A5083768969- Gut microbiota and health
- Microbial Community Ecology and Physiology
- Genomics and Phylogenetic Studies
- Diet and metabolism studies
- Clostridium difficile and Clostridium perfringens research
- Oral microbiology and periodontitis research
- Probiotics and Fermented Foods
- Bacteriophages and microbial interactions
- Insect symbiosis and bacterial influences
- Protist diversity and phylogeny
- Metabolism and Genetic Disorders
- Oral Health Pathology and Treatment
- Salivary Gland Disorders and Functions
- RNA and protein synthesis mechanisms
- Methane Hydrates and Related Phenomena
- Genetics, Bioinformatics, and Biomedical Research
- Birth, Development, and Health
- Mosquito-borne diseases and control
- RNA modifications and cancer
- Clinical Nutrition and Gastroenterology
- Inorganic Chemistry and Materials
- Mycobacterium research and diagnosis
- Colorectal Cancer Screening and Detection
- Machine Learning in Bioinformatics
- Microbial Metabolic Engineering and Bioproduction
Marine Biological Laboratory
2016-2025
Max Planck Institute for Marine Microbiology
2023-2025
Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung
2023-2025
Helmholtz Institute for Functional Marine Biodiversity
2022-2025
Carl von Ossietzky Universität Oldenburg
2022-2025
University of Chicago
2015-2024
University of Calgary
2021
Wellcome Centre for Mitochondrial Research
2018
University of Newcastle Australia
2018
Newcastle University
2018
We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of Minimum Information about Any (x) Sequence (MIxS). The a Single Amplified Genome (MISAG) Metagenome-Assembled (MIMAG), including, but not limited to, assembly quality, estimates completeness contamination. These can be used in combination with other GSC checklists, including (MIGS), Metagenomic (MIMS), Marker Gene (MIMARKS). Community-wide...
Advances in high-throughput sequencing and 'omics technologies are revolutionizing studies of naturally occurring microbial communities. Comprehensive investigations lifestyles require the ability to interactively organize visualize genetic information incorporate subtle differences that enable greater resolution complex data. Here we introduce anvi'o, an advanced analysis visualization platform offers automated human-guided characterization genomes metagenomic assemblies, with interactive...
Bacteria comprise the most diverse domain of life on Earth, where they occupy nearly every possible ecological niche and play key roles in biological chemical processes. Studying composition ecology bacterial ecosystems understanding their function is prime importance. High-throughput sequencing technologies enable comprehensive descriptions diversity through 16S ribosomal RNA gene amplicons. Analyses these communities generally rely upon taxonomic assignments reference databases, or...
Abstract Molecular microbial ecology investigations often employ large marker gene datasets, for example, ribosomal RNAs, to represent the occurrence of single-cell genomes in communities. Massively parallel DNA sequencing technologies enable extensive surveys libraries that sometimes include nearly identical sequences. Computational approaches rely on pairwise sequence alignments similarity assessment and de novo clustering with facto thresholds partition high-throughput datasets constrain...
Although recent research revealed an impact of westernization on diversity and composition the human gut microbiota, exact consequences metacommunity characteristics are insufficiently understood, underlying ecological mechanisms have not been elucidated. Here, we compared fecal microbiota adults from two non-industrialized regions in Papua New Guinea (PNG) with that United States (US) residents. Guineans harbor communities greater bacterial diversity, lower inter-individual variation,...
Abstract Nitrogen fixation in the surface ocean impacts global marine nitrogen bioavailability and thus microbial primary productivity. Until now, cyanobacterial populations have been viewed as main suppliers of bioavailable this habitat. Although PCR amplicon surveys targeting nitrogenase reductase gene revealed existence diverse non-cyanobacterial diazotrophic populations, subsequent quantitative suggest that they generally occur low abundance. Here, we use state-of-the-art metagenomic...
