The Kobe University Human Intestinal Microbiota Model for gut intervention studies

The Role of Early Life Gut Mycobiome on Child Health

The human gut microbiota is composed of bacteria (microbiota or microbiome), fungi (mycobiome), viruses, and archaea, but most of the research is primarily focused on the bacterial component of this ecosystem. Besides bacteria, fungi have been shown to play a role in host health and physiologic functions. However, studies on mycobiota composition during infancy, the factors that might shape infant gut mycobiota, and implications to child health and development are limited. In this review, we discuss the factors likely shaping gut mycobiota, interkingdom interactions, and associations with child health outcomes and highlight the gaps in our current knowledge of this ecosystem.

Culturing the unculturables: strategies, challenges, and opportunities for gut microbiome study

Metagenome sequencing techniques revolutionized the field of gut microbiome study. However, it is equipped with experimental and computational biases, which affect the downstream analysis results. Also, live microbial strains are needed for a better understanding of host-microbial crosstalks and for designing next-generation treatment therapies based on probiotic strains and postbiotic molecules. Conventional culturing methodologies are insufficient to get the dark gut matter on the plate; therefore, there is an urgent need to propose novel culturing methods that can fill the limitations of metagenomics. The current work aims to provide a consolidated evaluation of the available methods for host-microbe interaction with an emphasis on in vitro culturing of gut microbes using organoids, gut on a chip, and gut bioreactor. Further, the knowledge of microbial crosstalk in the gut helps us to identify core microbiota, and key metabolites that will aid in designing culturing media and co-culturing systems for gut microbiome study. After the deeper mining of the current culturing methods, we recommend that 3D-printed intestinal cells in a multistage continuous flow reactor equipped with an extended organoid system might be a good practical choice for gut microbiota-based studies.

Calorie restriction mimetic drugs could favorably influence gut microbiota leading to lifespan extension

Calorie restriction (CR) can prolong human lifespan, but enforcing long-term CR is difficult. Thus, a drug that reproduces the effects of CR without CR is required. More than 10 drugs have been listed as CR mimetics (CRM), and some of which are conventionally categorized as upstream-type CRMs showing glycolytic inhibition, whereas the others are categorized as downstream-type CRMs that regulate or genetically modulate intracellular signaling proteins. Intriguingly, recent reports have revealed the beneficial effects of CRMs on the body such as improving the host body condition via intestinal bacteria and their metabolites. This beneficial effect of gut microbiota may lead to lifespan extension. Thus, CRMs may have a dual effect on longevity. However, no reports have collectively discussed them as CRMs; hence, our knowledge about CRM and its physiological effects on the host remains fragmentary. This study is the first to present and collectively discuss the accumulative evidence of CRMs improving the gut environments for healthy lifespan extension, after enumerating the latest scientific findings related to the gut microbiome and CR. The conclusion drawn from this discussion is that CRM may partially extend the lifespan through its effect on the gut microbiota. CRMs increase beneficial bacteria abundance by decreasing harmful bacteria rather than increasing the diversity of the microbiome. Thus, the effect of CRMs on the gut could be different from that of conventional prebiotics and seemed similar to that of next-generation prebiotics.

Effects of blackcurrant extract on indole and ammonia productions in an in vitro human fecal culture model

Blackcurrant is available as a traditional medicine in Europe. However, the detailed effects of blackcurrant on the human gut microbiota remain unknown. In this study, we investigated the prebiotic effects of a blackcurrant extract using a human fecal culture model in six healthy subjects. Feces were individually inoculated into a medium with or without the blackcurrant extract and then fermented for 48 hr under anaerobic conditions. The results obtained from analysis of samples from the fermented medium demonstrated that after 48 hr of fermentation, the pH of the medium with the blackcurrant extract was significantly decreased (control, 6.62 ± 0.20; blackcurrant extract, 6.41 ± 0.33; p=0.0312). A 16S rRNA gene sequencing analysis of the microbiota of the fermented medium showed a significant increase in the relative abundance of Bifidobacteriaceae. In measuring the concentrations of putrefactive components in the fermented medium, we found that the blackcurrant extract significantly reduced ammonia levels and displayed a tendency toward reduced indole levels. Our results suggest that blackcurrant extract could be a potential ingredient for relief of putrefactive components in the gut.

