Effect of maternal HIV status on the early neonatal microbiome.

Microbiome disruption is a proposed mechanism for the observed differences in child health outcomes by maternal HIV status, but the early neonatal microbiome of HIV-exposed (HE) newborns is not well studied. We used 16S ribosomal ribonucleic acid sequencing to analyze the microbiome composition of nasal, skin, and rectal samples collected ≤72 hours after birth from 57 hospitalized neonates in Botswana, 33% of whom were HE. Beta diversity differed by anatomic compartment (p=.

Increased reflux secondary bile acids are associated with changes to the microbiome and transcriptome in Barrett's esophagus.

Bile acids are a major component of gastro-esophageal refluxate, thought to contribute to the development of Barrett's esophagus (BE) and esophageal adenocarcinoma (EAC). As the microbiome shifts with EAC progression and bile acids influence bacterial composition, we examined these connections in a multi-center, cross-sectional study. We analyzed biospecimens from patients undergoing endoscopy using LC-MS to quantify bile acids in gastric aspirates, 16S rRNA sequencing for tissue microbiome profiling, and RNA sequencing on BE or cardia tissue.

Developing Predictive Models for Periodontitis Progression Using Artificial Intelligence: A Longitudinal Cohort Study.

Aim: To construct predictive models of periodontitis progression by applying Machine Learning (ML) to baseline data from a study of periodontitis progression.

Materials And Methods: Logistic regression (LR), multi-layer perceptron (MLP) and probabilistic graphic model (PGM) were utilised on data from a multi-centre longitudinal study in which periodontally healthy (n = 113) and periodontitis participants (n = 302) were examined bi-monthly for 12 months without treatment. Periodontal examination was performed, and salivary levels of 10 analytes were determined.

Enhancing outcomes in medically inoperable early-stage NSCLC with gut-targeted antibiotics and stereotactic body radiotherapy: results from a randomized pilot study.

Background: Gut microbiota modulation is an emerging strategy to improve cancer therapy outcomes. This study evaluated the safety and therapeutic potential of combining oral vancomycin-a non-absorbed, gut-restricted antibiotic with primary activity against gram-positive bacteria-with stereotactic body radiotherapy (SBRT) in early-stage non-small cell lung cancer (NSCLC). The underlying hypothesis was that vancomycin-induced changes in gut microbiota could enhance the antitumor effects of SBRT.

The effect of dietary zinc on the microbiome and resistome of the gestating sow and neonatal piglets.

Zinc is an important trace element for animal health and physiology, and it is routinely provided as a supplement in livestock diets. High levels of dietary zinc have been found to be beneficial for weanling pigs in preventing diarrhea and improving growth. It has also been associated with better reproductive performance in gestating sows and survival of neonatal piglets.

Digestive parameters and gut microbiota load and composition along the in vivo piglet gastrointestinal tract.

The increased attention toward the role of the gut microbiome in health and disease for both animals and humans has fueled the demand for more relevant and accurate research models. In this study, we present an overview of biochemical and microbial parameters measured throughout the digestive tract of ten TopigsNorsvin × German Piétrain piglets to better understand the in vivo dynamics of digestive and fermentative processes in different gastrointestinal segments, as pigs are suggested to be a representative animal model for the human gastrointestinal tract. Our key findings include region-specific and significantly differing (P < 0.

Dietary Fiber Modulates the Window of Susceptibility to Clostridioides difficile Infection.

Background & Aims: Clostridioides difficile epidemiology is rapidly evolving, and understanding the factors that contribute to one's risk of C difficile infection (CDI) is urgently needed. Based on our observations in a dietary intervention study, we hypothesized that fiber modulates susceptibility to C difficile after antibiotic exposure and investigated this using human specimens and murine models.

Methods: To determine whether fiber impacts factors known to mediate colonization resistance against C difficile, we investigated bile acid and microbiota composition in human subjects consuming a low-fiber diet.

Goblet Cell Loss Linked to NOD2 and Secondary Resection in Crohn's Disease is Induced by Dysbiosis and Epithelial MyD88.