Pangenomes offer detailed characterizations of core and accessory genes found in a set closely related microbial genomes, generally by clustering based on sequence homology. In comparison, metagenomes facilitate highly resolved investigations the relative distribution genomes individual across environments through read recruitment analyses. Combining these complementary approaches can yield unique insights into functional basis niche partitioning fitness, however, advanced software solutions...
The Human Microbiome Project provided a census of bacterial populations in healthy individuals, but an understanding the biomedical significance this has been hindered by limited taxonomic resolution. A high-resolution method termed oligotyping overcomes limitation evaluating individual nucleotide positions using Shannon entropy to identify most information-rich positions, which then define oligotypes. We have applied comprehensively analyze oral microbiome. Using 16S rRNA gene sequence data...
Consensus between independent reads improves the accuracy of genome and transcriptome analyses, however lack consensus very similar sequences in metagenomic studies can often does represent natural variation biological significance. The common use machine-assigned quality scores on next generation platforms not necessarily correlate with accuracy. Here, we describe using overlap paired-end, short sequence to identify error-prone marker gene analyses their contribution spurious OTUs following...
ABSTRACT Bacteria living on the aerial parts of plants (the phyllosphere) are globally abundant and ecologically significant communities can have effects their plant hosts. Despite importance, little is known about ecological processes that drive phyllosphere dynamics. Here, we describe development bacterial over time model Arabidopsis thaliana in a controlled greenhouse environment. We used large number replicate to identify repeatable dynamics community assembly reconstructed history by...
ABSTRACT Molecular characterizations of the gut microbiome from individual human stool samples have identified community patterns that correlate with age, disease, diet, and other characteristics, but resources for marker gene studies consider trends among populations scale number individuals sampled each population. As an alternative strategy sampling populations, we examined whether sewage accurately reflects microbial a mixture samples. We used oligotyping high-throughput 16S rRNA...
OBJECTIVES: Exploring associations between the gut microbiota and colonic inflammation assessing sequential changes during exclusive enteral nutrition (EEN) may offer clues into microbial origins of Crohn’s disease (CD). METHODS: Fecal samples (n=117) were collected from 23 CD 21 healthy children. From children fecal before, EEN, when patients returned to their habitual diets. Microbiota composition functional capacity characterized using sequencing 16SrRNAgene shotgun metagenomics. RESULTS:...
The advent of next-generation DNA sequencing platforms has revolutionized molecular microbial ecology by making the detailed analysis complex communities over time and space a tractable research pursuit for small groups. However, ability to generate 105–108 reads with relative ease brings it many downstream complications. Beyond computational resources skills needed process analyze data, is difficult compare datasets in an intuitive interactive manner that leads hypothesis generation...
We introduce DESMAN for De novo Extraction of Strains from Metagenomes. Large multi-sample metagenomes are being generated but strain variation results in fragmentary co-assemblies. Current algorithms can bin contigs into metagenome-assembled genomes unable to resolve strain-level variation. identifies variants core genes and uses co-occurrence across samples link haplotypes abundance profiles. These then searched against non-core determine the accessory genome each strain. validated on a...
Abstract Introduction Microbial residents of the human oral cavity have long been a major focus microbiology due to their influence on host health and intriguing patterns site specificity amidst lack dispersal limitation. However, determinants niche partitioning in this habitat are yet be fully understood, especially among taxa that belong recently discovered branches microbial life. Results Here, we assemble metagenomes from tongue dental plaque samples multiple individuals reconstruct 790...
To explore differences in the vaginal microbiome between preterm and term deliveries.Nested case-control study 3D cohort (design, develop, discover).Quebec, Canada.Ninety-four women with spontaneous birth as cases [17 early (<34 weeks) 77 late (34-36 birth] 356 controls delivery (≥37 weeks).To assess by sequencing V4 region of 16S ribosomal RNA (rRNA) gene swabs self-collected during pregnancy.Comparison relative abundance bacterial operational taxonomic units oligotypes identifying...
Marine planktonic eukaryotes play critical roles in global biogeochemical cycles and climate. However, their poor representation culture collections limits our understanding of the evolutionary history genomic underpinnings ecosystems. Here, we used 280 billion