Junjie Qin's research while affiliated with IT University of Copenhagen and other places

Publications (47)

Article
Full-text available
Most current approaches for analyzing metagenomic data rely on comparisons to reference genomes, but the microbial diversity of many environments extends far beyond what is covered by reference databases. De novo segregation of complex metagenomic data into specific biological entities, such as particular bacterial strains or viruses, remains a lar...
Article
Full-text available
doi:10.1038/nature09944 and corrigendum 474, 666 (2011); doi:10.1038/nature10187 It has been drawn to our attention that the methods described in the main text and the Supplementary Information of this Article have been considered by some researchers to be insufficient to enable them to identify enterotypes in their own data sets. Enterotypes were...
Article
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We are facing a global metabolic health crisis provoked by an obesity epidemic. Here we report the human gut microbial composition in a population sample of 123 non-obese and 169 obese Danish individuals. We find two groups of individuals that differ by the number of gut microbial genes and thus gut bacterial richness. They contain known and previo...
Article
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The human gut microbiota is a reservoir of antibiotic resistance genes, but little is known about their diversity and richness within the gut. Here we analyse the antibiotic resistance genes of gut microbiota from 162 individuals. We identify a total of 1,093 antibiotic resistance genes and find that Chinese individuals harbour the highest number a...
Article
Full-text available
We are facing a global metabolic health crisis provoked by an obesity epidemic. Here we report the human gut microbial composition in a population sample of 123 non-obese and 169 obese Danish individuals. We find two groups of individuals that differ by the number of gut microbial genes and thus gut bacterial richness. They contain known and previo...
Data
Raw and high quality read and base statistics for the three metagenomic data sets used in this study. (DOCX)
Data
Maximum computational resources and processing time required for each processing step, for each of the datasets used in this article. (DOC)
Data
Comparison of mapping rates of 5′ untrimmed and 5′ trimmed reads. (DOCX)
Data
Mapping used when summarizing the estimated abundances for the simulated metagenome. (DOC)
Article
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MOCAT is a highly configurable, modular pipeline for fast, standardized processing of single or paired-end sequencing data generated by the Illumina platform. The pipeline uses state-of-the-art programs to quality control, map, and assemble reads from metagenomic samples sequenced at a depth of several billion base pairs, and predict protein-coding...
Data
Reference sequences to which reads from the even HMP mock community were mapped. (DOCX)
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Aligned raw reads form the mock community to known Illumina adapters. (DOCX)
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Output files and statistics from each of the processing steps in MOCAT. (DOCX)
Data
Number of raw and high quality (HQ) bases and reads, calculated Kmer size, and the computational resources (RAM and HDD) required to assemble the 124 fecal metagenomics samples. (DOCX)
Article
Full-text available
Guinea pig (Cavia porcellus) is an important model for human intestinal research. We have characterized the faecal microbiota of 60 guinea pigs using Illumina shotgun metagenomics, and used this data to compile a gene catalogue of its prevalent microbiota. Subsequently, we compared the guinea pig microbiome to existing human gut metagenome data fro...
Data
Figure S1.a) Gene rarefaction curve showing that the number of new genes decreases with each sample added. b) Comparative assignment of human and guine pig samples to their respective gene catalogue (H-H, G-G) and cross species assignment fractions (G-H, H-G).
Data
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Figure S2. Sample-wise rarefaction curves for guinea pig and human samples on a) genus and b) COG data. On these two data levels, differences in richness are significantly different on the highest rarefaction depth (3.5*106).
Data
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Figure S3. Phylogenetic assignment of guinea pig and human metagenomic reads using Blast with an identity cutoff of 95% against bacterial database. Question marks designates reads that were not assignable to a bacterial genome.
Data
Table S1. Significantly different genera (q < 0.1, p < 0.05) between human and guinea pig gut microbiome. The depth taxonomic of taxonomic classification is not consistent (due to the PhymmBL algorithm) and this is marked by “?” if the phylogenetic level could not be determined with high confidence.
Data
Table S2. Significant functional differences (q < 0.1) between guinea pig and human gut microbiome. These were summarized in five Worksheets: COG categories, KEGG module subsubcategories, SEED categories, SEED families and MetaCyc.
Data
Table S3. Assembly statistics for the 8 guinea pig metagenomes, each based on samples from 7 or 8 individual animals. ‘Matched Reads’ designates the number of reads that could be matched to the non-redundant contig set. These were used for subsequent results on functional or phylogenetic characteristics.
Article
Full-text available
Assessment and characterization of gut microbiota has become a major research area in human disease, including type 2 diabetes, the most prevalent endocrine disease worldwide. To carry out analysis on gut microbial content in patients with type 2 diabetes, we developed a protocol for a metagenome-wide association study (MGWAS) and undertook a two-s...
