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

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

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

No abstract available.
Microbiota*

Aims: Different studies have shown that members of the Vibrio such as Vibrio coralliilyticus and Vibrio shiloi are opportunistic pathogens which can cause coral lysis. The aims of this study were to assess whether this results of the virulence of V. coralliilyticus are transmittable to Acropora hyacinthus and Porites lobata, and what role the microbiome of the corals plays during exposure to V. coralliilyticus. Methodology and results: In laboratory-based experiments, we examined the impact of V. coralliilyticus (ATCC BAA- 450) to the microbiome of Acropora hyacinthus and Porites lobata. A. hyacinthus and P. lobata were exposed to ampicillin, V. coralliilyticus, and a combination of both. Results indicate a resistance of A. hyacinthus to V. coralliilyticus through the microbiome and underpin the importance of the microbiome for the coral’s health. Conclusion, significance and impact study: Further studies are needed to identify the bacteria responsible for the coral resistance and could in future lead to the development of a probiotic treatment or prevention of bleaching for sensitive corals.
Microbiota

Early environmental exposure is recognized as a key factor for long-term health based on the Developmental Origins of Health and Disease hypothesis. It considers that early-life nutrition is now being recognized as a major contributor that may permanently program change of organ structure and function toward the development of diseases, in which epigenetic mechanisms are involved. Recent researches indicate early-life environmental factors modulate the microbiome development and the microbiome might be mediate diet-epigenetic interaction. This review aims to define which nutrients involve microbiome development during the critical window of susceptibility to disease, and how microbiome modulation regulates epigenetic changes and influences human health and future prevention strategies.
Environmental Exposure ; Epigenomics ; Gastrointestinal Microbiome ; Humans ; Microbiota

Fecal microbiota transplantation (FMT) has been used as a core therapy for treating dysbiosis-related diseases by remodeling gut microbiota. The methodology and technology for improving FMT are stepping forward, mainly including washed microbiota transplantation (WMT), colonic transendoscopic enteral tubing (TET) for microbiota delivery, and purified Firmicutes spores from fecal matter. To improve the understanding of the clinical applications of FMT, we performed a systematic literature review on FMT published from 2011 to 2021. Here, we provided an overview of the reported clinical benefits of FMT, the methodology of processing FMT, the strategy of using FMT, and the regulations on FMT from a global perspective. A total of 782 studies were included for the final analysis. The present review profiled the effectiveness from all clinical FMT uses in 85 specific diseases as eight categories, including infections, gut diseases, microbiota-gut-liver axis, microbiota-gut-brain axis, metabolic diseases, oncology, hematological diseases, and other diseases. Although many further controlled trials will be needed, the dramatic increasing reports have shown the promising future of FMT for dysbiosis-related diseases in the gut or beyond the gut.
Humans ; Fecal Microbiota Transplantation/methods* ; Dysbiosis/therapy* ; Gastrointestinal Microbiome ; Feces ; Microbiota

A symbiotic relationship between humans and the microbiota is critical for the maintenance of our health, including development of the immune system, enhancement of the epithelial barrier, and acquisition of nutrients. Recent research has shown that the microbiota impacts immune cell development and differentiation. These findings suggest that the microbiota may also influence adjuvant and vaccine efficacy. Indeed, several factors such as malnutrition and poor sanitation, which affect gut microbiota composition, impair the efficacy of vaccines. Although there is little evidence that microbiota alters vaccine efficacy, further understanding of human immune system-microbiota interactions may lead to the effective development of adjuvants and vaccines for the treatment of diseases.
Gastrointestinal Microbiome ; Humans ; Immune System ; Malnutrition ; Microbiota* ; Sanitation ; Vaccines

A massive depletion of CD4+ T lymphocytes has been described in early and acute human immunodeficiency virus (HIV) infection, leading to an imbalance between the human microbiome and immune responses. In recent years, a growing interest in the alterations in gut microbiota in HIV infection has led to many studies; however, only few studies have been conducted to explore the importance of oral microbiome in HIV-infected individuals. Evidence has indicated the dysbiosis of oral microbiota in people living with HIV (PLWH). Potential mechanisms might be related to the immunodeficiency in the oral cavity of HIV-infected individuals, including changes in secretory components such as reduced levels of enzymes and proteins in saliva and altered cellular components involved in the reduction and dysfunction of innate and adaptive immune cells. As a result, disrupted oral immunity in HIV-infected individuals leads to an imbalance between the oral microbiome and local immune responses, which may contribute to the development of HIV-related diseases and HIV-associated non-acquired immunodeficiency syndrome comorbidities. Although the introduction of antiretroviral therapy (ART) has led to a significant decrease in occurrence of the opportunistic oral infections in HIV-infected individuals, the dysbiosis in oral microbiome persists. Furthermore, several studies with the aim to investigate the ability of probiotics to regulate the dysbiosis of oral microbiota in HIV-infected individuals are ongoing. However, the effects of ART and probiotics on oral microbiome in HIV-infected individuals remain unclear. In this article, we review the composition of the oral microbiome in healthy and HIV-infected individuals and the possible effect of oral microbiome on HIV-associated oral diseases. We also discuss how ART and probiotics influence the oral microbiome in HIV infection. We believe that a deeper understanding of composition and function of the oral microbiome is critical for the development of effective preventive and therapeutic strategies for HIV infection.
Dysbiosis ; Gastrointestinal Microbiome ; HIV Infections/drug therapy* ; Humans ; Microbiota ; Mouth

Fecal microbiota transplantation (FMT) refers to using the intestinal microorganisms present in the feces or processed feces from healthy people for treating various types of diseases, such as digestive and metabolic diseases. The rapid development of metagenomic and culturomic technologies in gut microbiome analysis provides powerful tools for the FMT research and its clinical applications. Metagenomics technologies comprehensively revealed the diversity and functions of gut microbiota under health and disease conditions, while culturomics technologies helped isolation and identification of "unculturable" bacteria in the human gut under conventional culture conditions. The combination of these two technologies not only enabled us better understand the FMT regularities of cause and effect in clinical practices, but also effectively promoted its applications. Considering the above advantages, this article summarized the applications of metagenomics and culturomics technologies in FMT and prospected its future development trend.
Humans ; Fecal Microbiota Transplantation ; Metagenomics ; Feces/microbiology* ; Gastrointestinal Microbiome ; Bacteria