How informative is the mouse for human gut microbiota research?

As an important part of ecosystem, microbes are widely distributed in various habitats. In recent years, more and more attention has been paid to the study on gut microbiota. The gut microbiota and their metabolites influence human and animal nutrition processing, metabolic balance, immune function, gastrointestinal development and other physiological activities. With the deepening of studies on human and animal gut microbiota, it has been found that some factors, such as diet, age, gender, and living environment, impacting on the composition of gut microbiota, while the differences among animal species have more significant influence on the gut microbiota composition. In relatively primitive grassland ecosystems, soil microbes interact with human and animal activities. On the one hand, microbes in the soil environment are the driving forces for the transformation and circulation of organic matter and nutrients. The improvement of soil microbial community diversity is beneficial for the soil fertility. On the other hand, human and animal activities will affect the diversity of soil microbial community. Although there are a lot of researches on soil microbiota, animal and human gut microbiota, their differences in diversity and composition within the same environment have not been studied. The advent of sequencing technology provides an effective mean for the accurate and comprehensive understanding of microbes, especially for the study of uncultivable microorganisms. The PacBio single-molecule real-time (SMRT) technology is advantageous in producing long sequence reads with high accuracy. Based on sequencing the full length 16S rRNA genes, the microbiota composition can be identified to the species level. Therefore, it is an effective approach for studying microbial diversity. We collected 56 stool and soil samples from Xilinguole, including 6, 10, 11, 9, and 10 stool samples from human, goat, cattle, horse, and sheep, respectively, as well as 10 soil samples. Genomic DNA was extracted from the samples. After DNA extraction and quality check, the 16S rRNA genes of all samples were amplified from the genomic DNA. The PCR products were sequenced using the PacBio RS II instrument. The QIIME software (V1.7) was used to analyze the sequencing data, and the R software (version 3.5.0) was used to further analyze and visualize the results. Firstly, it was found that the gut microbiota diversity of human was significantly lower than other samples ( P 0.01). The overall composition of the human and animal gut microbiota were dominated by the Firmicutes and Bacteroidetes phyla. However, the soil microbiota was dominated by Proteobacteria and Acidobacteria. At the genus level, the sheep, goat and cattle gut microbiota were dominated by Clostridium , Bacteroides , and Oscillibacter , while the horse gut microbiota was mainly composed of Clostridium , Eubacterium , and Treponema . The soil microbiota was composed mainly of Blastocatella and Bacillus . The human gut microbiota comprised much of Veillonella , Clostridium , Escherichia/Shigella . At the species level, the human gut microbiota mainly contained Escherichia/Shigella , dysenteriae , Streptococcus salivarius . The sheep, goat, cattle, and horse gut microbiota were dominated by Oscillibacter valericigenes and Eubacterium coprostanoligenes . The major species in soil were Blastocatella fastidiosa and Bacillus longiquaesitum . Moreover, principal coordinate analysis (PCoA) and hierarchical clustering analysis showed some differences in the microbiota structure among human gut, animal gut and soil samples. The gut microbiota structure was similar among cattle, goats and sheep. They were more different from the samples collected from human, horse and soil. We classified all samples into four clusters. Cluster 1 only included human samples; cluster 2 comprised the horse samples; cluster 3 was consisted of the sheep, goat, and cattle samples; while cluster 4 contained only the soil samples. Lastly, we identified the discriminatory OTUs and assigned them taxonomically to the species level. In conclusion, there were significant differences between animal gut microbiota and soil microbiota. The soil microbiota was more complex. As an omnivore, human gut microbiota diversity was significantly lower than other herbivorous animal (namely cattle, goat, horse and sheep). Although cattle, sheep, goat and horses are all herbivorous animals, the distinct features of the digestive systems could contribute to the difference in gut microbiota composition of horse from those of sheep, goat and cattle. This study revealed the differences of gut microbiota diversity between human and other animals, as well as from the soil microbial community. This work has laid a theoretical foundation for further studies on microbial diversity in different habitats.

