. Results: Infants (n = 106) were randomly assigned to either the interventional (n = 48) or placebo (n = 49) group; 9 infants were exclusively breastfed throughout the entire intervention period of 12 mo. Infants exposed to bifidobacteria-supplemented formula showed decreased occurrence of Bacteroides and Blautia spp. associated with changes in lipids and unknown metabolites at month 1. Microbiota and metabolite profiles of intervention and placebo groups converged during the study period, and long-term colonization (24 mo) of the supplemented Bifidobacterium strains was not detected. Significant differences in microbiota and metabolites were detected between infants fed breast milk and those fed formula (P , 0.005) and between infants birthed vaginally and those birthed by cesarean delivery (P , 0.005). No significant differences were observed between infant feeding groups regarding growth, antibiotic uptake, or other health variables (P . 0.05). Conclusion:The supplementation of bifidobacteria to infant diet can modulate the occurrence of specific bacteria and metabolites during early life with no detectable long-term effects. This trial was registered at germanctr.de as DRKS00003660. Am J Clin Nutr 2017;106: 1274-86.

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Gut metabolites and bacterial community networks during a pilot intervention study with flaxseeds in healthy adult men

Abstract: Flaxseeds increase enterolignan production but do not markedly alter fecal metabolome and dominant bacterial communities. The data underline the possible role of members of the family Ruminococcaceae in the regulation of enterolignan production and blood lipids.

Cited by 106 publications

References 90 publications

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

Increased Pancreatic Protease Activity in Response to Antibiotics Impairs Gut Barrier and Triggers Colitis

Randomized controlled trial on the impact of early-life intervention with bifidobacteria on the healthy infant fecal microbiota and metabolome

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