Featured Research

The publications below have been authored or co-authored by members of the Clinical-Microbiomics team and showcases some of our capabilities within microbiome research, including host-microbiome interactions in health and disease and development of novel bioinformatics methods. We invite you to explore this research further and see how the microbiome can impact your own scientific efforts.

Transcriptional interactions suggest niche segregation among microorganisms in the human gut Plichta DR et al., Nature Microbiology. 2016 Aug 26; 16152

Human gut microbes impact host serum metabolome and insulin sensitivity Pedersen HK*, Gudmundsdottir V*, Nielsen HB*, Hyotylainen T*, Nielsen T* et al., (* contributed equally to this work). Nature. 2016 Jul 21;535(7612):376-81

Capturing one of the human gut microbiome’s most wanted: reconstructing the genome of a novel butyrate-producing, clostridial scavenger from metagenomic sequence data P. Jeraldo et al., Front Microbiol. 2016 May 26;7:783

Disentangling disease- and drug signatures of the human gut microbiome: the case of type 2 diabetes mellitus K. Forslund et al., Nature. 2015 Dec 10;528(7581):262-6

Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago Rasmussen S et al., Cell. 2015 Oct 22;163(3):571-82

A catalog of the mouse gut metagenome Xiao L et al., Nat Biotechnol. 2015 Oct;33(10):1103-8

A Retrospective Metagenomics Approach to Studying Blastocystis Andersen LO et al., FEMS Microbiol Ecol. 2015 Jul;91(7). pii: fiv072

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes Nielsen HB et al., Nat Biotechnol. 2014 Aug;32(8):822-8

An integrated catalog of reference genes in the human gut microbiome Li J et al., Nat Biotechnol. 2014 Aug;32(8):834-41

Metagenomic species profiling using universal phylogenetic marker genes Sunagawa S et al., Nat Methods. 2013 Dec;10(12):1196-9

Richness of human gut microbiome correlates with metabolic markers Le Chatelier E et al., Nature. 2013 Aug 29;500(7464):541-6

Transcriptome profiling of mice testes following low dose irradiation Belling KC et al., Reprod Biol Endocrinol. 2013 May 28;11:50

Transcriptome responses to combinations of stresses in Arabidopsis Rasmussen S et al., Plant Physiol. 2013 Apr;161(4):1783-94

The chemical interactome space between the human host and the genetically defined gut metabotypes Jacobsen UP et al., ISME J. 2013 Apr;7(4):730-42

A comparative analysis of the intestinal metagenomes present in guinea pigs (Cavia porcellus) and humans (Homo sapiens) Hildebrand F et al., BMC Genomics. 2012 Sep 28;13:514

FARO server: Meta-analysis of gene expression by matching gene expression signatures to a compendium of public gene expression data Manijak MP, Nielsen HB, BMC Res Notes. 2011 Jun 11;4:181

Enterotypes of the human gut microbiome Arumugam M et al., Nature. 2011 May 12;473(7346):174-80

A human gut microbial gene catalogue established by metagenomic sequencing Qin J et al., Nature. 2010 Mar 4;464(7285):59-65

The transcriptionally active regions in the genome of Bacillus subtilis Rasmussen S et al., Nielsen HB, Jarmer H, Mol Microbiol. 2009 Sep;73(6):1043-57