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The mammalian digestive tract harbors a vast microbial community that has the potential to modulate numerous health-related processes. Multicompartment dynamic gut models have been developed to study microbial communities in a controlled environment. To verify the assumption that the experimental results produced in vitro in a mechanical device would be highly similar to those obtained from an in vivo study, in this study fecal samples from four pigs were inoculated in a simulator of the porcine intestinal microbial ecosystem (SPIME) and cultured until reaching steady state. The composition and structure of the resultant microbial communities, and the metabolites produced were compared with those harvested from the intestine of the same pigs. Taxonomic abundance identification based on shallow shotgun metagenomic sequencing revealed only 12.1% of species or 15% of metagenome-assembled genomes (MAGs) being shared across the colon compartments of the source pigs and the SPIME. Despite these overwhelming compositional shifts, higher functional conservation was indicated as measured by functional richness, MAG-level traits, CAZymes, and untargeted metabolomics. Environmental selection and bacterial functional redundancy were considered the two key elements in microbial compositional shifts and functional preservation.

The recent ban of the antimicrobial compound triclosan from use in consumer soaps followed research that showcased the risk it poses to the environment and to human health. Triclosan has been found in human plasma, urine and milk, demonstrating that it is present in human tissues. Previous work has also demonstrated that consumption of triclosan disrupts the gut microbial community of mice and zebrafish. Due to the widespread use of triclosan and ubiquity in the environment, it is imperative to understand the impact this chemical has on the human body and its symbiotic resident microbes. To that end, this study is the first to explore how triclosan impacts the human gut microbial community in vitro both during and after treatment. Through our in vitro system simulating three regions of the human gut; the ascending colon, transverse colon, and descending colon regions, we found that treatment with triclosan significantly impacted the community structure in terms of reduced population, diversity, and metabolite production, most notably in the ascending colon region. Given a 2 week recovery period, most of the population levels, community structure, and diversity levels were recovered for all colon regions. Our results demonstrate that the human gut microbial community diversity and population size is significantly impacted by triclosan at a high dose in vitro, and that the community is recoverable within this system.

The consumption of probiotics is widely encouraged due to reports of their positive effects on human health. In particular, Lacticaseibacillus rhamnosus strain GG (LGG) is an approved probiotic that has been reported to improve health outcomes, especially for gastrointestinal disorders. However, how LGG cooperates with the gut microbiome has not been fully explored. To understand the interaction between LGG and its ability to survive and grow within the gut microbiome, this study introduced LGG into established microbial communities using an in vitro model of the colon. LGG was inoculated into the simulated ascending colon and its persistence in, and transit through the subsequent transverse and descending colon regions was monitored over two weeks. The impact of LGG on the existing bacterial communities was investigated using 16S rRNA sequencing and short-chain fatty acid analysis. LGG was able to engraft and proliferate in the ascending region for at least 10 days but was diminished in the transverse and descending colon regions with little effect on short-chain fatty acid abundance. These data suggest that the health benefits of the probiotic LGG rely on its ability to transiently engraft and modulate the host microbial community.

The genus Senna contains globally distributed plant species of which the leaves, roots, and seeds have multiple traditional medicinal and nutritional uses. Notable chemical compounds derived from Senna spp. include sennosides and emodin which have been tested for antimicrobial effects in addition to their known laxative functions. However, studies of the effects of the combined chemical components on intact human gut microbiome communities are lacking. This study evaluated the effects of Juemingzi ( Senna sp.) extract on the human gut microbiome using SIFR ® (Systemic Intestinal Fermentation Research) technology. After a 48-hour human fecal incubation, we measured total bacterial cell density and fermentation products including pH, gas production and concentrations of short chain fatty acids (SCFAs). The initial and post-incubation microbial community structure and functional potential were characterized using shotgun metagenomic sequencing. Juemingzi ( Senna seed) extracts displayed strong, taxon-specific anti-microbial effects as indicated by significant reductions in cell density (40%) and intra-sample community diversity. Members of the Bacteroidota were nearly eliminated over the 48-hour incubation. While generally part of a healthy gut microbiome, specific species of Bacteroides can be pathogenic. The active persistence of the members of the Enterobacteriaceae and selected Actinomycetota despite the reduction in overall cell numbers was demonstrated by increased fermentative outputs including high concentrations of gas and acetate with correspondingly reduced pH. These large-scale shifts in microbial community structure indicate the need for further evaluation of dosages and potential administration with prebiotic or synbiotic supplements. Overall, the very specific effects of these extracts may offer the potential for targeted antimicrobial uses or as a tool in the targeted remodeling of the gut microbiome.

In traditional Chinese medicine, the rhizome of (Baizhu), the leaves of (Daqingye), and the flowers of (Hehuanhua) have been used to treat gastrointestinal illnesses, epidemics, and mental health issues. Modern researchers are now exploring the underlying mechanisms responsible for their efficacy. Previous studies often focused on the impact of purified chemicals or mixed extracts from these plants on cells in tissue culture or in rodent models. As modulation of the human gut microbiome has been linked to host health status both within the gastrointestinal tract and in distant tissues, the effects of lipid-free ethanol extracts of Baizhu, Daqingye, and Hehuanhua on the human adult gut microbiome were assessed using Systemic Intestinal Fermentation Research (SIFR ) technology (n=6). Baizhu and Daqingye extracts similarly impacted microbial community structure and function, with the extent of effects being more pronounced for Baizhu. These effects included decreases in the Bacteroidetes phylum and increases in health-related spp. and short chain fatty acids which may contribute to Baizhu's efficacy against gastrointestinal ailments. The changes upon Hehuanhua treatment were larger and included increases in multiple bacterial species, including , , and , known to produce secondary metabolites beneficial to mental health. In addition, many of the changes induced by Hehuanhua correlated with a rise in spp., which may make the tested dose of this herb contraindicated for some individuals. Overall, there is some evidence to suggest that the palliative effect of these herbs may be mediated, in part, by their impact on the gut microbiome, but more research is needed to elucidate the exact mechanisms.