Background & Aims: The role of goblet cells in small intestinal inflammation in Crohn's disease (CD) is unknown. Polymorphisms of NOD2 confer risk for CD and associate with small intestinal disease location. We previously showed in mice that Nod2 deficiency leads to overexpansion of Phocaeicola vulgatus in the gut and downstream goblet cell defects, which preceded small intestinal inflammation.

Gut metagenomes reveal interactions between dietary restriction, ageing and the microbiome in genetically diverse mice.

The gut microbiome changes with age and has been proposed to mediate the benefit of lifespan-extending interventions such as dietary restriction. However, the causes and consequences of microbiome ageing and the potential of such interventions remain unclear. Here we analysed 2,997 metagenomes collected longitudinally from 913 deeply phenotyped, genetically diverse mice to investigate interactions between the microbiome, ageing, dietary restriction (caloric restriction and fasting), host genetics and a range of health parameters.

Microbiota and metabolite-based prediction tool for colonic polyposis with and without a known genetic driver.

Despite extensive investigations into the microbiome and metabolome changes associated with colon polyps and colorectal cancer (CRC), the microbiome and metabolome profiles of individuals with colonic polyposis, including those with (Gene-pos) and without (Gene-neg) a known genetic driver, remain comparatively unexplored. Using colon biopsies, polyps, and stool from patients with Gene-pos adenomatous polyposis ( = 9), Gene-neg adenomatous polyposis ( = 18), and serrated polyposis syndrome (SPS,  = 11), we demonstrated through 16S rRNA sequencing that the mucosa-associated microbiota in individuals with colonic polyposis is representative of the microbiota associated with small polyps, and that both Gene-pos and SPS cohorts exhibit differential microbiota populations relative to Gene-neg polyposis cohorts. Furthermore, we used these differential microbiota taxa to perform linear discriminant analysis to differentiate Gene-neg subjects from Gene-pos and from SPS subjects with an accuracy of 89% and 93% respectively.

Utilizing the biosimulator to analyze the environmental microbiome within the intensive care units of a hospital.

Hospital-acquired infections (HAIs), also known as nosocomial infections, are illnesses contracted during treatment at a healthcare facility and can result in severe or life-threatening complications. HAIs are caused by microorganisms that exhibit resistance to standard antibiotics. HAIs can lead to severe complications, longer stays, and increased mortality, particularly in vulnerable patients.

Role of the Microbiome in Neonatal Infection: Pathogenesis and Implications for Management.

The human microbiome refers to the collective genome of microorganisms, including bacteria, fungi, and viruses residing on human body surfaces that are in contact with the environment. Together these communities protect against invasive infections. Conversely, when disrupted, the microbiome can be the source of pathogens causing invasive infection.

A pro-inflammatory diet is associated with growth and virulence of Escherichia coli in pediatric Crohn's disease.

Background And Aims: Epidemiological studies have suggested an association between the inflammatory potential of dietary patterns and Crohn's disease (CD). However, the relationships of these inflammatory dietary determinants with the microbiome remain largely unknown. In this cross-sectional study, we evaluate the association between the inflammatory potential of habitual diet, as assessed by the modified Children-Dietary Inflammatory Index (mC-DII), and the fecal microbiome and metabolome of children with CD in comparison to healthy children.

Antibiotic exposure is associated with minimal gut microbiome perturbations in healthy term infants.

Background: The evolving infant gut microbiome influences host immune development and later health outcomes. Early antibiotic exposure could impact microbiome development and contribute to poor outcomes. Here, we use a prospective longitudinal birth cohort of n = 323 healthy term African American children to determine the association between antibiotic exposure and the gut microbiome through shotgun metagenomics sequencing as well as bile acid profiles through liquid chromatography-mass spectrometry.

Concomitant suppression of COX-1 and COX-2 is insufficient to induce enteropathy associated with chronic NSAID use.

Nonsteroidal anti-inflammatory drugs (NSAIDs) are the most widely used medications for the management of chronic pain; however, they are associated with numerous gastrointestinal (GI) adverse events. Although many mechanisms have been suggested, NSAID-induced enteropathy has been thought to be primarily due to inhibition of both cyclooxygenases (COX) -1 and -2, which results in suppression of prostaglandin synthesis. Yet surprisingly, we found that concomitant postnatal deletion of and over 10 months failed to cause intestinal injury in mice unless they were treated with naproxen or its structural analog, phenylpropionic acid, which is not a COX inhibitor.