Article
Full-text available
Assessment and characterization of gut microbiota has become a major research area in human disease, including type 2 diabetes, the most prevalent endocrine disease worldwide. To carry out analysis on gut microbial content in patients with type 2 diabetes, we developed a protocol for a metagenome-wide association study (MGWAS) and undertook a two-s...
Article
Species in genus Nannochloropsis are promising candidates for both biofuel and biomass production due to their ability to accumulate rich fatty acids and grow fast; however, their sexual reproduction has not been studied. It is clear that the construction of their metabolic pathways, such as that of polyunsaturated fatty acid (PUFA) biosynthesis, a...
Article
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An outbreak caused by Shiga-toxin–producing Escherichia coli O104:H4 occurred in Germany in May and June of 2011, with more than 3000 persons infected. Here, we report a cluster of cases associated with a single family and describe an open-source genomic analysis of an isolate from one member of the family. This analysis involved the use of rapid,...
Article
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An outbreak caused by Escherichia coli serotype O104:H4 strains has hit northern Germany since May 2011, with 3,222 patients infected and 39 of them died until June 18 (4).…
Article
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With the rapid development of next-generation sequencing techniques, metagenomics, also known as environmental genomics, has emerged as an exciting research area that enables us to analyze the microbial environment in which we live. An important step for metagenomic data analysis is the identification and taxonomic characterization of DNA fragments...
Article
Full-text available
Our knowledge of species and functional composition of the human gut microbiome is rapidly increasing, but it is still based on very few cohorts and little is known about variation across the world. By combining 22 newly sequenced faecal metagenomes of individuals from four countries with previously published data sets, here we identify three robus...
Article
Full-text available
Our knowledge of species and functional composition of the human gut microbiome is rapidly increasing, but it is still based on very few cohorts and little is known about variation across the world. By combining 22 newly sequenced faecal metagenomes of individuals from four countries with previously published data sets, here we identify three robus...
Article
We thank Brantingham et al. for their interest in our study; we agree that both molecular and archaeological evidence should be used to understand the demographic history of the Tibetan people. Our Report focused not on the demographic history of the Tibetan population, but rather the selection
Article
A major challenge in the human metagenomics field is to identify associations of the bacterial genes and human phenotypes and act to modulate microbial populations in order to improve human health and wellbeing. MetaHIT project addresses this ambitious challenge by developing and integrating a number of necessary approaches within the context of th...
Article
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Residents of the Tibetan Plateau show heritable adaptations to extreme altitude. We sequenced 50 exomes of ethnic Tibetans, encompassing coding sequences of 92% of human genes, with an average coverage of 18× per individual. Genes showing population-specific allele frequency changes, which represent strong candidates for altitude adaptation, were i...
Article
Full-text available
To understand the impact of gut microbes on human health and well-being it is crucial to assess their genetic potential. Here we describe the Illumina-based metagenomic sequencing, assembly and characterization of 3.3 million non-redundant microbial genes, derived from 576.7 gigabases of sequence, from faecal samples of 124 European individuals. Th...
Conference Paper
Full-text available
Limited by the laboratory technique, traditional microorganism research usually focuses on one single individual species. This significantly limits the deep analysis of intricate biological processes among complex microorganism communities. With the rapid development of genome sequencing techniques, the traditional research methods of microorganism...
Article
Full-text available
Here we integrate the de novo assembly of an Asian and an African genome with the NCBI reference human genome, as a step toward constructing the human pan-genome. We identified approximately 5 Mb of novel sequences not present in the reference genome in each of these assemblies. Most novel sequences are individual or population specific, as reveale...
Article
Bombyx mori, the domesticated silkworm, is a major insect model for research, and the first lepidopteran for which draft genome sequences became available in 2004. Two independent data sets from whole-genome shotgun sequencing were merged and assembled together with newly obtained fosmid- and BAC-end sequences. The remarkably improved new assembly...
Article
Full-text available
Here we present the first diploid genome sequence of an Asian individual. The genome was sequenced to 36-fold average coverage using massively parallel sequencing technology. We aligned the short reads onto the NCBI human reference genome to 99.97% coverage, and guided by the reference genome, we used uniquely mapped reads to assemble a high-qualit...
Article
Full-text available
TreeFam (http://www.treefam.org) was developed to provide curated phylogenetic trees for all animal gene families, as well as orthologue and paralogue assignments. Release 4.0 of TreeFam contains curated trees for 1314 families and automatically generated trees for another 14,351 families. We have expanded TreeFam to include 25 fully sequenced anim...

