The microbiome, which has been defined as ‘the ecological community of commensal, symbiotic and pathogenic microorganisms that share our body space, may be distinguished from the microbiota as it includes the collective genomes. An increasing level of evidence reveals that the human microbiome plays a major role in health. For this reason, it is often referred to as the ‘forgotten organ.’ All surfaces of the human body that are exposed to the environment are colonized, including skin, respiratory system, urogenital tract and gastrointestinal (GI) tract, totaling at least 100 trillion microbial cells. The known roles of the GI microbiome include metabolic functions, synthesis functions, and immune roles. Recent studies indicate that the human gut microbiome plays a significant role in health and disease. Dysbiosis, defined as a pathological imbalance in a microbial community, is becoming increasingly appreciated as a ‘central environmental factor’ that is both associated with complex phenotypes and affected by host genetics, diet, and antibiotic use. More recently, a link has been established between the dysmetabolism of bile acids (BAs) in the gut and the gut-liver axis, and this relationship with the microbiome has been highlighted. This review summarizes the microbiome of the hepatobiliary system and how microbiome is related to diseases of the liver and biliary tract.
Bile Acids and Salts ; Biliary Tract ; Biota ; Colon ; Diet ; Dysbiosis ; Gallbladder ; Gastrointestinal Microbiome ; Genetics ; Genome ; Human Body ; Humans ; Liver ; Microbiota* ; Pancreas ; Phenotype ; Respiratory System ; Skin

BACKGROUND/AIMS: Recently, a number of studies have reported that the gut microbiota could contribute to human conditions, including obesity, inflammation, cancer development, and behavior. We hypothesized that the composition and distribution of gut microbiota are different according to stool frequency, and attempted to identify the association between gut microbiota and stool frequency. METHODS: We collected fecal samples from healthy individuals divided into 3 groups according to stool frequency: group 1, a small number of defecation (≤2 times/wk); group 2, normal defecation (1 time/day or 1 time/2 day); and group 3, a large number of defecation (≥2–3 times/day). We evaluated the composition and distribution of the gut microbiota in each group via 16S rRNA-based taxonomic profiling of the fecal samples. RESULTS: Fecal samples were collected from a total of 60 individuals (31 men and 29 women, aged 34.1±5.88 years), and each group comprised 20 individuals. The microbial richness of group 1 was significantly higher than that of group 3 and tended to decrease with increasing number of defecation (P<0.05). The biological community composition was fairly different according to the number of defecation, and Bacteroidetes to Firmicutes ratio was higher in group 1 than in the other groups. Moreover, we found specific strains at the family and genus levels in groups 1 and 3. CONCLUSIONS: Bacteroidetes to Firmicutes ratio and the abundance of Bifidobacterium were different according to the stool frequency, and specific bacteria were identified in the subjects with large and small numbers of defecation, respectively. These findings suggest that stool frequency might be associated with the richness and community composition of the gut microbiota.
Bacteria ; Bacteroidetes ; Bifidobacterium ; Biota ; Defecation ; Feces ; Female ; Firmicutes ; Gastrointestinal Microbiome ; Humans ; Inflammation ; Male ; Obesity

OBJECTIVETo study the effects of Chrysanthemum morifolium based on functional diversity in soil microbial community with different cropping system and fertilization and offer scientific basis for the establishment of the reasonable planting patterns.

METHODCombined yield and quality of Ch. morifolium, 8 treatments of different cropping system and fertilization on functional diversity in soil microbial community of Ch. morifolium were investigated by the Biolog.

RESULTThe AWCD of Ch. morifolium paddy-dryland rotation was higher than that of the continuous cropping, the AWCD of organic fertilizer and compound NPK > single organic fertilizer > single compound NPK > no fertilizer. The principal component analysis about Ch. morifolium soil microbial carbon source use showed that the contribution rate of principal component 1 was 45.5% and principal component 2 was 12.1%, which could explain most information about the variation. Different cropping system of Ch. morfolium differentiated in principal component 1 axis, different fertilization differentiated in principal component 2 axis. The yield of Ch. morifolium and volatile oil content paddy-dryland rotation was significantly higher than that of continuous cropping.