The Gut Microbiome in Health and Disease

Influence of the co-exposure of microplastics and tetrabromobisphenol A on human gut: Simulation in vitro with human cell Caco-2 and gut microbiota

The human gut microbiota is a complex ecosystem consisting of trillions of microorganisms that symbiotically inhabit the human gut. Through the production of a number of metabolites, they perform many important metabolic functions that complement mammalian enzyme activity and play an essential role in digestion. Interindividual variability in the structure of the microbiota and hence the expression of its genes (microbiome) has been largely explained by diet. Nutrition affects the composition and function of the microbiota with short- and long-term effects. Although an extensive number of studies are available, the molecular mechanisms underlying these effects still remain incompletely understood. In this article, we summarized and concretized the available data on the effects of diet on the composition of the gut microbiota. Nutrition has short- and long-term effects on microbial colonies, accomplishing a profound impact on human health. In fact, diet-induced changes in the microbiota are progressively associated not only with human physiology but also with chronic diseases, including obesity, immune, metabolic and inflammatory bowel diseases. The relationship between human health, gut microbiota and nutrition represents one of the most promising and challenging topics for researchers. Indeed, the microbiota is a dynamic community undergoing changes according to dietary habits throughout the human lifespan and has a great metabolic potential to act on pharmacological targets and bioactive compounds.

In a majority of the solar/thermal studies to date, a utility economic methodology has been used to assess the potential of solar power systems. The utility sector is precluded from taking advantage of loan leveraging because the effective rate of return is artificially set. Utilities are regulated by public commissions and thus must finance new capital investments according to a prescribed set of rules on after tax cost of capital and fixed charge rates. Commercial ventures have no such externally imposed constraints and make decisions for capital expenditures which include the effect of loan leveraging. The relevant parameters for a commercial institution are interest rate on debt, a discount rate which accounts for risk, and the effect of favorable tax incentives. An expression is developed for a capital cost factor which contains these parameters. Results are shown for various downpayments and discount rates. It will be shown that the effect of loan leveraging can be substantial in affecting the penetration of solar process heat into the commercial energy market. In addition, the relation between loan leveraging and risk is investigated.

BackgroundSulfoquinovose (SQ) is a green-diet-derived sulfonated glucose and a selective substrate for a limited number of human gut bacteria. Complete anaerobic SQ degradation via interspecies metabolite transfer to sulfonate-respiring bacteria produces hydrogen sulfide, which has dose- and context-dependent health effects. Here, we studied potential SQ degradation by the mammalian host and the impact of SQ supplementation on human and murine gut microbiota diversity and metabolism.Results13CO2 breath tests with germ-free C57BL/6 mice gavaged with 13C-SQ were negative. Also, SQ was not degraded by human intestinal cells in vitro, indicating that SQ is not directly metabolized by mice and humans. Addition of increasing SQ concentrations to human fecal microcosms revealed dose-dependent responses of the microbiota and corroborated the relevance of Agathobacter rectalis and Bilophila wadsworthia in cooperative degradation of SQ to hydrogen sulfide via interspecies transfer of 2,3-dihydroxy-1-propanesulfonate (DHPS). Similar to the human gut microbiome, the genetic capacity for SQ or DHPS degradation is sparsely distributed among bacterial species in the gut of conventional laboratory mice. Escherichia coli and Enterocloster clostridioformis were identified as primary SQ degraders in the mouse gut. SQ and DHPS supplementation experiments with conventional laboratory mice and their intestinal contents showed that SQ was incompletely catabolized to DHPS. Although some E. clostridioformis genomes encode an extended sulfoglycolytic pathway for both SQ and DHPS fermentation, SQ was only degraded to DHPS by a mouse-derived E. clostridioformis strain.ConclusionsOur findings suggest that SQ is solely a nutrient for the gut microbiota and not for mice and humans, emphasizing its potential as a prebiotic. SQ degradation by the microbiota of conventional laboratory mice differs from the human gut microbiota by absence of DHPS degradation activity. Hence, the microbiota of conventional laboratory mice does not fully represent the SQ metabolism in humans, indicating the need for alternative model systems to assess the impact of SQ on human health. This study advances our understanding of how individual dietary compounds shape the microbial community structure and metabolism in the gut and thereby potentially influence host health.Video Supplementary InformationThe online version contains supplementary material available at 10.1186/s40168-025-02175-x.

