Your gut microbiota are what you eat. Nat Rev Microbiol. 2014;12:8. [PMID: 24336181 DOI: 10.1038/nrmicro3186]

The interaction among gut microbes, the intestinal barrier and short chain fatty acids

The mammalian gut is inhabited by a massive and complicated microbial community, in which the host achieves a stable symbiotic environment through the interdependence, coordination, reciprocal constraints and participation in an immune response. The interaction between the host gut and the microbiota is essential for maintaining and achieving the homeostasis of the organism. Consequently, gut homeostasis is pivotal in safeguarding the growth and development and potential productive performance of the host. As metabolites of microorganisms, short chain fatty acids are not only the preferred energy metabolic feedstock for host intestinal epithelial cells, but also exert vital effects on antioxidants and the regulation of intestinal community homeostasis. Herein, we summarize the effects of intestinal microorganisms on the host gut and the mechanisms of action of short chain fatty acids on the four intestinal barriers of the organism, which will shed light on the manipulation of the intestinal community to achieve precise nutrition for specific individuals and provide a novel perspective for the prevention and treatment of diseases.

Metagenomics assembled genome scale analysis revealed the microbial diversity and genetic polymorphism of Lactiplantibacillus plantarum in traditional fermented foods of Hainan, China

Exploring the microbiome in fermented foods and their effects on food quality and sustainability is beneficial to provide data support for understanding how they affects human physiology. Here, metagenomic sequencing and metagenomic assembled genomes (MAGs) were applied to appraise the microbial diversity of fermented Yucha (FYC) and fermented vegetables (FVE). The antibiotic resistance genes (ARGs) enrichment and genetic polymorphism of Lactiplantibacillus plantarum in fermented foods of different regions were compared. The results showed that Lactiplantibacillus plantarum was the dominant species in FYC, while Lactiplantibacillus fermentum in FVE occupied the dominant position. From 32 high-quality MAGs, the central differential Lactic acid bacteria were higher in FVE. By comparing the Lactiplantibacillus plantarum MAGs in Hainan and Other regions, we found that the total Single Nucleotide Polymorphisms of Lactiplantibacillus plantarum in Hainan were significantly higher than other areas. Six non-synonymous mutations were included in the primary differential mutation, especially TrkA family potassium uptake protein and MerR family transcriptional regulator, which may be related to the hypersaline environment and highest ARGs enrichment in Hainan. This research provides valuable insight into our understanding of the microbiome of fermented food. Meanwhile, the analysis of Lactiplantibacillus plantarum genetic polymorphism based on MAGs helps us understand this strain's evolutionary history.

Gut microbiota in healthy and unhealthy long-living people

The human gut microbiota in long-living people has been characterized, however, its metabolic potential is still largely unknown in this group. In this study, the gut microbiota was assessed in 37 Chinese long-living participants (aged 90 + years) by metagenomic sequencing of stool samples. Participants were categorized into two groups, healthy long-living (n = 28) and unhealthy long-living (n = 9). Gut microbiota composition and function were compared among these two groups. We found that the gut microbiota in the healthy long-living group was significantly separated from the unhealthy group. The healthy long-living group contained a higher abundance of Bacteroidetes and more functional pathways in energy metabolism, glycan biosynthesis and metabolism, metabolism of cofactors and vitamins, and biosynthesis of other secondary metabolites. The unhealthy group contained a higher abundance of Streptococcus and other pathogenic bacteria, and also contained more functional pathways for xenobiotics biodegradation and metabolism than the healthy group. Additionally, the unhealthy group had decreased levels of carbohydrate-active enzymes, including host-glycan and fiber degrading enzymes, and an increase in starch-degrading enzymes. In conclusion, the gut microbiota of unhealthy long-living people contains more pathogenic bacteria, and the overall gut microbiota may be in an unhealthy state, "dysbiosis", which leads to a decrease in carbohydrate digestion, glycan and thiamine (B1) metabolites, and fatty acid biosynthesis.

Gut microbiota influence tumor development and Alter interactions with the human immune system

Recent scientific advances have greatly enhanced our understanding of the complex link between the gut microbiome and cancer. Gut dysbiosis is an imbalance between commensal and pathogenic bacteria and the production of microbial antigens and metabolites. The immune system and the gut microbiome interact to maintain homeostasis of the gut, and alterations in the microbiome composition lead to immune dysregulation, promoting chronic inflammation and development of tumors. Gut microorganisms and their toxic metabolites may migrate to other parts of the body via the circulatory system, causing an imbalance in the physiological status of the host and secretion of various neuroactive molecules through the gut-brain axis, gut-hepatic axis, and gut-lung axis to affect inflammation and tumorigenesis in specific organs. Thus, gut microbiota can be used as a tumor marker and may provide new insights into the pathogenesis of malignant tumors.

