scholarly journals Analysis of metagenome-assembled genomes from the mouse gut microbiota reveals distinctive strain-level characteristics

2020 ◽  
Author(s):  
Shenghui Li ◽  
Siyi Zhang ◽  
Bo Li ◽  
Shanshan Sha ◽  
Jian Kang ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Ribosomal Rna ◽  
Strain Level ◽  
Gut Contents ◽  
Gut Content ◽  
Gut Flora ◽  
Human Gut ◽  
Gene Catalogue ◽  
Taxonomic Characterization ◽  
Mouse Gut Microbiota

AbstractThe laboratorial mouse harbors a unique gut microbiota with potential value for human microbiota-associated studies. Mouse gut microbiota has been explored at the genus and species levels, but features rarely been showed at the strain level. The identification of 833,051 and 658,438 nonredundant genes of faeces and gut content samples from the laboratorial C57/BL mice showed over half of these genes were newly found compared to the previous mouse gut microbial gene catalogue. Metagenome-assembled genomes (MAGs) was used to reconstruct 46 nonredundant MAGs belonging to uncultured specieses. These MAGs included members across all phyla in mouse gut (i.e. Firmicutes, Bacteroidetes, Proteobacteria, Deferribacteres, Verrucomicrobia, and Tenericutes) and allowed a strain-level delineating of the mouse gut microbiota. Comparison of MAGs with human gut colonies revealed distinctive genomic and functional characteristics of mouse’s Bacteroidetes and Firmicutes strains. Genomic characteristics of rare phyla in mouse gut microbiota were demonstrated by MAG approach, including strains of Mucispirillum schaedleri, Parasutterella excrementihominis, Helicobacter typhlonius, and Akkermansia muciniphila.ImportanceThe identification of nonredundant genes suggested the existence of unknown microbes in the mouse gut samples. The metagenome-assembled genomes (MAGs) instantiated the specificity of mouse gut species and revealed an intestinal microbial correlation between mouse and human. The cultivation of faeces and gut contents sample validated the existence of MAGs and estimate their accuracy. Full-length 16S ribosomal RNA gene sequencing enabled taxonomic characterization. This study highlighted a unique ecosystem in the gut of laboratorial mice that obviously differed with the human gut flora at the strain level. The outcomes may be beneficial to researches based on laboratorial mouse models.

Molecular biological methods for studying the gut microbiota: the EU human gut flora project

2002 ◽  
Vol 87 (6) ◽  
pp. 203-211 ◽  
Author(s):  
Blaut M.* ◽  
M.D. Collins ◽  
G.W. Welling ◽  
J. Doré ◽  
J. van Loo ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gut Flora ◽  
Human Gut ◽  
Biological Methods ◽  
The Eu

scholarly journals Galactooligosaccharides and Xylo-oligosaccharides Altering the Caecal Microbiome, Metabolome, and Transcriptome of Chickens Revealed by a Multi-Omics Analysis

2021 ◽  
Author(s):  
Chaowu Yang ◽  
Mohan Qiu ◽  
Chunlin Yu ◽  
Han Peng ◽  
Xiaoyan Song ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Meat Quality ◽  
Myristic Acid ◽  
Transcriptome Sequencing ◽  
Underlying Mechanism ◽  
Gut Contents ◽  
Chicken Breast ◽  
Gut Content ◽  
Flavor Compound ◽  
Different Levels