Effects of partially hydrolyzed guar gums of different molecular weights on a human intestinal in vitro fermentation model

Partially hydrolyzed guar gums (PHGGs) are prebiotic soluble dietary fibers. High molecular-weight PHGGs have rapid fermentation and high short-chain fatty acid (SCFA) productivity rates, compared to low molecular-weight PHGGs. Therefore, low molecular-weight PHGGs may have less pronounced prebiotic effects than high molecular-weight PHGGs. However, the effects of PHGGs of different molecular weights on the human intestinal microbiota, as well as their fermentation ability and prebiotic effects, have not been investigated. The aim of this study was to evaluate the effects of two PHGGs of different molecular weights, Sunfiber-R (SF-R; 20 kDa) and Sunfiber-V (SF-V; 5 kDa), on human colonic microbiota and SCFA production. A human intestinal in vitro fermentation model was operated by fecal samples with and without the PHGGs. The addition of 0.2% SF-R or SF-V increased the relative abundance of Bacteroides spp., especially that of Bacteroides uniformis. This increase corresponded to a significant (p = 0.030) and non-significant (p = 0.073) increase in propionate production in response to SF-R and SF-V addition, respectively. Both fibers increased the relative abundance of Faecalibacterium and stimulated an increase in the abundance of unclassified Lachnospiraceae and Bifidobacterium. In conclusion, the low molecular-weight PHGG exerted prebiotic effects on human colonic microbiota to increase SCFA production and bacteria that are beneficial to human health in a manner similar to that of the high molecular-weight forms of PHGG.

Effects of Xylo-Oligosaccharide on the Gut Microbiota of Patients With Ulcerative Colitis in Clinical Remission

Gut microbiota dysbiosis is closely associated with ulcerative colitis (UC). Prebiotic therapy is a potential approach for UC management especially remission maintaining. Xylo-oligosaccharide (XOS) is an efficient prebiotic with proven health benefits and few side effects. However, the effects of XOS on the gut microbiota of patients with UC have not been investigated previously. The aim of this study was to evaluate the prebiotic effects of XOS on the fecal microbiota of patients with UC in clinical remission using an in vitro fermentation model. Five patients with UC in clinical remission and five healthy volunteers were enrolled in this study. Fresh fecal samples of UC patients were diluted and inoculated in yeast extract, casitone and fatty acid (YCFA) medium alone or with XOS. After fermentation for 48 h, samples were collected for 16S rDNA sequencing to investigate the gut microbiota composition. Differences in the gut microbiota between healthy volunteers and UC patients in clinical remission were detected using original fecal samples. Subsequently, the differences between the YCFA medium alone or with XOS samples were analyzed to illustrate the effects of XOS on the gut microbiota of UC patients. In both principal coordinate analysis (PCoA) and principal component analysis (PCA), the fecal samples of UC patients differed from those of healthy volunteers. Linear discriminant analysis effect size (LEfSe) analysis revealed that the relative abundances of g_Roseburia and g_Lachnospiraceae_ND3007_group were higher in healthy volunteers than in UC patients, while o_Lactobacillales abundance showed the opposite trend (P < 0.05). Wilcoxon rank-sum test bar plot showed that the abundances of g_Eubacterium_halli_group and g_Lachnospiraceae_ND3007_group were higher in the healthy volunteers than in the UC patients (P < 0.05). In addition, in UC patients, the Wilcoxon rank-sum test showed that XOS fermentation promoted the growth of bacterial groups including g_Roseburia, g_Bifidobacterium, and g_Lactobacillus, which is beneficial for recovery of intestinal diseases. These results suggest that XOS can relieve dysbiosis in the feces of UC patients in clinical remission and thus represent a potential prebiotic material for maintaining remission.

Time to integrate biotechnological approaches into fish gut microbiome research

Like for other vertebrates, the fish microbiome is critical to the health of its host and has complex and dynamic interactions with the surrounding environment. Thus, the study of the fish microbiome can benefit from the new prospects gained by innovative biotechnological applications in human and other animals, that include manipulation of the associated microbial communities (to improve the health, productivity, and sustainability of fish production), in vitro gut simulators, synthetic microbial communities, and others. Here, we summarize the current state of knowledge on such biotechnological approaches to better understand and engineer the fish microbiome, as well as to advance our knowledge on host-microbes interactions. A particular focus is given to the most recent strategies for fish microbiome manipulation to improve fish health, food safety and environmental sustainability.