A gene catalogue of the Sprague-Dawley rat gut metagenome

Pan, Hudan; Guo, Ruijin; Zhu, Jun; Wang, Qi; Ju, Yanmei; Xie, Ying; Zheng, Yanfang; Wang, Zhifeng; Li, Ting; Liu, Zhongqiu; Lu, Linlin; Li, Fēi; Tong, Bin; Xiao, Liang; Xu, Xun; Li, Runze; Yuan, Zhongwen; Yang, Huanming; Wang, Jian; Kristiansen, Karsten; Jia, Huijue; Liu, Liang

doi:10.1093/gigascience/giy055

Cited by 68 publications

(66 citation statements)

References 36 publications

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“…The universally present species were Streptococcus thermophilus and Bifidobacterium animalis instead of commonly tested probiotics from Lactobacillus . An orally administered strain of B. longum has been shown to persist in 30% of individuals for at least 6 months 87 , while we failed to detect in feces an L. casei strain gavaged to rats 88, 89 , suggesting general differences between Bifidobacterium and Lactobacillus . The strains used by Zmora et al included a number of Lactobacillus , Bifidobacterium , as well as Streptococcus and Lactococcus , all detectable in various gastrointestinal sites despite laxative and colonoscopy 11 .…”

Section: Discussioncontrasting

confidence: 61%

A multi-omic cohort as a reference point for promoting a healthy human gut microbiome

Jie

Liang

Ding

et al. 2019

Preprint

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1 More than a decade of gut microbiome studies have a common goal for human 2 health. As most of the disease studies sample the elderly or the middle-aged, a 3 reference cohort for young individuals has been lacking. It is also not clear what 4 other omics data need to be measured to better understand the gut microbiome.5 Here we present high-depth metagenomic shotgun sequencing data for the fecal 6 microbiome together with other omics data in a cohort of 2,183 adults, and observe 7 a number of vitamins, hormones, amino acids and trace elements to correlate with 8 the gut microbiome and cluster with T cell receptors. Associations with physical 9 fitness, sleeping habits and dairy consumption are identified in this large multi-omic 1 0 cohort. Many of the associations are validated in an additional cohort of 1,404 1 1 individuals. Our comprehensive data are poised to advise future study designs to 1 2 better understand and manage our gut microbiome both in population and in 1 3 mechanistic investigations.

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Section: Discussioncontrasting

confidence: 61%

A multi-omic cohort as a reference point for promoting a healthy human gut microbiome

Jie

Liang

Ding

et al. 2019

Preprint

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“…Interestingly, the two new RA dental markers appeared more abundant in control saliva samples. The strongest marker from healthy saliva remained Lactococcus lactis 5 , and Lactobacillus paracasei, Streptococcus infantarius, w ere identified, reminiscent of beneficial effects of L. casei gavage in rat model of RA 42, 43 . The assembled genomes allowed matching of different species in the Veillonella genus as RA saliva markers.…”

Section: Resultsmentioning

confidence: 98%

Over 50000 metagenomically assembled draft genomes for the human oral microbiome reveal new taxa