CONCLUSIONThe Ch. morifolium should be cultivated with organic fertilizer and compound NPK by paddy-dryland rotation patters.

Four strains of Penicillium and Talaromyces species are described and illustrated in an inventory of fungal species belonging to Eurotiales. The strains, CNUFC-DDS17-1, CNUFC-DDS27-1, CNUFC-PTM72-1, and CNUFC-YJW3-31, were isolated from soil and freshwater samples from South Korea. Based on their morphological characteristics and sequence analyses by the combined β-tubulin and calmodulin gene, the CNUFC-DDS17-1, CNUFC-DDS27-1, CNUFC-PTM72-1, and CNUFC-YJW3-31 isolates were identified as Penicillium pasqualense, Penicillium sanguifluum, Talaromyces apiculatus, and Talaromyces liani, respectively. The designated strains were found to represent a previously undescribed species of Korean fungal biota. In this study, detailed morphological descriptions and phylogenetic relationships of these species are provided.
Biota ; Calmodulin ; Eurotiales ; Fresh Water ; Korea ; Penicillium ; Sequence Analysis ; Soil ; Talaromyces

This study analyzed the distribution of endophytic fungi in 3 coastal environments with different climatic, geographical, and geological characteristics: the volcanic islands of Dokdo, the East Sea, and the West Sea of Korea. The isolated fungal endophytes were characterized and analyzed with respect to the characteristics of their host environments. For this purpose, we selected common native coastal halophyte communities from three regions. Molecular identification of the fungal endophytes showed clear differences among the sampling sites and halophyte host species. Isolates were also characterized by growth at specific salinities or pH gradients, with reference to previous geographical, geological, and climate studies. Unlike the East Sea or West Sea isolates, some Dokdo Islands isolates showed endurable traits with growth in high salinity, and many showed growth under extremely alkaline conditions. A smaller proportion of West Sea coast isolates tolerate compared to the East Sea or Dokdo Islands isolates. These results suggest that these unique fungal biota developed through a close interaction between the host halophyte and their environment, even within the same halophyte species. Therefore, this study proposes the application of specific fungal resources for restoring sand dunes and salt-damaged agricultural lands and industrialization of halophytic plants.
Biota ; Climate ; Endophytes ; Fungi ; Islands ; Korea ; Proton-Motive Force ; Salinity ; Salt-Tolerant Plants

There are a large number of natural microbial communities in nature. Different populations inside the consortia expand the performance boundary of a single microbial population through communication and division of labor, reducing the overall metabolic burden and increasing the environmental adaptability. Based on engineering principles, synthetic biology designs or modifies basic functional components, gene circuits, and chassis cells to purposefully reprogram the operational processes of the living cells, achieving rich and controllable biological functions. Introducing this engineering design principle to obtain structurally well-defined synthetic microbial communities can provide ideas for theoretical studies and shed light on versatile applications. This review discussed recent progresses on synthetic microbial consortia with regard to design principles, construction methods and applications, and prospected future perspectives.
Microbial Consortia/genetics* ; Synthetic Biology ; Microbiota ; Models, Theoretical

The human body is actually a super-organism that is composed of 10 times more microbial cells than our body cells. Metagenomic study of the human microbiome has demonstrated that there are 3.3 million unique genes in human gut, 150 times more genes than our own genome, and the bacterial diversity analysis showed that about 1000 bacterial species are living in our gut and a majority of them belongs to the divisions of Firmicutes and Bacteriodetes. In addition, most people share a core microbiota that comprises 50-100 bacterial species when the frequency of abundance at phylotype level is not considered, and a core microbiome harboring more than 6000 functional gene groups is present in the majority of human gut surveyed till now. Gut bacteria are not only critical for regulating gut metabolism, but also important for host immune system as revealed by animal studies.
Animals ; Biota ; Cell Culture Techniques ; Digestive System ; immunology ; microbiology ; Digestive System Diseases ; microbiology ; Humans ; Immune System ; Metagenome ; Obesity ; microbiology ; Symbiosis

