Biology subjects

Roager, H. M.

Publications and source records attributed to Roager, H. M..

5 recordsLinked to original sources

bioRxiv2026

Ultra-High Multiplexing Enables Near-Full-Length 16S rRNA Gene Amplicon Sequencing of Over 1,200 Gut Microbiome Samples on a Single Nanopore Flow Cell

Next-generation sequencing (NGS) of the prokaryotic 16S rRNA gene revolutionized gut microbiome research two decades ago. However, short read lengths remain an inherent limitation of platforms such as the widely used Illumina platforms (2 x 150-300 bp). Recent advances in Oxford Nanopore Technologies (ONT) flow cell chemistry (R10.4.1) have substantially improved sequencing accuracy. Combined with a custom multiple-primer strategy that comprehensively targets 16S rRNA gene variants to generate near-full-length amplicons, this approach enables read-by-read taxonomic classification, a feature not feasible with short-read sequencing platforms. Although our multiple-primer strategy could enable parallel sequencing of more than 18,000 samples (192 x 96), current flow cell capacity offers sufficient sequencing depth for approximately 1,000-1,500 samples. To validate the scalability and our per-read classification pipeline, we show that more than a thousand human fecal microbiome samples spiked with two bacterial strains (Imtechella halotolerans and Allobacillus halotolerans), not otherwise present in human fecal samples, can be successfully sequenced on a single flow cell, achieving a per-molecule error rate sufficient for direct per-read classification and at an adequate read depth for downstream analysis. This level of scalability significantly reduces per-sample costs, making the approach more accessible to a broader research community. To embrace these advancements, we have developed RubyRed, a pipeline that processes raw sequencing data and assigns taxonomic classifications on a per-read basis. Using spike-in references (I. halotolerans and A. halotolerans), we demonstrate high mean single-read sequencing accuracy (99% and 98.9%, respectively), with the majority of reads exceeding the canonical threshold required for species-level taxonomic classification based on the 16S rRNA gene.

microbiology↗

bioRxiv2026

Daily Bowel Movements are Associated with Stronger Gut-Brain Phase-Amplitude Coupling and Better Cognitive Performance

Gut-brain communication has emerged as a rapidly expanding field of research, with recent electrophysiological studies revealing rhythmic gut-brain coupling between gastric activity and brain oscillations in humans. Gut motility is a key determinant of gastrointestinal function, but it remains unclear whether individual differences in gut motility reflected by weekly bowel movements (e.g., defecation frequency) are associated with differences in gut-brain coupling. Here, we address this question by examining women with self-reported daily bowel movements (N = 38) and women with less frequent bowel movements (N = 38). We recorded simultaneous electroencephalography (EEG) and electrogastrography (EGG) at fasting state, performed cognitive assessments, and analysed faecal short-chain fatty acids (SCFAs) as markers of colonic fermentation. In a subset of participants, EEG-EGG coupling was assessed twice over an interval of at least eight weeks to assess test-retest reliability. In this group, EEG-EGG coupling showed moderate test-retest reliability (Intraclass Correlation Coefficient (ICC) = 0.50). When comparing the two groups of women, the phase-amplitude coupling (PAC) analysis between EEG and EGG signals revealed a significantly stronger gut-brain coupling in women with daily bowel movements compared to women with less frequent bowel movements (p = 0.03). We additionally found that women with daily bowel movements made less errors in the cognitive tasks and had higher levels of faecal SCFAs. A path analysis suggested that bowel movements significantly affect gut-brain phase-amplitude coupling through faecal SCFAs. However, neither faecal SCFAs nor phase-amplitude coupling significantly predicted cognitive performance, suggesting the existence of alternative pathways for the association between bowel movements and cognitive performance. Together, our findings suggest that the strength of gut-brain coupling is associated with bowel movements and cognitive performance, making EEG-EGG coupling a promising marker of human gut-brain interactions.

neuroscience↗

bioRxiv2024

Gut environmental factors explain variations in the gut microbiome composition and metabolism within and between healthy adults