Abstract Backgroud Studies have shown that prebiotics could affect meat quality, but the underlying mechanism are poorly understood. This study aimed to investigate whether prebiotics affect chicken’s meat quality through gut microbiome and metabolome. Methods The gut content were collected from chickens fed with or without prebiotics (galactooligosaccharides or xylo-oligosaccharides) and subjected to microbiome and metabolome analyses, and chicken breast was performed transcriptome sequencing. Results The prebiotics altered proportions of microbiota in gut contents at different levels, especially microbiota in the phylum of Bacteroidetes and Firmicutes, such as genus of Alistipes, Bacteroides, and Faecalibacterium. The prebiotics also altered contents of caecal metabolites such as lysophosphatidylcholine (lysoPC), intramuscular fat and flavor compound (Benzaldehyde and myristic acid). Differentially expressed genes (DEGs) induced by prebiotics were significantly involved in regulation of lipolysis inadipocytes and adipocytokine signaling pathway. Changes in gut microbiota and metabolites were remarkably correlated such as Bacteroidetes and Firmicutes was respectively positively and negatively correlated with lysoPC. DEGs were also interacted with caecal metabolites. Conclusion These findings integrated and incorporated link among gut microbiota, metabolites and transcriptome, which proposed prebiotics may affect meat quality and flavor of chickens.

scholarly journals Bacterial Atlas of Mouse Gut Microbiota

2021 ◽  
Author(s):  
Mengqi Chu ◽  
Xiaobo Zhang
Keyword(s):  
Complex System ◽  
Gut Microbiota ◽  
Bacterial Communities ◽  
Large Scale ◽  
Gut Bacteria ◽  
Human Gut ◽  
The Core ◽  
Human Gut Microbiota ◽  
Human Immunity ◽  
Mouse Gut Microbiota

Abstract Background: Mouse model is one of of the most widely used animal models for exploring the roles of human gut microbiota, a complex system involving in human immunity and metabolism. However, the structure of mouse gut bacterial community has not been explored at a large scale. To address this concern, the diversity and composition of the gut bacteria of 600 mice was characterized in this study. Results: The results showed that the bacteria belonging to 8 genera were found in the gut microbiota of all mouse individuals, indicating that the 8 bacteria were the core bacteria of mouse gut microbiota. The dominant genera of the mouse gut bacteria contained 15 bacterial genera. It was found that the bacteria in the gut microbiota were mainly involved in host’s metabolisms via the collaborations between the gut bacteria. The further analysis demonstrated that the composition of mouse gut microbiota was similar to that of human gut microbiota. Conclusion: Our study presented a bacterial atlas of mouse gut microbiota, providing a solid basis for investing the bacterial communities of mouse gut microbiota.

Strain-level functional variation in the human gut microbiota based on bacterial binding to artificial food particles

2021 ◽  
Vol 29 (4) ◽  
pp. 664-673.e5
Author(s):  
Michael L. Patnode ◽  
Janaki L. Guruge ◽  
Juan J. Castillo ◽  
Garret A. Couture ◽  
Vincent Lombard ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Strain Level ◽  
Human Gut ◽  
Functional Variation ◽  
Artificial Food ◽  
Human Gut Microbiota ◽  
Bacterial Binding ◽  
Food Particles

scholarly journals Comprehensive mouse gut metagenome catalog reveals major difference to the human counterpart

2021 ◽  
Author(s):  
Silas Kieser ◽  
Evgeny M. Zdobnov ◽  
Mirko Trajkovski
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
New Order ◽  
Human Gut ◽  
Rarefaction Analysis ◽  
Human Counterpart ◽  
The Impact ◽  
Human And Mouse ◽  
Gut Metagenome ◽  
Mouse Gut Microbiota

AbstractMouse is the most used model for studying the impact of microbiota on its host, but the repertoire of species from the mouse gut microbiome remains largely unknown. Here, we construct a Comprehensive Mouse Gut Metagenome (CMGM) catalog by assembling all currently available mouse gut metagenomes and combining them with published reference and metagenome-assembled genomes. The 50’011 genomes cluster into 1’699 species, of which 78.1% are uncultured, and we discovered 226 new genera, 7 new families, and 1 new order. Rarefaction analysis indicates comprehensive sampling of the species from the mouse gut. CMGM enables an unprecedented coverage of the mouse gut microbiome exceeding 90%. Comparing CMGM to the human gut microbiota shows an overlap 64% at the genus, but only 16% at the species level, demonstrating that human and mouse gut microbiota are largely distinct.