Arabinoxylan combined with different glucans improve lipid metabolism disorder by regulating bile acid and gut microbiota in mice fed with high-fat diet

The effect of arabinoxylan (AX) combined with β-glucan and xyloglucan on lipid metabolism by regulating bile acids and gut microbiota was investigated in mice fed with high-fat diet. Fifty male ICR/KM mice were randomly divided into five groups: control diet (CON) group, high-fat diet (HFD) group, high-fat diet with AX (HFAX) group, high-fat diet with AX and β-glucan (HFAB) group, and high-fat diet with AX and xyloglucan (HFAG) group. After 8 weeks of feeding, the mice were sacrificed and samples were collected. In contrast to CON, HFD disturbed lipid metabolism, bile acids, and gut microbiota in mice. Mice in HFD group had increase in weight, blood lipids and liver fat, and circulating bile acid as well as abnormal liver tissue morphology and disordered gut microbiota. Compared with HFD, HFAB and HFAG mice had reduced body weight and cholesterol and triglyceride levels; Fxr was activated, Cyp7a1 was inhibited to reduce bile acids, the microbial species diversity increased, the number of beneficial bacteria increased, and the number of conditional pathogenic bacteria decreased. HFAG uniquely activated intestinal bile acid receptors (Fxr and Tgr5) and increased the abundance of Bacteroidetes and Akkermansia. In summary, the effect of AX compounded glucans (β-glucan or xyloglucan) on lipid metabolism was better than that of single AX by regulating bile acid metabolism and gut microbiota possibly due to the more complex chemical structure of combined polysaccharides.

Intestinal Bacteroides sp. Imbalance Associated With the Occurrence of Childhood Undernutrition in China

Undernutrition (UN) is a worldwide concern affecting morbidity and mortality among children, but the safety and long-term efficacy of its current treatments remain controversial. Recent evidence showing the roles of the gut microbiome (GM) in nutrient absorption indicates its usefulness in alternative interventions to treat UN safely with sustainable amelioration. To enhance our understanding of the GM and childhood undernutrition, we deep sequenced the gut metagenomes of 65 children with moderate or severe undernutrition (UN group) and 61 healthy children (HC group) to identify associated taxa and genes using a two-stage validation scheme. At stage I, 54 UN patients and 51 healthy children were enrolled for the discovery of GM markers in UN children. The accuracy of the markers was then tested in an additional 11 UN patients and 10 healthy children at stage II. Compared to the HC group, the UN group had lower richness in microbial genes (P = 0.005, FDR = 0.005) and species (P = 0.002, FDR = 0.002). The distributions of bacterial genes enable the identification of 16 gene markers with which to discriminate UN patients with high accuracy [averaged areas under the receiver operating curve (AUC) = 0.87], including three Bacteroides uniformis genes that are responsible for the synthesis of iron transporters. We also identified four species markers that enable the UN patients to be confidently discriminated from the HC children (averaged AUC = 0.91), namely Bacteroides ovatus, Bacteroides uniformis, Bacteroides uniformis, and Bacteroides vulgatus. In addition, metabolic comparison showed significantly decreased isobutyric acid (P = 0.005, FDR = 0.017) and increased isovaleric acid (P = 0.006, FDR = 0.017) in UN patients. We also identified notable correlations between microbial species and short-chain fatty acids (SCFAs) and several nutritional indicators, including acetic acid and iron (r = 0.436, P = 0.029), butyric acid and iron (r = 0.422, P = 0.036), butyric acid and lymphocyte (r = -0.309, P = 0.011), and acetic acid and total protein (r = -0.303, P = 0.043). Taken together, the distinct features of gut microbiota in UN patients highlight the taxonomic and functional shift during the development of UN and provide a solid theoretical basis for intervention in childhood undernutrition through gut microbes.

More Pathogenicity or Just More Pathogens?-On the Interpretation Problem of Multiple Pathogen Detections with Diagnostic Multiplex Assays