Metal availability shapes early life microbial ecology and community succession.

The gut microbiota plays a critical role in human health and disease. Microbial community assembly and succession early in life are influenced by numerous factors. In turn, assembly of this microbial community is known to influence the host, including immune system development, and has been linked to outcomes later in life.

Gingival Crevicular Fluid Biomarkers During Periodontitis Progression and After Periodontal Treatment.

Objective: To identify gingival crevicular fluid (GCF)-derived inflammatory markers of periodontitis progression and periodontal treatment impact.

Methods: Periodontally healthy (H; n = 112) and periodontitis (P; n = 302) patients were monitored bi-monthly for 1 year without therapy. Periodontitis patients were re-examined 6 months after non-surgical periodontal therapy (NSPT).

A quantitative approach to measure and predict microbiome response to antibiotics.

Unlabelled: Although antibiotics induce sizable perturbations in the human microbiome, we lack a systematic and quantitative method to measure and predict the microbiome's response to specific antibiotics. Here, we introduce such a method, which takes the form of a microbiome response index (MiRIx) for each antibiotic. Antibiotic-specific MiRIx values quantify the overall susceptibility of the microbiota to an antibiotic, based on databases of bacterial phenotypes and published data on intrinsic antibiotic susceptibility.

Effects of dietary zinc on the gut microbiome and resistome of the gestating cow and neonatal calf.

Zinc is an essential trace element required in the diet of all species. While the effects of zinc have been studied in growing calves, little is known about the effect of zinc on the microbiota of the gestating cow or her neonatal calf. Understanding factors that shape the gut health of neonatal animals and evaluating the effect of dietary supplements in adult gestating animals is important in promoting animal health and informing feeding practices.

Disruption of intestinal oxygen balance in acute colitis alters the gut microbiome.

The juxtaposition of well-oxygenated intestinal colonic tissue with an anerobic luminal environment supports a fundamentally important relationship that is altered in the setting of intestinal injury, a process likely to be relevant to diseases such as inflammatory bowel disease. Herein, using two-color phosphorometry to non-invasively quantify both intestinal tissue and luminal oxygenation in real time, we show that intestinal injury induced by DSS colitis reduces intestinal tissue oxygenation in a spatially defined manner and increases the flux of oxygen from the tissue into the gut lumen. By characterizing the composition of the microbiome in both DSS colitis-affected gut and in a bioreactor containing a stable human fecal community exposed to microaerobic conditions, we provide evidence that the increased flux of oxygen into the gut lumen augments glycan degrading bacterial taxa rich in glycoside hydrolases which are known to inhabit gut mucosal surface.

Unassigning bacterial species for microbiome studies.

The method of 16S rRNA marker gene sequencing has fueled microbiome research and continues to be relevant. A perceived weakness of the method is that taxonomic assignments are not possible to make at the rank of species. We show that by working to bacterial or archaeal species membership, we can provide an answer that is more accurate and useful.

Supplementation with soluble or insoluble rice-bran fibers increases short-chain fatty acid producing bacteria in the gut microbiota .

Introduction: Studies have shown that a diet high in fiber and prebiotics has a positive impact on human health due largely to the fermentation of these compounds by the gut microbiota. One underutilized source of fiber may be rice bran, a waste product of rice processing that is used most frequently as an additive to livestock feed but may be a good source of fibers and other phenolic compounds as a human diet supplement. Previous studies focused on specific compounds extracted from rice bran showed that soluble fibers extracted from rice bran can improve glucose response and reduce weight gain in mouse models.

Surgery for Crohn's Disease Is Associated With a Dysbiotic Microbiome and Metabolome: Results From Two Prospective Cohorts.

Background & Aims: Crohn's disease is associated with alterations in the gut microbiome and metabolome described as dysbiosis. We characterized the microbial and metabolic consequences of ileal resection, the most common Crohn's disease surgery.

Methods: Patients with and without intestinal resection were identified from the Diet to Induce Remission in Crohn's Disease and Study of a Prospective Adult Research Cohort with Inflammatory Bowel Disease studies.