Ankur Naqib

Background: Although shifts in nasal microbiota have been well‐documented in inflammatory upper airway conditions, microbiota tumor‐associated alterations remain uncharacterized. This study is the first to compare sinonasal microbiota profiles of patients with malignant tumors (MT), benign tumors (BT), and controls, offering insights into tumor‐associated microbiomes. Methods: This prospective, cross‐sectional, observational study assessed intraoperative sinus swabs from 70 adult research participants (MT = 23, BT = 15, control = 32). Sinonasal microbial communities were characterized using 16S rRNA gene amplicon sequencing to determine if microbial community structures differed between groups. Results: Tumor‐associated sinonasal microbiota profiles showed clear dysbiosis, with reduced relative abundance of beneficial microbes and increased putative pathogenic taxa. Both MT and BT had significantly lower microbial diversity and distinct compositions compared to controls. MT samples had significantly higher relative abundance of Firmicutes and reduced relative abundance of Actinobacteria. These phylum‐level alterations were accompanied by elevated proinflammatory microbial taxa, paired with reduced relative abundance of keystone, beneficial taxa consistent with healthy nasal microbiomes. Microbial communities in BT and MT samples were similar, but Alcaligenes was more abundant, and Corynebacterium was less abundant in MT than in BT. Conclusion: This study observed that sinonasal microbial communities in MT exhibited marked dysbiosis with a reduction in the relative abundance of putative sinonasal commensal taxa compared to controls. These alterations were present to a lesser extent in BT. Future investigations should aim to determine whether these microbial shifts contribute to tumor development or represent secondary effects, with an aim to quantify their impact on outcomes and guide therapeutic strategies.

We developed a home-based electronic nose (E-Nose) to passively monitor volatile organic compounds (VOCs) emitted following bowel movements and assessed its validity by correlating the output with prebiotic fiber intake. Healthy, non-overweight participants followed a three-week protocol which included the following: (1) installing the E-Nose in their bathroom; (2) activating the device following each bowel movement; (3) recording their dietary intake; (4) consuming a fiber bar (RiteCarbs) containing a blend of 10 g of prebiotic fiber daily during weeks two and three; and (5) submit stool specimens at the beginning and end of the study for 16S rRNA gene sequencing and analysis. Participants’ fecal microbiome displayed significantly increased relative abundance of putative total SCFA-producing genera (p = 0.0323) [total acetate-producing genera (p = 0.0214), total butyrate-producing genera (p = 0.0131)] and decreased Gram-negative proinflammatory genera (p = 0.0468). Prebiotic intervention significantly increased the participants’ fiber intake (p = 0.0152), E-Nose Min/Max (p = 0.0339), and area over the curve in VOC–to–fiber output (p = 0.0044). Increased fiber intake was negatively associated (R² = 0.53, p = 0.026) with decreased relative abundance of putative Gram-negative proinflammatory genera. This proof-of-concept study demonstrates that a prototype E-Nose can noninvasively detect a direct connection between fiber intake and VOC outputs in a home-based environment.

Human inducible pluripotent stem cell (hiPSC)-derived astrocytes (iAs) are critical to study astrocytes in health and disease. They provide several advantages over human fetal astrocytes in research, which include consistency, availability, disease modeling, customization, and ethical considerations. The generation of iAs is hampered by the requirement of Matrigel matrix coating for survival and proliferation. We provide a protocol demonstrating that human iAs cultured in the absence of Matrigel are viable and proliferative. Further, through a side-by-side comparison of cultures with and without Matrigel, we show significant similarities in astrocyte-specific profiling, including morphology (shape and structure), phenotype (cell-specific markers), genotype (transcriptional expression), metabolic (respiration), and functional aspects (glutamate uptake and cytokine response). In addition, we report that, unlike other CNS cell types, such as neuronal progenitor cells and neurons, iAs can withstand the absence of Matrigel coating. Our study demonstrates that Matrigel is dispensable for the culture of human iPSC-derived astrocytes, facilitating an easy, streamlined, and cost-effective method of generating these cells.

