Gut Microbes

ObjectiveThe small intestine (SI) microbiome is increasingly implicated in both functional gastrointestinal (GI) disorders and a wide range of systemic diseases. However, owing to limitations of traditional GI sampling approaches, the SI remains challenging to directly access on a large scale. This work presents the Small Intestinal MicroBiome Aspiration Capsule (SIMBA) as an effective means for sampling SI luminal content. DesignIn an observational clinical study, SIMBA capsules were ingested ...

BackgroundBifidobacterium longum supplementation can be used to regulate bowel movement; however, individuals vary in the response to B. longum treatment. One putative factor is the gut microbiota; recent studies have reported that the gut microbiota mediates diet or drug effects. Here, we investigated intestinal features related to B. longum effectiveness in increasing bowel movement frequency. ResultsA randomized, double-blind controlled crossover trial was conducted with twenty Japanese subj...

BackgroundBlastocystis, the most prevalent eukaryotic gut microbe in humans, has a global distribution. Studies have linked its presence with distinct gut microbiome and metabolome profiles compared to those where the organism is absent. However, the in vivo effect of antibiotics on Blastocystis and the surrounding gut microbiome remains understudied. This case study aimed to explore how antibiotic consumption influences the presence of Blastocystis and the subsequent changes in the gut microbio...

BackgroundThe gut microbiome is crucial for maintaining overall host homeostasis and metabolism, but it can be significantly affected by dietary changes, leading to substantial temporal variations in microbial composition both within and between individuals. Despite these variations, fecal sampling remains the standard for microbiome assessment. Recently, the blood microbiome, which reflects the microbial DNA circulating in the bloodstream, has emerged as a potentially more stable and integrated...

The invasive nature of sample collection for studying the small intestinal (SI) microbiome often results in its poor characterization. This study evaluated a novel ingestible medical device (MD) for SI luminal sample collection. A monocentric interventional trial (NCT05477069) was conducted on 15 healthy subjects. Metagenomics, metabolomics and culturomics assessed the MDs effectiveness in characterizing the healthy SI microbiome and identifying potential biomarkers. The SI microbiota differed s...

BackgroundPost-discharge morbidity and mortality is high in acute pancreatitis (AP) and pathophysiological mechanisms remain poorly understood. ObjectivesWe aim to investigate the composition of gut microbiota and clinical long-term outcomes of prospectively enrolled AP patients to predict post-discharge complications. DesignIn this long-term follow-up study, we analysed clinical and microbiome data of 277 patients from the prospective multi-centre P-MAPS trial. Primary endpoint was the associ...

BackgroundDysbiosis of gut microbial community is associated with the pathogenesis of CD and may serve as a promising non-invasive diagnostic tool. We aimed to compare the performances of the microbial markers of different biological levels by conducting a multidimensional analysis on the microbial metagenomes of CD. MethodsWe collected fecal metagenomic datasets generated from eight cohorts that altogether include 870 CD patients and 548 healthy controls. The microbial alterations in CD patien...

Defining the "health" of the gut microbiome or microbial organ has been elusive and controversial. This in turn makes defining gut dysbiosis (imbalances in gut microbiota) an enigma particularly in determining what, how, and when to intervene to restore eubiosis. Taxonomical profiles of gut microbiota have typically been used but are unreliable because of highly variable interindividual taxa and arbitrary functional assignments generalized to microbial groups. We therefore developed a functional...

ObjectiveLittle is known about the interplay between gut microbiome and SARS-CoV-2 vaccine immunogenicity. In this prospective observational study, we investigated associations between the gut microbiome, habitual dietary fibre intake, and mRNA vaccine-elicited immune responses, including anti-Spike IgG, avidity, and ACE-2 competition (surrogate neutralization). Design16S rRNA sequencing and short-chain fatty acid analyses were undertaken using stool samples collected from 48 healthy individual...

BackgroundCrohns disease (CD), ulcerative colitis (UC) and pouchitis are multifactorial and chronic inflammatory diseases of the gastrointestinal tract, termed together as inflammatory bowel diseases (IBD). Pouchitis develops in former patients with UC after total proctocolectomy and ileal pouch-anal anastomosis ("pouch surgery") and is characterized by inflammation of the previously normal small intestine comprising the pouch. It has been extensively shown that broad taxonomic and functional al...