To explore the effect of ultra-strong static magnetic field on gut microbiota, 16 T static magnetic field was used to study the changes in the structure and composition of human and mouse gut microbiota in this environment. In the mouse gut microbiota, at the genus level, the magnetic field significantly decreased the relative abundances of Escherichia-Shigella, Lactobacillus, Enterococcus, Burkholderia-Caballeronia-Paraburkholderia, Parasutterella, and Ralstonia and significantly increased those of Parabacteroides, Alloprevotella, Alistipes, Odoribacter, Bacteroides, Mucispirillum, Sutterella, and Prevotellaceae_UCG-001. Similarly, at the genus level, the relative abundances of Bacteroides, Parabacteroides, Romboutsia, and Streptococcus significantly decreased in the human gut microbiota. Contrary to the changing trend of the abundance in the mouse gut, the abundances of Bacteroides and Parabacteroides in the human gut were significantly reduced under magnetic field. The BugBase phenotypic prediction analysis showed that the relative abundances of five phenotypes, including anaerobism, mobile elements, potential pathogenicity, stress-tolerant, and biofilm formation, changed significantly in the mouse gut microbiota, while the relative abundances of two phenotypes, including Gram-positive and Gram-negative phenotypes, changed significantly in the human gut microbiota. The 16 T magnetic field could differently affect the composition, structure, and phenotypes of gut microbiota in human and mice, suggesting the importance of model selection in studying the biological effects of magnetic field.

Bile Acids as Modulators of Gut Microbiota Linking Dietary Habits and Inflammatory Bowel Disease: A Potentially Dangerous Liaison

Eliminating Pathobionts With Bacteriophages: A Novel Approach to Reduce Gut Inflammation in Inflammatory Bowel Diseases?

Effects of oral antibiotics and isotretinoin on the murine gut microbiota

BackgroundLittle is known regarding the pool of mobile genetic elements associated with the human gut microbiome. In this study we employed the culture independent TRACA system to isolate novel plasmids from the human gut microbiota, and a comparative metagenomic analysis to investigate the distribution and relative abundance of functions encoded by these plasmids in the human gut microbiome.ResultsNovel plasmids were acquired from the human gut microbiome, and homologous nucleotide sequences with high identity (>90%) to two plasmids (pTRACA10 and pTRACA22) were identified in the multiple human gut microbiomes analysed here. However, no homologous nucleotide sequences to these plasmids were identified in the murine gut or environmental metagenomes. Functions encoded by the plasmids pTRACA10 and pTRACA22 were found to be more prevalent in the human gut microbiome when compared to microbial communities from other environments. Among the most prevalent functions identified was a putative RelBE toxin-antitoxin (TA) addiction module, and subsequent analysis revealed that this was most closely related to putative TA modules from gut associated bacteria belonging to the Firmicutes. A broad phylogenetic distribution of RelE toxin genes was observed in gut associated bacterial species (Firmicutes, Bacteroidetes, Actinobacteria and Proteobacteria), but no RelE homologues were identified in gut associated archaeal species. We also provide indirect evidence for the horizontal transfer of these genes between bacterial species belonging to disparate phylogenetic divisions, namely Gram negative Proteobacteria and Gram positive species from the Firmicutes division.ConclusionsThe application of a culture independent system to capture novel plasmids from the human gut mobile metagenome, coupled with subsequent comparative metagenomic analysis, highlighted the unexpected prevalence of plasmid encoded functions in the gut microbial ecosystem. In particular the increased relative abundance and broad phylogenetic distribution was identified for a putative RelBE toxin/antitoxin addiction module, a putative phosphohydrolase/phosphoesterase, and an ORF of unknown function. Our analysis also indicates that some plasmids or plasmid families are present in the gut microbiomes of geographically isolated human hosts with a broad global distribution (America, Japan and Europe), and are potentially unique to the human gut microbiome. Further investigation of the plasmid population associated with the human gut is likely to provide important insights into the development, functioning and evolution of the human gut microbiota.

