scholarly journals Dynamics of the human gut microbiome in inflammatory bowel disease

2017 ◽  
Vol 2 (5) ◽  
Author(s):  
Jonas Halfvarson ◽  
Colin J. Brislawn ◽  
Regina Lamendella ◽  
Yoshiki Vázquez-Baeza ◽  
William A. Walters ◽  
...  
Keyword(s):  
Inflammatory Bowel Disease ◽  
Bowel Disease ◽  
Gut Microbiome ◽  
Human Gut ◽  
Human Gut Microbiome ◽  
Inflammatory Bowel

scholarly journals The taxonomic distribution of histamine-secreting bacteria in the human gut microbiome

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Zhongyu Mou ◽  
Yiyan Yang ◽  
A. Brantley Hall ◽  
Xiaofang Jiang
Keyword(s):  
Inflammatory Bowel Disease ◽  
Bowel Disease ◽  
Gut Microbiome ◽  
Human Gut ◽  
Taxonomic Distribution ◽  
Human Gut Microbiome ◽  
Endogenous Histamine ◽  
Histamine Production ◽  
Significant Enrichment ◽  
Inflammatory Bowel

Abstract Background Biogenic histamine plays an important role in immune response, neurotransmission, and allergic response. Although endogenous histamine production has been extensively studied, the contributions of histamine produced by the human gut microbiota have not been explored due to the absence of a systematic annotation of histamine-secreting bacteria. Results To identify the histamine-secreting bacteria from in the human gut microbiome, we conducted a systematic search for putative histamine-secreting bacteria in 36,554 genomes from the Genome Taxonomy Database and Unified Human Gastrointestinal Genome catalog. Using bioinformatic approaches, we identified 117 putative histamine-secreting bacteria species. A new three-component decarboxylation system including two colocalized decarboxylases and one transporter was observed in histamine-secreting bacteria among three different phyla. We found significant enrichment of histamine-secreting bacteria in patients with inflammatory bowel disease but not in patients with colorectal cancer suggesting a possible association between histamine-secreting bacteria and inflammatory bowel disease. Conclusions The findings of this study expand our knowledge of the taxonomic distribution of putative histamine-secreting bacteria in the human gut.

scholarly journals Biomass distances from personalized multispecies dynamic flux balance analysis of the human gut microbiome identify dietary influences for patients with and without inflammatory bowel disease

2019 ◽  
Author(s):  
Alexandros C. Dimopoulos ◽  
Martin Reczko
Keyword(s):  
Inflammatory Bowel Disease ◽  
Flux Balance Analysis ◽  
Bowel Disease ◽  
Gut Microbiome ◽  
Human Gut ◽  
Human Gut Microbiome ◽  
Dynamic Flux Balance Analysis ◽  
Flux Balance ◽  
Balance Analysis ◽  
Inflammatory Bowel

A parallelized version of a multispecies dynamic flux balance analysis (msdFBA) algorithm is implemented and applied to the AGORA collection of genome-scale metabolic reconstructions for 818 members of the human gut microbiome. The msdFBA method assumes the well stirred interaction mode of all organisms to exchange external metabolites. In each msdFBA simulation, the biomasses the gut microbiome composition of one of 149 patients from NIH Human Microbiome Project is used for initialization in combination with one of 11 different diets used as substrates as defined in the Virtual Metabolic Human database. The union of all species in the patient data comprises 255 different microbes. The patients are either healthy or suffer from inflammatory bowel disease (IBD). The msdFBA simulation is performed for 50 time steps. For all combinations of patients and time steps, the euclidean distance between the vector of the biomasses of the 255 patient species and the evolving vector of biomasses for the same species is calculated, providing the information about the biomass distance to each patient during each simulation. To quantify the overall influence of a diet for all patients, a diet score is defined as the sum of the reciprocal distances to the closest patient at the last time step, in case the closest patient is diseased, subtracted from the respective sum for the case that the closest patient is healthy. With this score, the known beneficial influences both of a high fiber and a gluten free diet for IBD is verified. Noteworthy is the utility of a Mediterranean diet in this context, having similar distance patterns. The proposed method provides an universal platform for the in-silico analysis of different environmental influences like diets for different microbiotas defined by metagenomic quantifications from individual patients and has the potential to generate additional dietary recommendations for the management of various other diseases.

scholarly journals Decoding the Language of Microbiomes: Leveraging Patterns in 16S Public Data using Word-Embedding Techniques and Applications in Inflammatory Bowel Disease

2019 ◽  
Author(s):  
Christine A. Tataru ◽  
Maude M. David
Keyword(s):  
Inflammatory Bowel Disease ◽  
Bowel Disease ◽  
Gut Microbiome ◽  
Metabolic Pathways ◽  
Community Level ◽  
Human Gut ◽  
Human Gut Microbiome ◽  
Inflammatory Bowel ◽  
Microbiome Data ◽  
Positive Results

