Missing microbes in infants and children in the COVID-19 pandemic: a study of 1,126 participants in Beijing, China.

The COVID-19 pandemic has caused many fatalities worldwide and continues to affect the health of the recovered patients in the form of long-COVID. In this study, we compared the gut microbiome of uninfected infants and children before the pandemic began (BEFORE cohort, n=906) to that of after the pandemic (AFTER cohort, n=220) to examine the potential impact of social distancing and life habit changes on infant/children gut microbiome. Based on 16S rRNA sequencing, we found a significant change in microbiome composition after the pandemic, with Bacteroides enterotype increasing to 35.45% from 30.46% before the pandemic. qPCR quantification indicated that the bacterial loads of seven keystone taxa decreased by 91.69%-19.58%. Quantitative microbiome profiling, used to enhance the resolution in detecting microbiome differences, revealed a greater explained variance of pandemic on microbiome compared to gender, as well as a significant decrease in bacterial loads in 15 of the 20 major genera. The random forest age-predictor indicated the gut microbiomes were less mature in the after-pandemic cohort than in the before-pandemic cohort in the children group (3-12 years old) and had features of a significantly younger age (average of 1.86 years). Lastly, body weight and height were significantly lower in the after-pandemic cohort than in the before-pandemic cohort in infants (<1 year of age), which was associated with a decrease in bacterial loads in the fecal microbiome.

ChatGPT and generative AI are revolutionizing the scientific community: A Janus-faced conundrum.

The advent of generative artificial intelligence (AI) technologies marks a transformative moment for the scientific sphere, unlocking novel avenues to elevate scientific writing's efficiency and quality, expedite insight discovery, and enhance code development processes. Essential to leveraging these advancements is prompt engineering, a method that enhances AI interaction efficiency and quality. Despite its benefits, effective application requires blending researchers' expertise with AI, avoiding overreliance. A balanced strategy of integrating AI with independent critical thinking ensures the advancement and quality of scientific research, leveraging innovation while maintaining research integrity.

The Microbiome Protocols eBook initiative: Building a bridge to microbiome research.

The Microbiome Protocols eBook (MPB) serves as a crucial bridge, filling gaps in microbiome protocols for both wet experiments and data analysis. The first edition, launched in 2020, featured 152 meticulously curated protocols, garnering widespread acclaim. We now extend a sincere invitation to researchers to participate in the upcoming 2nd version of MPB, contributing their valuable protocols to advance microbiome research.

Dynamical alterations of brain function and gut microbiome in weight loss.

Objective: Intermittent energy restriction (IER) is an effective weight loss strategy. However, little is known about the dynamic effects of IER on the brain-gut-microbiome axis. Methods: In this study, a total of 25 obese individuals successfully lost weight after a 2-month IER intervention. FMRI was used to determine the activity of brain regions. Metagenomic sequencing was performed to identify differentially abundant gut microbes and pathways in from fecal samples. Results: Our results showed that IER longitudinally reduced the activity of obese-related brain regions at different timepoints, including the inferior frontal orbital gyrus in the cognitive control circuit, the putamen in the emotion and learning circuit, and the anterior cingulate cortex in the sensory circuit. IER longitudinally reduced E. coli abundance across multiple timepoints while elevating the abundance of obesity-related Faecalibacterium prausnitzii, Parabacteroides distasonis, and Bacterokles uniformis. Correlation analysis revealed longitudinally correlations between gut bacteria abundance alterations and brain activity changes. Conclusions: There was dynamical alteration of BGM axis (the communication of E. coli with specific brain regions) during the weight loss under the IER.

Specially designed yogurt supplemented with combination of pro- and prebiotics relieved constipation in mice and humans.

OBJECTIVE: Functional constipation is a gastrointestinal disorder that affects millions of people and is correlated with gut microbiome dysbiosis. The currently available treatments are ineffective; therefore, novel treatment schemes targeting the gut microbiome are desired. The aim of this study was to assess the effects of yogurt supplemented with seven probiotic strains and six types of dietary fibers on functional constipation. METHODS: In the mouse study, mice with induced constipation were administered the yogurt once a day for 1 wk, with fecal parameters and intestinal transit rate measured. In the clinical study, participants with constipation (N = 86) were given the yogurt once daily (200 g) for 4 wk. Fecal and blood samples along with Patient Assessment of Constipation-symptoms and Patient Assessment of Constipation-Quality of Life Scale questionnaires were collected to evaluate the safety and efficacy of the yogurt. Shotgun metagenomic sequencing was performed to analyze fecal samples of both mice and humans. RESULTS: We found that constipated mice had different gut microbiomes compared with those in healthy controls; yogurt treatment significantly relieved constipation-related symptoms and resulted in shifts in the microbiome. Yogurt also relieved symptoms of antibiotic-induced constipation in mice and restored the gut microbiome to a certain extent. In the clinical trial with 86 patients, yogurt administration significantly improved constipation symptoms and showed no serious adverse effects (was generally considered safe). However, subsequent metagenomic profiling of the gut microbiome did not reveal significant changes in the microbial composition, in contrast to the results in mice. We hypothesize that the differences in dosage between mice and humans may attribute to such discrepancies, and microbiome changes may not be necessary for improvements of constipation symptoms in humans. CONCLUSION: Results from this study showed that yogurt can potentially be used for the treatment of constipation.

Sequence variation and consensus sequence of V3 loop on HIV-1 gp120.

Mutation in the V3 loop of HIV-1 gp120 could affect syncytium formation, virus infectivity and neutralization. To acquire more information of the V3 loop mutation, we analyzed amino acid sequences of the V3 loop of 24504 isolates from most HIV-1 clades (including A, B, C, D, E, F, G and H clades). The consensus sequence of the V3 loop of each subtype with the highest frequency emerging on each position is constituted and the conservation of each amino acid in this region is also calculated. Exploring the restricted mutation of the V3 region could help to understand mechanism of HIV entry and to develop new strategy against HIV-1.

Antibody to CD14 like CXCR4-specific antibody 12G5 could inhibit CXCR4-dependent chemotaxis and HIV Env-mediated cell fusion.

The expression of HIV-1 coreceptors (CXCR4 and CCR5) on monocyte surface can be regulated by the ligand of CD14 (LPS), which stimulate the susceptibility of the cells to HIV-1. To investigate whether it exists potential association between CD14 and HIV-1 coreceptor CXCR4, we tested the impact of CD14-specific monoclonal antibodies (mAbs) upon CXCR4-dependent responses, such as SDF-induced chemotaxis and HIV Env-mediated membrane fusion. The anti-CD14 mAb TUK4 like CXCR4-specific mAb 12G5 could block SDF-induced chemotaxis of U937 cells in a dose-dependent manner, while another CD14-specific mAb UCHM-1 did not show any activity. More interestingly, syncytium assay indicated that only the CD14-specific mAb TUK4 inhibited HIV Env-mediated CXCR4-dependent cell fusion between U937 cells and HIV-1(HXB2) Env transfected CHO cells distinctly, consistent with its activity against CXCR4-dependent chemotaxis. These results provided experimental evidence for existence of close association between CD14 and HIV coreceptor CXCR4 on human monocytic cells.