Modern molecular diagnostic approaches in the diagnostic microbiological laboratory like real-time quantitative polymerase chain reaction (qPCR) have led to a considerable increase of diagnostic sensitivity. They usually outperform the diagnostic sensitivity of culture-based approaches. Culture-based diagnostics were found to be insufficiently sensitive for the assessment of the composition of biofilms in chronic wounds and poorly standardized for screenings for enteric colonization with multi-drug resistant bacteria. However, the increased sensitivity of qPCR causes interpretative challenges regarding the attribution of etiological relevance to individual pathogen species in case of multiple detections of facultative pathogenic microorganisms in primarily non-sterile sample materials. This is particularly the case in high-endemicity settings, where continuous exposition to respective microorganisms leads to immunological adaptation and semi-resistance while considerable disease would result in case of exposition of a non-adapted population. While biofilms in chronic wounds show higher pathogenic potential in case of multi-species composition, detection of multiple pathogens in respiratory samples is much more difficult to interpret and asymptomatic enteric colonization with facultative pathogenic microorganisms is frequently observed in high endemicity settings. For respiratory samples and stool samples, cycle-threshold-value-based semi-quantitative interpretation of qPCR results has been suggested. Etiological relevance is assumed if cycle-threshold values are low, suggesting high pathogen loads. Although the procedure is challenged by lacking standardization and methodical issues, first evaluations have led to promising results. Future studies should aim at generally acceptable quantitative cut-off values to allow discrimination of asymptomatic colonization from clinically relevant infection.

Gut microbiota and allogeneic transplantation

The latest high-throughput sequencing technologies show that there are more than 1000 types of microbiota in the human gut. These microbes are not only important to maintain human health, but also closely related to the occurrence and development of various diseases. With the development of transplantation technologies, allogeneic transplantation has become an effective therapy for a variety of end-stage diseases. However, complications after transplantation still restrict its further development. Post-transplantation complications are closely associated with a host's immune system. There is also an interaction between a person's gut microbiota and immune system. Recently, animal and human studies have shown that gut microbial populations and diversity are altered after allogeneic transplantations, such as liver transplantation (LT), small bowel transplantation (SBT), kidney transplantation (KT) and hematopoietic stem cell transplantation (HTCT). Moreover, when complications, such as infection, rejection and graft versus host disease (GVHD) occur, gut microbial populations and diversity present a significant dysbiosis. Several animal and clinical studies have demonstrated that taking probiotics and prebiotics can effectively regulate gut microbiota and reduce the incidence of complications after transplantation. However, the role of intestinal decontamination in allogeneic transplantation is controversial. This paper reviews gut microbial status after transplantation and its relationship with complications. The role of intervention methods, including antibiotics, probiotics and prebiotics, in complications after transplantation are also discussed. Further research in this new field needs to determine the definite relationship between gut microbial dysbiosis and complications after transplantation. Additionally, further research examining gut microbial intervention methods to ameliorate complications after transplantation is warranted. A better understanding of the relationship between gut microbiota and complications after allogeneic transplantation may make gut microbiota as a therapeutic target in the future.

Human colon-derived soluble factors modulate gut microbiota composition

The commensal microbiota modulates immunological and metabolic aspects of the intestinal mucosa contributing to development of human gut diseases including inflammatory bowel disease. The host/microbiota interaction often referred to as a crosstalk, mainly focuses on the effect of the microbiota on the host neglecting effects that the host could elicit on the commensals. Colonic microenvironments from three human healthy controls (obtained from the proximal and distal colon, both in resting conditions and after immune – IL-15- and microbiota – LPS-in vitro challenges) were used to condition a stable fecal population. Subsequent 16S rRNA gene-based analyses were performed to study the effect induced by the host on the microbiota composition and function. Non-supervised principal component analysis (PCA) showed that all microbiotas, which had been conditioned with colonic microenvironments clustered together in terms of relative microbial composition, suggesting that soluble factors were modulating a stable fecal population independently from the treatment or the origin. Our findings confirmed that the host intestinal microenvironment has the capacity to modulate the gut microbiota composition via yet unidentified soluble factors. These findings indicate that an appropriate understanding of the factors of the host mucosal microenvironment affecting microbiota composition and function could improve therapeutic manipulation of the microbiota composition.

Application of metagenomics in the human gut microbiome

There are more than 1000 microbial species living in the complex human intestine. The gut microbial community plays an important role in protecting the host against pathogenic microbes, modulating immunity, regulating metabolic processes, and is even regarded as an endocrine organ. However, traditional culture methods are very limited for identifying microbes. With the application of molecular biologic technology in the field of the intestinal microbiome, especially metagenomic sequencing of the next-generation sequencing technology, progress has been made in the study of the human intestinal microbiome. Metagenomics can be used to study intestinal microbiome diversity and dysbiosis, as well as its relationship to health and disease. Moreover, functional metagenomics can identify novel functional genes, microbial pathways, antibiotic resistance genes, functional dysbiosis of the intestinal microbiome, and determine interactions and co-evolution between microbiota and host, though there are still some limitations. Metatranscriptomics, metaproteomics and metabolomics represent enormous complements to the understanding of the human gut microbiome. This review aims to demonstrate that metagenomics can be a powerful tool in studying the human gut microbiome with encouraging prospects. The limitations of metagenomics to be overcome are also discussed. Metatranscriptomics, metaproteomics and metabolomics in relation to the study of the human gut microbiome are also briefly discussed.