A5049927688- Gut microbiota and health
- Clostridium difficile and Clostridium perfringens research
- Diabetes and associated disorders
- Infant Nutrition and Health
- Neural Networks and Applications
- Bacterial Identification and Susceptibility Testing
- Bacteriophages and microbial interactions
- Diet and metabolism studies
- Protein Structure and Dynamics
- Genomics and Phylogenetic Studies
- Probiotics and Fermented Foods
- Diabetes Management and Research
- Adolescent and Pediatric Healthcare
- Neonatal Respiratory Health Research
- Viral gastroenteritis research and epidemiology
- Pancreatic function and diabetes
- Inflammatory Bowel Disease
- Bioinformatics and Genomic Networks
- Microscopic Colitis
- Machine Learning in Bioinformatics
- Anomaly Detection Techniques and Applications
- Gastrointestinal motility and disorders
- Enzyme Structure and Function
- Bayesian Methods and Mixture Models
- Urinary Tract Infections Management
University of Helsinki
2011-2025
Broad Institute
2016-2025
University of Auckland
2019-2025
Helsinki University Hospital
2023
National University of Singapore
2021
NIHR Southampton Biomedical Research Centre
2021
Massachusetts Institute of Technology
2016-2021
Harvard University
2016-2021
Tampere University
2021
Aalto University
2010-2017
“Normal” for the gut microbiota For benefit of future clinical studies, it is critical to establish what constitutes a “normal” microbiome, if exists at all. Through fecal samples and questionnaires, Falony et al. Zhernakova targeted general populations in Belgium Netherlands, respectively. Gut composition correlated with range factors including diet, use medication, red blood cell counts, chromogranin A, stool consistency. The data give some hints possible biomarkers normal communities....
The development of the microbiome from infancy to childhood is dependent on a range factors, with microbial–immune crosstalk during this time thought be involved in pathobiology later life diseases1–9 such as persistent islet autoimmunity and type 1 diabetes10–12. However, our knowledge, no studies have performed extensive characterization early large, multi-centre population. Here we analyse longitudinal stool samples 903 children between 3 46 months age by 16S rRNA gene sequencing (n =...
The gut microbial community is dynamic during the first 3 years of life, before stabilizing to an adult-like state. However, little known about impact environmental factors on developing human microbiome. We report a longitudinal study microbiome based DNA sequence analysis monthly stool samples and clinical information from 39 children, half whom received multiple courses antibiotics life. Whereas most children born by vaginal delivery was dominated Bacteroides species, four cesarean...
Type 1 diabetes (T1D) is an autoimmune disease that targets pancreatic islet beta cells and incorporates genetic environmental factors1, including complex elements2, patient exposures3 the gut microbiome4. Viral infections5 broader dysbioses6 have been identified as potential causes or contributing factors; however, human studies not yet microbial compositional functional triggers are predictive of autoimmunity T1D. Here we analyse 10,913 metagenomes in stool samples from 783 mostly white,...
Inflammatory bowel disease (IBD) is characterized by chronic inflammation of the gastrointestinal tract that associated with changes in gut microbiome. Here, we sought to identify strain-specific functional correlates IBD outcomes.We performed metagenomic sequencing monthly stool samples from 20 patients and 12 controls (266 total samples). These were taxonomically profiled MetaPhlAn2 functionally using HUMAnN2. Differentially abundant species identified MaAsLin pangenome haplotypes analyzed...
Abstract The rapid increase in the number of proteins sequence databases and diversity their functions challenge computational approaches for automated function prediction. Here, we introduce DeepFRI, a Graph Convolutional Network predicting protein by leveraging features extracted from language model structures. It outperforms current leading methods sequence-based Neural Networks scales to size repositories. Augmenting training set experimental structures with homology models allows us...
Significance Type 1 diabetes (T1D) is a major autoimmune disease with increasing incidence in recent years. In this study, we found that the intestinal viromes of cases were less diverse than those controls. We identified eukaryotic viruses and bacteriophage contigs are associated presence or absence autoimmunity. These provide targets for future mechanistic studies to differentiate causal incidental associations between virome protection against development T1D.
A gluten-free diet (GFD) is the most commonly adopted special worldwide. It an effective treatment for coeliac disease and also often followed by individuals to alleviate gastrointestinal complaints. known there important link between gut microbiome, but it largely unknown how a switch GFD affects human microbiome. We studied changes in microbiomes of 21 healthy volunteers who four weeks. collected nine stool samples from each participant: one at baseline, during period, when they returned...
Industrialization has impacted the human gut ecosystem, resulting in altered microbiome composition and diversity. Whether bacterial genomes may also adapt to industrialization of their host populations remains largely unexplored. Here, we investigate extent which rates targets horizontal gene transfer (HGT) vary across thousands strains from 15 spanning a range industrialization. We show that HGTs have accumulated over recent generations HGT occurs at high frequency within individuals....
Gut microbiome dysbiosis has been demonstrated in subjects with newly diagnosed and chronic inflammatory bowel disease (IBD). In this study we sought to explore longitudinal changes ascertain associations between markers of activity treatment outcome. We performed a prospective cohort 19 treatment-naïve pediatric IBD 10 healthy controls, measuring fecal calprotectin assessing the gut via repeated stool samples. Associations clinical characteristics were tested using generalized estimating...
The microbiota in the lumen of patients with Crohn's disease (CD) is characterized by reduced diversity, particularly Firmicutes and Bacteroidetes. It unknown whether introduction intestinal from healthy individuals could correct this dysbiosis reverse mucosal inflammation. We investigated response to fecal microbial transplantation (FMT) subjects active CD. performed a prospective open-label study (uncontrolled) FMT donors A single was colonoscopy. Recipients' T-cell phenotypes, clinical...
Abstract The development of the gut microbiome from birth plays important roles in short- and long-term health, but factors influencing preterm are poorly understood. In present study, we use metagenomic sequencing to analyse 1,431 longitudinal stool samples 123 very infants (<32 weeks’ gestation) who did not develop intestinal disease or sepsis over a study period 10 years. During period, one cohort had no probiotic exposure whereas two cohorts were given different products: Infloran (...
Abstract For the past half-century, structural biologists relied on notion that similar protein sequences give rise to structures and functions. While this assumption has driven research explore certain parts of universe, it disregards spaces don’t rely assumption. Here we areas universe where functions can be achieved by different structures. We predict ~200,000 for diverse from 1,003 representative genomes across microbial tree life annotate them functionally a per-residue basis. Structure...
<h3>Importance</h3> Treatment of pediatric obesity is challenging. Preclinical studies in mice indicated that weight and metabolism can be altered by gut microbiome manipulation. <h3>Objective</h3> To assess efficacy fecal transfer (FMT) to treat adolescent improve metabolism. <h3>Design, Setting, Participants</h3> This randomized, double-masked, placebo-controlled trial (October 2017-March 2019) with a 26-week follow-up was conducted among adolescents aged 14 18 years body mass index (BMI;...