The gut microbiota plays a key role in the maintenance of healthy gut function as well as many other aspects of health. High-throughput sequence analyses have revealed the composition of the gut microbiota, showing that there is a core signature to the human gut microbiota, as well as variation in its composition between people. The gut microbiota of animals is also being investigated. We are interested in the relationship between bacterial taxa of the human gut microbiota and those in the gut microbiota of domestic and semi-wild animals. While it is clear that some human gut bacterial pathogens come from animals (showing that human – animal transmission occurs), the extent to which the usually non-pathogenic commensal taxa are shared between humans and animals has not been explored. To investigate this we compared the distal gut microbiota of humans, cattle and semi-captive chimpanzees in communities that are geographically sympatric in Uganda. The gut microbiotas of these three host species could be distinguished by the different proportions of bacterial taxa present. We defined multiple operational taxonomic units (OTUs) by sequence similarity and found evidence that some OTUs were common between human, cattle and chimpanzees, with the largest number of shared OTUs occurring between chimpanzees and humans, as might be expected with their close physiological similarity. These results show the potential for the sharing of usually commensal bacterial taxa between humans and other animals. This suggests that further investigation of this phenomenon is needed to fully understand how it drives the composition of human and animal gut microbiotas.

Gut Microbiota and Its Possible Relationship With Obesity

Human gut microbiota is the complex community of microorganisms that live in the digestive tracts, including bacteria, archaea, virus, fungi and protists. These microorganisms coevolved together with human body for a long history, forming a balanced micro-ecosystem. Recent researches discovered the close association between gut microbiota and human health. The gut microbiota was thought to be the biggest endocrine organ, which keeps and restores human health by regulating the its composition and structure. Dysregulation in the composition and diversity of microbiota (dysbiosis) is closely associated with diverse metabolism and immune disorders, such as diabetes, allergy, autoimmunity, and gastrointestinal inflammatory disorders. Thus, a balanced network between gut microbiota and human body will be of great help for diagnosis, treatment and prognosis in the field of precision medicine. Gut microbiota also interacts with diet to degrade nutrients and provide additional nutrients. Meanwhile, faecal bacteria can exert a fundamental role in modulating energy metabolism. Studies have shown that in obesity individuals, the gut microbiota composition can be significantly different from that of lean individuals, and that modifications of gut microbiota composition can be associated with increases or reductions of body weight and body mass index. On the other hand, gut bacterial was related with nutrients absorption. Such as, decreased abundance of Lactobacillus maybe relate with iron (Fe) deficiency, which indicated the intimate connection between gut microbiota and nutrients. Development of nutriology has contributed greatly to human health. A well-balanced diet is the basis for a healthy life. Both the western diet and special diets can have a relevant impact on the microbiome and promote the development of various diseases. An increasing in food-related disorders in recent years, largely associated with dramatic changes in food consumption trends and main nutrients. Nutrition has a very special influence on the microbiome as it is an important factor throughout age. Gut bacteria are specialized in the fermentation of various substrates, thus, complex diets can lead to a number of metabolic products, especially vitamins and SCFAs, which are important to human health. Dietary-associated changes in compositional and functional microbiota traits should be correlated with the health status for the future development of dietary recommendations and potential clinical interventions. We have realized the close relationship between human body, gut microbiota, nutrients and immunity, which will bring an unprecedented opportunity for developing precision nutrition. This review will focus on the gut microbiota, nutrition and health. Due to rapid advances in this inter-discipline, we here only choose several facets to discuss.

The human genome codes for approximately 23,000 genes,1 yet some experts have suggested that the total information coded by the human genome alone is not enough to carry out all of the body’s biological functions.2 A growing number of studies suggest that part of what determines how the human body functions may be not only our own genes, but also the genes of the trillions of microorganisms that reside on and in our bodies. The genomes of the bacteria and viruses of the human gut alone are thought to encode 3.3 million genes.3 “The genetic richness and complexity of the bugs we carry is much richer than our own,” says Jayne Danska, an immunologist at the Hospital for Sick Children Research Institute in Ontario, Canada. “They serve as a buffer and interpreter of our environment. We are chimeric organisms.” Figure 1 False-color scanning electron micrograph shows the surface of the colon mucosa with pink clusters of rod-shaped bacteria, possibly Escherichia coli, attached. The genomes of the bacteria and viruses of the human gut alone are thought to encode 3.3 million ... A role for gut microbes in gastrointestinal function has been well documented since researchers first described differences in the fecal bacteria of people with inflammatory bowel disease.4 The molecular mechanisms responsible for the gut microbiome’s impact on metabolism and diseases throughout the body remain largely unknown. However, researchers are beginning to decipher how the microorganisms of the human intestinal tract influence biological functions beyond the gut and play a role in immunological, metabolic, and neurological diseases.