Background A major bottleneck in the use of metagenome sequencing for human gut
microbiome studies has been the lack of a comprehensive genome collection to be used as a …

The recent introduction of metagenome-assembled genomes (MAGs) has marked a major
milestone in the human gut microbiome field (Almeida et al., 2019; Nayfach et al., 2019; …

Butyrate and propionate represent two of three main short-chain fatty acids produced by the
intestinal microbiota. In healthy populations, their levels are reportedly equimolar, whereas a …

We present a novel liquid array diagnostics (LAD) method, which enables rapid and inexpensive
detection of microbial markers in a single-tube multiplex reaction. We evaluated LAD …

The microbial species residing in the human gut exercise vital functions for the host. They
produce different metabolites that are crucial for human wellbeing. A variety of such molecules …

Genomics research has greatly increased understanding of the human gut microbiome, but
the existing reference databases remain insu cient, failing to map up to half of the sequences …

Background Traditional gene annotation methods rely on characteristics that may not be
available in short reads generated from next generation technology, resulting in suboptimal …

… To Pranvera Hiseni, I can never thank you enough for all your help, time, patience and
engagement in this project. Our discussions have been priceless, as they always challenged my …

… I would also like to thank Pranvera Hiseni, co-supervisor from GA, for good conversations,
feedback, and guidance throughout the project. Additionally, thanks to the GA team for their …

… We thank Dylan Maghini and Boryana Doyle for thoughtful comments on the manuscript,
Stephen Nayfach and Pranvera Hiseni for helpful conversations, Jakob Wirbel for testing Phanta…