The human gut microbiome is highly personal. However, the contribution of the gut environment to variations in the gut microbiome remains elusive. Here, we profiled the gut microbiome composition and metabolism over 9 consecutive days in 61 healthy adults and assessed gut environmental factors including segmental transit time and pH using a wireless motility capsule. Day-to-day fluctuations in gut environmental factors as well as segmental transit time and pH varied substantially between individuals. The gut environment explained more variations in gut microbiome and urine metabolome than dietary macronutrients or personal characteristics. Finally, we identified coffee-derived metabolites to be negatively correlated with small intestinal transit time and several microbial metabolites to be associated with colonic transit time including urinary proteolytic markers, faecal short-chain fatty acids, and breath methane. Our work suggests that the gut environment is key for understanding the individuality of the human gut microbiome composition and metabolism.

microbiology↗

bioRxiv2023

Substrate availability and dietary fibre regulate metabolism of tryptophan by human gut microbes

Tryptophan is catabolized by gut microbes, resulting in a wide range of metabolites implicated in both beneficial and adverse host effects. However, it remains elusive how the gut microbial tryptophan metabolism is governed either towards indole, associated with adverse effects in chronic kidney disease, or towards indolelactic acid (ILA) and indolepropionic acid (IPA), associated with protective effects in type 2 diabetes and inflammatory bowel disease. Here, we used human fecal cultures in combination with a controlled three-species model to test competition for tryptophan, and measured the resulting metabolites both in vitro and in gnotobiotic mice colonized with the three species. We revealed that the generation of specific tryptophan-derived metabolites was not predominantly determined by the abundance of tryptophan metabolizing bacteria, but rather by substrate-dependent regulation of specific metabolic pathways. In vitro and in vivo, indole-producing Escherichia coli and ILA- and IPA-producing Clostridium sporogenes competed for tryptophan. Importantly, the fibre degrading Bacteroides thetaiotaomicron affected this competition by cross-feeding monosaccharides to E. coli, which inhibited indole production through catabolite repression, and thereby made more tryptophan available to C. sporogenes, increasing ILA and IPA production. We thus present the first mechanistic explanation for why consumption of fermentable fibres suppress indole production but promote the generation of other tryptophan metabolites associated with health benefits. We conclude that the availability of tryptophan and dietary fibre regulates gut microbiome tryptophan metabolism pathways, and consequently influences the balance between the different tryptophan catabolites generated. This balance has implications for host-microbial cross-talk affecting human health.

microbiology↗

bioRxiv2020

Breastmilk-promoted bifidobacteria produce aromatic lactic acids in the infant gut

Breastfeeding profoundly shapes the infant gut microbiota, which is critical for early life immune development. However, few breastmilk-dependent microbial metabolites mediating host-microbiota interactions are currently known. We here demonstrate that breastmilk-promoted Bifidobacterium species convert aromatic amino acids (tryptophan, phenylalanine and tyrosine) into their respective aromatic lactic acids (indolelactate, phenyllactate and 4-hydroxyphenyllactate) via a previously unrecognised aromatic lactate dehydrogenase. By longitudinal profiling of the gut microbiota composition and metabolome of stool samples of infants obtained from birth until 6 months of age, we show that stool concentrations of aromatic lactic acids are determined by the abundance of human milk oligosaccharide degrading Bifidobacterium species containing the aromatic lactate dehydrogenase. We demonstrate that stool concentrations of Bifidobacterium-derived indolelactate, the most abundant aromatic lactic acid in vivo, are associated with the capacity of infant stool samples to activate the aryl hydrocarbon receptor (AhR), a receptor important for controlling intestinal homeostasis and immune responses. Finally, we show that indolelactate modulates ex vivo immune responses of human CD4+ T-cells and monocytes in a dose-dependent manner by acting as an agonist of both, the AhR and hydroxycarboxylic acid receptor 3 (HCAR3). Our findings reveal that breastmilk-promoted Bifidobacterium produce aromatic lactic acids in the gut of infants and suggest that these microbial metabolites may impact immune function in early life.

microbiology↗