Zhu

Liang

Chen

et al. 2019

Preprint

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21The oral cavity of each person is home for hundreds of bacterial species. While 22 taxa for oral diseases have been well studied using culture-based as well as 23 amplicon sequencing methods, metagenomic and genomic information remain 24 scarce compared to the fecal microbiome. Here we provide metagenomic shotgun 25 data for 3346 oral metagenomics samples, and together with 808 published 26 samples, assemble 56,213 metagenome-assembled genomes (MAGs). 64% of the 27 3,589 species-level genome bins contained no publicly available genomes, others 28 with only a handful. The resulting genome collection is representative of samples 29 around the world and across physiological conditions, contained many genomes 30 from Candidate phyla radiation (CPR) which lack monoculture, and enabled 31 discovery of new taxa such as a family within the Acholeplasmataceae order. 32 New biomarkers were identified for rheumatoid arthritis or colorectal cancer, 33 which would be more convenient than fecal samples. The large number of 34 metagenomic samples also allowed assembly of many strains from important 35 oral taxa such as Porphyromonas and Neisseria. Predicted functions enrich in 36 drug metabolism and small molecule synthesis. Thus, these data lay down a 37 genomic framework for future inquiries of the human oral microbiome. 38 39The human microbiome has been implicated in a growing number of diseases. 40The majority of microbial cells is believed to reside in the large intestine 1 and cohorts 41 with fecal metagenomic data contain over 1000 individuals 2, 3 . For the oral 42 microbiome, hundreds of metagenomic shotgun-sequenced samples have been 43 available from the Human Microbiome Project (HMP) and for rheumatoid arthritis 4-6 . 44A number of other diseases studied by Metagenome-wide association studies (MWAS) 45 using gut microbiome data also indicated potential contribution from the oral 46 microbiome in disease etiology 7-12 . Although the MWAS on rheumatoid arthritis was 47 the oral microbiome is believed to be well covered by culturing 13 , and analyses by 54 16S rRNA gene amplicon sequencing or polymerase chain reaction (PCR) are 55 common. Recently published large-scale metagenomic assembly efforts mostly 56 included fecal metagenomic data [14][15][16] . It is not clear how much is really missing for 57 the oral microbiome. The saliva, in particular, seems to have more bacterial species 58 per individual than the fecal microbiome 17 . 59After getting contigs using assembly algorithms suitable for metagenomic 60 data 18 , a central idea used by metagenomic binning algorithms is that genes or contigs 61 that co-vary in abundance among many samples belong to the same microbial 62 genome 8,[19][20][21] . Large cohorts are therefore prerequisites for high-quality assembly. 63Here we present 3346 new oral metagenomic samples, and 56,213 64 metagenome-assembled genomes (MAGs) which represent 3,589 species-level clades, 65revealing new taxa as well as substantially complementing the genomic content of 66 known species. This ...

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“…On the basis that the overlap between microbial genes in rats and humans is larger than between mice and humans and that 97% of the functional pathways in the human catalog are present in the rat catalog (48), we here established an experimental arthritis model in rats rather than mice to obtain more convincing conclusions. According to the results of metagenomic shotgun sequencing and a metagenome‐wide association study, patients with RA exhibit gut microbiota dysbiosis (7, 8, 49).…”

Section: Discussionmentioning

confidence: 99%

The gut microbiota modulator berberine ameliorates collagen‐induced arthritis in rats by facilitating the generation of butyrate and adjusting the intestinal hypoxia and nitrate supply

Yue

Yu²,

Fang³

et al. 2019

The FASEB Journal

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The commensal microbiota is one of the environmental triggers of rheumatoid arthritis (RA). Recent studies have identified the characteristics of the gut microbiota in patients with RA. However, it is still unclear how the microbiota can be modulated to slow down disease progression. In the present study, berberine, a modulator of gut microbiota with substantial anti‐RA effect, was chosen to explore the mechanisms by which the microbiota modulators ameliorate RA. The results showed that oral administration of berberine alleviated collagen‐induced arthritis (CIA) in rats in a gut microbiota‐dependent manner. Berberine down‐regulated the diversity and richness of the gut bacteria, reduced the abundance of Prevotella, and elevated the abundance of butyrate‐producing bacteria in CIA rats as determined by the 16S rRNA gene sequence, which might function through limiting the generation of nitrate and stabilizing the physiologic hypoxia in the intestine. Moreover, berberine treatment significantly increased the intestinal butyrate level and promoted the expression and activity of butyryl‐CoA:acetate‐CoA transferase (BUT). The coadministration of a BUT inhibitor largely diminished the adjustment of intestinal environment and the antiarthritic effect of berberine. In conclusion, modulators of the gut microbiota might serve as therapeutic agents for RA by inducing the butyrate generation through promoting the expression and activity of BUT.—Yue, M., Tao, Y., Fang, Y., Lian, X., Zhang, Q., Xia, Y., Wei, Z., Dai, Y. The gut microbiota modulator berberine ameliorates collagen‐induced arthritis in rats by facilitating the generation of butyrate and adjusting the intestinal hypoxia and nitrate supply. FASEB J. 33,12311‐12323 (2019). http://www.fasebj.org

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A gene catalogue of the Sprague-Dawley rat gut metagenome

Cited by 68 publications

References 36 publications

A multi-omic cohort as a reference point for promoting a healthy human gut microbiome

A multi-omic cohort as a reference point for promoting a healthy human gut microbiome

Over 50000 metagenomically assembled draft genomes for the human oral microbiome reveal new taxa

The gut microbiota modulator berberine ameliorates collagen‐induced arthritis in rats by facilitating the generation of butyrate and adjusting the intestinal hypoxia and nitrate supply

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