Aims: The present study investigated the biodegradation and removal of dye mixture (Remazol Brilliant Violet 5R and Reactive Red 120) using a new bacterial consortium isolated from dye-contaminated soil. Methodology and results: Among the total 15 isolates screened, the two most efficient bacterial species (SS07 and SS09) were selected and identified as Enterobacter cloacae (MT573884) and Achromobacter pulmonis (MT573885). The removal efficiency of dye mixture by E. cloacae and A. pulmonis at an initial concentration of 100 mg/L was 82.78 and 84.96%, discretely. The bacterial consortium was developed using selected isolates and the optimum conditions for removing dyes were investigated. The maximum decolorization efficiency was achieved at pH 7; 35 °C; dye concentration, 100 mg/L; and initial inoculum concentration, 0.5 mL with mannitol and ammonium sulfate as carbon and nitrogen sources. The maximum removal efficiency of 91.3 ± 3.35% was achieved at the optimal conditions after 72 h of incubation. Conclusion, significance and impact of study Decolorization of azo dyestuff by the developed microbial consortia conforms to the zero-order reaction kinetics model. Consortia of E. cloacae and A. pulmonis was established as an effective decolorizer for the Remazol Brilliant violet 5R and Reactive Red 120 dye mixture with >90% color removal.
Azo Compounds ; Microbial Consortia

Recently, the gut microbiota-based live biotherapeutics (LBPs) development, the interaction between gut microbial species and the host, and the mining of new antimicrobial peptides, enzymes and metabolic pathway have received increasing attention. Culturing gut microbial species is therefore of great importance. This review systemically compared the construction advances of gut microbial culture banks and also analyzed the differences of methods used by research groups to give insight into the construction and enrichment of gut microbial resources. Presently, the gut microbial culture banks have included more than 1 000 bacterial species, belonging to 12 phyla, 22 classes, 39 orders, 96 families, and 358 genera. Among these, Firmicutes, Proteobacteria, Bacteroidota, and Actinomycetota exhibited the greatest diversities at the species level. The sequencing data showed that there are more than 2 000 species inhibited in the human gut. Therefore, the cultured gut microbial species are far from saturation. In terms of the construction method, the stool samples were pre-treated with ethanol or directly spread and cultured in the non-selective nutritional rich medium (represented by Gifu anaerobic medium) to obtain single colony. Then single colony was further purified. Generally, a simplified isolation and culture method is sufficient to obtain the most common and important intestinal bacterial species, such as Bifidobacteria-Lactobacillus, Akkermansia muciniphila, Faecalibacterium prausnitzii, Prevotella and S24-7 family strains. Finally, microbial resources with great diversities at the strain level are required for further functional research and product development. Samples covering hosts with distinct physiological status, diets or regions are necessary.
Humans ; Gastrointestinal Microbiome ; Microbiota ; Bacteria

Diet and nutrition have a substantial impact on the human microbiome, and interact with the microbiome, especially gut microbiome, to modulate various diseases and health status. Microbiome research has also guided the nutrition field to a more integrative direction, becoming an essential component of the rising area of precision nutrition. In this review, we provide a broad insight into the interplay among diet, nutrition, microbiome, and microbial metabolites for their roles in the human health. Among the microbiome epidemiological studies regarding the associations of diet and nutrition with microbiome and its derived metabolites, we summarize those most reliable findings and highlight evidence for the relationships between diet and disease-associated microbiome and its functional readout. Then, the latest advances of the microbiome-based precision nutrition research and multidisciplinary integration are described. Finally, we discuss several outstanding challenges and opportunities in the field of nutri-microbiome epidemiology.
Humans ; Diet ; Microbiota ; Gastrointestinal Microbiome