BackgroundThe relationship among the human gut microbiome, microbially produced metabolites, and health outcomes remains of great interest. To decrease participant burden, room-temperature storage methods for fecal samples have become increasingly important. However, kits for storing the fecal microbiome and metabolome have not been well explored. We hypothesized that storing fecal samples by drying them with silica gel may be suitable. ObjectivesThe objective was to evaluate the performance of...

BackgroundInflammatory bowel disease (IBD) is a set of conditions characterized by non-infectious chronic inflammation of the gastrointestinal tract. These primarily include Crohns disease (CD), ulcerative colitis (UC) and indeterminate colitis. Fecal microbiota transplantation (FMT) has proven to be an effective treatment for some patients with active UC. There is currently no procedure allowing to predict the patients response and to select the most adequate donor(s). AimInvestigate microbiom...

BackgroundMany disorders display dysbiosis of the enteric microbiome, compared with healthy controls. Different disorders share a pattern of dysbiosis that may reflect reverse causation, due to non-specific effects of illness-in-general. Combining a range of disorders into an aggregate non-healthy active control (ANHAC) group should highlight such non-specific dysbiosis. Differential dysbiosis between the ANHAC group and specific disorders may then reflect effects of treatment or bowel dysfunc...

ObjectiveEvidence on the association between the gut microbiome and metabolic conditions has been increasing during the past decades. Unlike the straightforward identification of beneficial non-pathogenic bacteria as a potential probiotic for clinical use, the analysis of gut microbiome diversity is more complex and required a better understanding of various measures. We aim to summarize an elaborated list of gut microbiome diversity measures. DesignSystematic search was conducted in three data...

Background Short-chain fatty acids (SCFAs) are widely used as functional readouts of gut microbial activity in vivo. The growing adoption of decentralised study designs and self-collection protocols has amplified the need for reliable room-temperature storage and shipment strategies. However, SCFAs volatility and the persistence of post-collection microbial metabolism raise concerns regarding pre-analytical stability and the interpretability of measured concentrations. Methods We assessed the te...

BackgroundDespite recent efforts, a single factor underlying the gut microbiota dysbiosis in intestinal diseases is not identified. We hypothesized that compromised intestinal barrier (CIB) could lead to increased host-derived contents including human cells in the gut, change its physio-metabolic properties, and globally alter gut microbiota and their metabolic capacities. ResultsConsistently, we found human DNA contents (HDCs), calculated as the percentage of metagenomic sequencing reads mappe...

Dysregulation of the gut microbiota/gut hormone axis contributes to the pathogenesis of irritable bowel syndrome (IBS). Melatonin plays a beneficial role in gut motility and immunity. However, altered expression of local mucosal melatonin in IBS and its relationship with the gut microbiota remain unclear. Therefore, we aimed to detect the colonic melatonin levels and microbiota profiles in patients with diarrhea-predominant IBS (IBS-D) and explore their relationship in germ-free (GF) rats and BO...

Recent studies have accumulated evidence that the intestinal environment is strongly correlated with host diet, which influences host health. A number of dietary products whose mechanisms of influence operate via the gut microbiota have been revealed, but they are still limited. Here, we investigated the dietary influence of Chlorella, a green alga commercially available as a dietary supplement. A randomized, double-blind, placebo-controlled crossover trial including 40 Japanese participants wit...

BackgroundGlobally, ulcerative colitis (UC) is the most common form of intestinal inflammation, which is believed to be the result of a deregulated immune system response to commensal microbiota in a genetically susceptible host. Multicellular organisms rely heavily on their commensal symbiotic microbiota, whose composition is closely related to intrinsic local characteristics and regulated or modified by environmental factors. In the present study we aim to describe the unknown gut microbiota o...

Progression of chronic liver diseases is precipitated by hepatocyte loss, inflammation and fibrosis. This process results in the loss of critical hepatic functions, increasing morbidity and the risk of infection. Medical interventions that treat complications of hepatic failure, including antibiotic administration for systemic infections, impact gut microbiome composition and metabolite production. Using a multi-omics approach on 850 fecal samples from 263 patients with acute or chronic liver di...