Citations

... Despite the importance of the gut microbiome, community composition varies significantly among host species, populations, and individuals (Benson et al., 2010;Yatsunenko et al., 2012;Brooks et al., 2016;Rehman et al., 2016;Amato et al., 2019). While a portion of this variation is expected to be selectively neutral, alterations of the gut microbiome are on the one hand linked to numerous human diseases (Carding et al., 2015;Lynch and Pedersen, 2016), including diabetes (Qin, 2012), inflammatory bowel disease (IBD) (Ott et al., 2004;Gevers et al., 2014), and mental disorders (Clapp et al., 2017). On the other hand, there is evidence that the gut microbiome can play an important role in adaptation on both recent (Hehemann et al., 2010;Suzuki and Ley, 2020b) and ancient evolutionary timescales (Rausch et al., 2019). ...
... However, a minor but statistically lower bacterial diversity was observed in toddlers with ASD compared to controls [71]. In particular, a low prevalence of Prevotella, a commensal microorganism involved in the metabolism of saccharides and in the biosynthesis of vitamins [72], was detected in salivary and dental samples of individuals with ASD [71]. ...
... 49 Predicted genes were clustered using BLAT by single linkage. 50 Genes were clustered if there was at least a 95% sequence similarity and at least 90% of the shorter gene was covered. This created a nonredundant gene catalog. ...
... Here, when microbial communities are sampled, they are found to vary either in the taxa present, or (more commonly) in the relative frequency of members of different taxa. In humans, initial analysis suggested the existence of 'enterotypes'—the microbial communities found within guts of different individuals cluster into three main community types[30]. While the presence of discrete clusters is under debate, the existence of inter-individual variation is not. ...
... Until the age of two, the process of microbiota maturation and stabilization is complete and it is defined for a lifetime, except in an extreme host changes and conditions (Sekirov, Russell, Antunes, & Finlay, 2010). In childhood, diet preference is the main tool that shapes the healthy microbiome with proper dynamics and this remains unchanged in adulthood (Dethlefsen, Eckburg, Bik, & Relman, 2006;Ehrlich, 2010;Lozupone, Stombaugh, Gordon, Jansson, & Knight, 2012). ...
... Adiposity, dyslipidemia, and insulin resistance are known to increase the risk of developing CMD. 1 Studies focusing on gut microbiota analysis have shown that such deleterious phenotypes are associated with low gut microbiota gene richness. 2 Furthermore, studies comparing geographically distinct populations, both close and distant, have shown that an increased consumption of fruits and vegetables, thus higher quantity in dietary fiber intake, is associated with higher gut microbiota diversity. [3][4][5][6][7] In overweight and obese subjects initially presenting a low gene count, a short-term energy-restricted diet including an increased quantity of dietary fibers, partly restored gut microbiota richness in parallel to improvement of the cardiometabolic profile. ...
... 101 Despite these limitations, strong correlations with phenotypic and clinical signals support the utility of sequence homology-based analyses of ARG for the interrogation of the abundance and distribution of ARGs in bacterial communities. [1][2][3]27,52,102 Another limitation in gut resistome studies is the nearly-exclusive profiling of stool samples as a proxy for the intestinal community. However, stool samples can differ significantly in microbial composition from the gut itself, and these community differences can lead to differences in ARG detection and quantification. ...
... CTX-M-55, CTX-M-79, CTX-M-15, and TEM have been identified not only in animals but also in humans and the environment (57)(58)(59). Evidence has shown that antibiotic resistance genes and antibiotic-resistant bacteria can spread to humans via contaminated meat, house dust, manure, and waste water discharge (60)(61)(62). Meanwhile, direct evidence has shown the environmental transmission of antibiotic resistance genes and their bacterial hosts among livestock and humans (63). ...
... Stratifying the patient cohort according to health status and feeding type showed no differences in microbial composition and bacterial diversity ( Supplementary Figure 1 C, D). Additionally, patients' comorbidities and disease history was tested for confounding, considering type 2 diabetes, 26,27 inflammatory bowel disease, 28 cancer, as well as chemotherapy and immunotherapy 29 within 6 months before stool sampling, or bowel resection 30 (Supplementary Table 3). We further tested whether age and gender, specific SARS-CoV-2 treatment (remdesivir, convalescent plasma, intravenous immunoglobulins, or baricitinib), immunosuppressive therapy, or secondary infections introduced bias in the microbial analysis. ...
... Besides human beings, A. muciniphila is also found in the gut of other mammals such as guinea pigs, swines and rabbits (31)(32)(33). The effects of A. muciniphila on obesity and metabolic disorders have been widely discussed. ...