  There are important conserved components of the gene network that regulate dauer formation, one being the nuclear hormone receptor DAF-12, which is important in free-living as well as parasitic nematode species [8-10]. [...]epistasis experiments show that dau-1 acts either downstream or in parallel to steroid hormone signaling, but is dependent on the nuclear hormone receptor gene daf-12 (Fig 1).

Tomatoes are a perishable and seasonal fruit with a high economic impact. Carbon dioxide (CO2), among several other reagents, is used to extend the shelf-life and preserve the quality of tomatoes during refrigeration or packaging. To obtain insight into CO2 stress during tomato ripening, tomatoes at the late green mature stage were conditioned with one of two CO2 delivery methods: 5% CO2 for 14 days (T1) or 100% CO2 for 3 h (T2). Conventional physical and chemical characterization found that CO2 induced by either T1 or T2 delayed tomato ripening in terms of color change, firmness, and carbohydrate dissolution. However, T1 had longer-lasting effects. Furthermore, ethylene production was suppressed by CO2 in T1, and promoted in T2. These physical observations were further evaluated via RNA-Seq analysis at the whole-genome level, including genes involved in ethylene synthesis, signal transduction, and carotenoid biosynthesis. Transcriptomics analysis revealed that the introduction of CO2 via the T1 method downregulated genes related to fruit ripening; in contrast, T2 upregulated the gene encoding for ACS6, the enzyme responsible for S1 ethylene synthesis, even though there was a large amount of ethylene present, indicating that T1 and T2 regulate tomato ripening via different mechanisms. Quantitative real-time PCR assays (qRT-PCR) were used for validation, which substantiated the RNA-Seq data. The results of the present research provide insight into gene regulation by CO2 during tomato ripening at the whole-genome level.

The food additive sodium benzoate (SB) has been used for decades as an antimicrobial to prevent food spoilage. SB has been deemed to pose no risk to human health when consumed at levels under 5 mg/kg body weight per day; however, when many of the supporting studies were conducted, the importance of the gut microbiome to human health was not yet appreciated. Given SB’s known antimicrobial qualities, it is important to assess the effect of this food additive on the human gut microbiome. The ex vivo SIFR® (Systemic Intestinal Fermentation Research) technology was used to test the effect of SB on microbial communities from 24 donors, aged infants to older adults. A dose of 3.5 g/L SB elicited a drop in the Pseudomonadota phylum for multiple age groups but did not alter the alpha or beta diversity within any of these groups. This was accompanied by changes in the functional outputs that included an overall rise in butyrate and a drop in propionate production. This higher butyrate correlates with an increase in the abundance of several known butyrate producers in the presence of SB, although the genetic potential for its production in the community did not change. Overall, despite using a dose ten times higher than the accepted daily intake limit, the effect on the gut microbiome was minimal.

In the present research, we investigated changes in the gut metabolome that occurred in response to the administration of the Laticaseibacillus rhamnosus strain GG (LGG). The probiotics were added to the ascending colon region of mature microbial communities established in a human intestinal microbial ecosystem simulator. Shotgun metagenomic sequencing and metabolome analysis suggested that the changes in microbial community composition corresponded with changes to metabolic output, and we can infer linkages between some metabolites and microorganisms. The in vitro method permits a spatially-resolved view of metabolic transformations under human physiological conditions. By this method, we found that tryptophan and tyrosine were mainly produced in the ascending colon region, while their derivatives were detected in the transverse and descending regions, revealing sequential amino acid metabolic pathways along with the colonic tract. The addition of LGG appeared to promote the production of indole propionic acid, which is positively associated with human health. Furthermore, the microbial community responsible for the production of indole propionic acid may be broader than is currently known.

Ivermectin is a an anti-helminthic that is critical globally for both human and veterinary care. To the best of our knowledge, information available regarding the influence of ivermectin (IVM) on the gut microbiota has only been collected from diseased donors, who were treated with IVM alone or in combination with other medicines. Results thus obtained were influenced by multiple elements beyond IVM, such as disease, and other medical treatments. The research presented here investigated the impact of IVM on the gut microbial structure established in a Triple-SHIME® (simulator of the human intestinal microbial ecosystem), using fecal material from three healthy adults. The microbial communities were grown using three different culture media: standard SHIME media and SHIME media with either soluble or insoluble fiber added (control, SF, ISF). IVM introduced minor and temporary changes to the gut microbial community in terms of composition and metabolite production, as revealed by 16S rRNA amplicon sequencing analysis, flow cytometry, and GC-MS. Thus, it was concluded that IVM is not expected to induce dysbiosis or yield adverse effects if administered to healthy adults. In addition, the donor’s starting community influences the relationship between IVM and the gut microbiome, and the soluble fiber component in feed could protect the gut microbiota from IVM; an increase in short-chain fatty acid production was predicted by PICRUSt2 and detected with IVM treatment.