In vitro study of the interaction between human gut microbiota and herbal extracts using willow bark extract as an example

Planta Medica ◽  
2016 ◽  
Vol 81 (S 01) ◽  
pp. S1-S381
Author(s):  
EM Pferschy-Wenzig ◽  
K Koskinen ◽  
C Moissl-Eichinger ◽  
R Bauer
Keyword(s):  
Gut Microbiota ◽  
In Vitro Study ◽  
Vitro Study ◽  
Bark Extract ◽  
Herbal Extracts ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
Willow Bark

Metabolization of the herbal combination STW-5 by human gut microbiota in vitro

2017 ◽  
Author(s):  
EM Pferschy-Wenzig ◽  
A Roßmann ◽  
K Koskinen ◽  
H Abdel-Aziz ◽  
C Moissl-Eichinger ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Human Gut ◽  
Human Gut Microbiota

Substrate use prioritization by a coculture of five species of gut bacteria fed mixtures of arabinoxylan, xyloglucan, β-glucan, and pectin

2020 ◽  
Author(s):  
Y Liu ◽  
AL Heath ◽  
B Galland ◽  
N Rehrer ◽  
L Drummond ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Dietary Fiber ◽  
Plant Cell Wall ◽  
Bacterial Species ◽  
Short Chain ◽  
Emergent Properties ◽  
Human Gut ◽  
Fermentation Products ◽  
Plant Polysaccharides ◽  
Human Gut Microbiota

© 2020 American Society for Microbiology. Dietary fiber provides growth substrates for bacterial species that belong to the colonic microbiota of humans. The microbiota degrades and ferments substrates, producing characteristic short-chain fatty acid profiles. Dietary fiber contains plant cell wall-associated polysaccharides (hemicelluloses and pectins) that are chemically diverse in composition and structure. Thus, depending on plant sources, dietary fiber daily presents the microbiota with mixtures of plant polysaccharides of various types and complexity. We studied the extent and preferential order in which mixtures of plant polysaccharides (arabinoxylan, xyloglucan, β-glucan, and pectin) were utilized by a coculture of five bacterial species (Bacteroides ovatus, Bifidobacterium longum subspecies longum, Megasphaera elsdenii, Ruminococcus gnavus, and Veillonella parvula). These species are members of the human gut microbiota and have the biochemical capacity, collectively, to degrade and ferment the polysaccharides and produce short-chain fatty acids (SCFAs). B. ovatus utilized glycans in the order β-glucan, pectin, xyloglucan, and arabinoxylan, whereas B. longum subsp. longum utilization was in the order arabinoxylan, arabinan, pectin, and β-glucan. Propionate, as a proportion of total SCFAs, was augmented when polysaccharide mixtures contained galactan, resulting in greater succinate production by B. ovatus and conversion of succinate to propionate by V. parvula. Overall, we derived a synthetic ecological community that carries out SCFA production by the common pathways used by bacterial species for this purpose. Systems like this might be used to predict changes to the emergent properties of the gut ecosystem when diet is altered, with the aim of beneficially affecting human physiology. This study addresses the question as to how bacterial species, characteristic of the human gut microbiota, collectively utilize mixtures of plant polysaccharides such as are found in dietary fiber. Five bacterial species with the capacity to degrade polymers and/or produce acidic fermentation products detectable in human feces were used in the experiments. The bacteria showed preferential use of certain polysaccharides over others for growth, and this influenced their fermentation output qualitatively. These kinds of studies are essential in developing concepts of how the gut microbial community shares habitat resources, directly and indirectly, when presented with mixtures of polysaccharides that are found in human diets. The concepts are required in planning dietary interventions that might correct imbalances in the functioning of the human microbiota so as to support measures to reduce metabolic conditions such as obesity.

Sign in / Sign up

Export Citation Format

Share Document