The composition and activity of the intestinal microbial community structures can be beneficially modulated by nutritional components such as non-digestible oligosaccharides and omega-3 poly-unsaturated fatty acids (n-3 PUFAs). These components affect immune function, brain development and behaviour. We investigated the additive effect of a dietary combination of scGOS:lcFOS and n-3 PUFAs on caecal content microbial community structures and development of the immune system, brain and behaviour from day of birth to early adulthood in healthy mice. Male BALB/cByJ mice received a control or enriched diet with a combination of scGOS:lcFOS (9:1) and 6% tuna oil (n-3 PUFAs) or individually scGOS:lcFOS (9:1) or 6% tuna oil (n-3 PUFAs). Behaviour, caecal content microbiota composition, short-chain fatty acid levels, brain monoamine levels, enterochromaffin cells and immune parameters in the mesenteric lymph nodes (MLN) and spleen were assessed. Caecal content microbial community structures displayed differences between the control and dietary groups, and between the dietary groups. Compared to control diet, the scGOS:lcFOS and combination diets increased caecal saccharolytic fermentation activity. The diets enhanced the number of enterochromaffin cells. The combination diet had no effects on the immune cells. Although the dietary effect on behaviour was limited, serotonin and serotonin metabolite levels in the amygdala were increased in the combination diet group. The combination and individual interventions affected caecal content microbial profiles, but had limited effects on behaviour and the immune system. No apparent additive effect was observed when scGOS:lcFOS and n-3 PUFAs were combined. The results suggest that scGOS:lcFOS and n-3 PUFAs together create a balance—the best of both in a healthy host.

Circadian misalignment—the misalignment between the central circadian “clock” and behavioral and environmental cycles (including sleep/wake, fasting/eating, dark/light)—results in adverse cardiovascular and metabolic effects. Potential underlying mechanisms for these adverse effects include alterations in the orogastrointestinal microbiota. However, it remains unknown whether human oral microbiota has endogenous circadian rhythms (i.e., independent of sleep/wake, fasting/eating, and dark/light cycles) and whether circadian misalignment influences oral microbiota community composition. Healthy young individuals [27.3 ± 2.3 years (18–35 years), 4 men and 2 women, body‐mass index range: 18–28 kg/m ² ] were enrolled in a stringently controlled 14‐day circadian laboratory protocol. This included a 32‐h constant routine (CR) protocol (endogenous circadian baseline assessment), a forced desynchrony protocol with four 28‐h “days” under ~3 lx to induce circadian misalignment, and a post‐misalignment 40‐h CR protocol. Microbiota assessments were performed on saliva samples collected every 4 h throughout both CR protocols. Total DNA was extracted and processed using high‐throughput 16S ribosomal RNA gene amplicon sequencing. The relative abundance of specific oral microbiota populations, i.e., one of the five dominant phyla, and three of the fourteen dominant genera, exhibited significant endogenous circadian rhythms. Importantly, circadian misalignment dramatically altered the oral microbiota landscape, such that four of the five dominant phyla and eight of the fourteen dominant genera exhibited significant circadian misalignment effects. Moreover, circadian misalignment significantly affected the metagenome functional content of oral microbiota (inferred gene content analysis), as indicated by changes in specific functional pathways associated with metabolic control and immunity. Collectively, our proof‐of‐concept study provides evidence for endogenous circadian rhythms in human oral microbiota and show that even relatively short‐term experimental circadian misalignment can dramatically affect microbiota community composition and functional pathways involved in metabolism and immune function. These proof‐of‐principle findings have translational relevance to individuals typically exposed to circadian misalignment, including night shift workers and frequent flyers.

Insoluble dietary fibers are typically known to be poorly fermented in the large intestine. However, their value may be high as evidence shows that important butyrogenic bacteria preferentially utilize insoluble substrates to support their energy needs. The objective of this study was to increase fermentability of an insoluble bran fiber (pearl millet) while keeping it mostly insoluble to promote bacteria in the community that rely on fermentable insoluble dietary fibers. Following pretests with different processing methods, a combination of microwave and enzymatic treatments were applied to isolated pearl millet fiber to increase its accessibility of gut bacteria. In vitro human fecal fermentation was conducted and analyses were made for short chain fatty acids and microbiota changes. Combined microwave and enzymatic processing increased the amount of insoluble fiber fermented in vitro from 36 to 59% of total dietary fiber, with a minor increase in soluble fiber (8%). Microwave/enzymatic processing doubled butyrate production and almost tripled acetate production at 6 h fermentation compared to the native millet fiber. 16S rRNA gene sequencing showed that the processing promoted a significant increase in Firmicutes/Bacteroidetes ratio compared to the native fiber with relative abundance increases in Blautia and Copprococcus genera and a decrease in Bacteroidetes. Overall, these data show that processing techniques can be used to increase the value of insoluble fiber, presumably by increasing accessibility of the fiber to degrading bacteria, and to support Firmicutes that preferentially compete on insoluble fibers.