AbstractMicrobiomes are complex ecological systems that play crucial roles in understanding natural phenomena from human disease to climate change. Especially in human gut microbiome studies, where collecting clinical samples can be arduous, the number of taxa considered in any one study often exceeds the number of samples ten to one hundred-fold. This discrepancy decreases the power of studies to identify meaningful differences between samples, increases the likelihood of false positive results, and subsequently limits reproducibility. Despite the vast collections of microbiome data already available, biome-specific patterns of microbial structure are not currently leveraged to inform studies. Instead, most microbiome survey studies focus on differential abundance testing per taxa in pursuit of specific biomarkers for a given phenotype. This methodology assumes differences in individual species, genera, or families can be used to distinguish between microbial communities and ignores community-level response. In this paper, we propose to leverage public microbiome databases to shift the analysis paradigm from a focus on taxonomic counts to a focus on comprehensive properties that more completely characterize microbial community members’ function and environmental relationships. We learn these properties by applying an embedding algorithm to quantify taxa co-occurrence patterns in over 18,000 samples from the American Gut Project (AGP) microbiome crowdsourcing effort. The resulting set of embeddings transforms human gut microbiome data from thousands of taxa counts to a latent variable landscape of only one hundred “properties”, or contextual relationships. We then compare the predictive power of models trained using properties, normalized taxonomic count data, and another commonly used dimensionality reduction method, Principal Component Analysis in categorizing samples from individuals with inflammatory bowel disease (IBD) and healthy controls. We show that predictive models trained using property data are the most accurate, robust, and generalizable, and that property-based models can be trained on one dataset and deployed on another with positive results. Furthermore, we find that these properties can be interpreted in the context of current knowledge; properties correlate significantly with known metabolic pathways, and distances between taxa in “property space” roughly correlate with their phylogenetic distances. Using these properties, we are able to extract known and new bacterial metabolic pathways associated with inflammatory bowel disease across two completely independent studies.More broadly, this paper explores a reframing of the microbiome analysis mindset, from taxonomic counts to comprehensive community-level properties. By providing a set of pre-trained embeddings, we allow any V4 16S amplicon study to leverage and apply the publicly informed properties presented to increase the statistical power, reproducibility, and generalizability of analysis.

scholarly journals Human Gut Microbiome Transplantation in Ileitis Prone Mice: A Tool for the Functional Characterization of the Microbiota in Inflammatory Bowel Disease Patients

2019 ◽  
Author(s):  
Abigail R Basson ◽  
Adrian Gomez-Nguyen ◽  
Paola Menghini ◽  
Ludovica F Buttó ◽  
Luca Di Martino ◽  
...  
Keyword(s):  
Inflammatory Bowel Disease ◽  
Mouse Model ◽  
Bowel Disease ◽  
Gut Microbiome ◽  
Fecal Microbiota Transplantation ◽  
Fecal Microbiota ◽  
Human Gut ◽  
Variable Effect ◽  
Inflammatory Bowel ◽  
Anti Inflammatory

Abstract Background Inflammatory bowel disease (IBD) is a lifelong digestive disease characterized by periods of severe inflammation and remission. To our knowledge, this is the first study showing a variable effect on ileitis severity from human gut microbiota isolated from IBD donors in remission and that of healthy controls in a mouse model of IBD. Methods We conducted a series of single-donor intensive and nonintensive fecal microbiota transplantation (FMT) experiments using feces from IBD patients in remission and healthy non-IBD controls (N = 9 donors) in a mouse model of Crohn’s disease (CD)-like ileitis that develops ileitis in germ-free (GF) conditions (SAMP1/YitFC; N = 96 mice). Results Engraftment studies demonstrated that the microbiome of IBD in remission could have variable effects on the ileum of CD-prone mice (pro-inflammatory, nonmodulatory, or anti-inflammatory), depending on the human donor. Fecal microbiota transplantation achieved a 95% ± 0.03 genus-level engraftment of human gut taxa in mice, as confirmed at the operational taxonomic unit level. In most donors, microbiome colonization abundance patterns remained consistent over 60 days. Microbiome-based metabolic predictions of GF mice with Crohn’s or ileitic-mouse donor microbiota indicate that chronic amino/fatty acid (valine, leucine, isoleucine, histidine; linoleic; P < 1e-15) alterations (and not bacterial virulence markers; P > 0.37) precede severe ileitis in mice, supporting their potential use as predictors/biomarkers in human CD. Conclusion The gut microbiome of IBD remission patients is not necessarily innocuous. Characterizing the inflammatory potential of each microbiota in IBD patients using mice may help identify the patients’ best anti-inflammatory fecal sample for future use as an anti-inflammatory microbial autograft during disease flare-ups.

scholarly journals Bacteria Effect On Health and Human-Review

2019 ◽  
Vol 1 (1) ◽  
pp. 23-27
Author(s):  
Saali Mohammed Lutfi
Keyword(s):  
Inflammatory Bowel Disease ◽  
Human Health ◽  
Chronic Diseases ◽  
Bowel Disease ◽  
Dietary Habits ◽  
Gut Bacteria ◽  
Nerve Function ◽  
Human Gut ◽  
Inflammatory Bowel ◽  
Bacteria Communities

Microbes are an important component of the microbiology  eco-system in the human gut, which is colonized by 1014 bacteria , ten times more than the human cells. Gut bacteria take  an important role in human health, like  supplying essential nutrients, synthesizing vit. K, aiding in the digestion of cellulose, and promoting angiogenesis and enteric nerve function. However, they can also be potentially harmful due to the change of their composition when the gut ecosystem undergoes abnormal changes in the light of the use of antibiotics, illness, stress, aging, bad dietary habits, and lifestyle. Dysbiosis of the gut bacteria communities can cause many chronic diseases, such as inflammatory bowel disease, obesity, cancer, and autism.

scholarly journals A Distinct Contractile Injection System Gene Cluster Found in a Majority of Healthy Adult Human Microbiomes

mSystems ◽  
2020 ◽  
Vol 5 (4) ◽  
Author(s):  
Maria I. Rojas ◽  
Giselle S. Cavalcanti ◽  
Katelyn McNair ◽  
Sean Benler ◽  
Amanda T. Alker ◽  
...  
Keyword(s):  
Inflammatory Bowel Disease ◽  
Gene Cluster ◽  
Bowel Disease ◽  
Human Microbiome ◽  
Gene Clusters ◽  
The United States ◽  
Injection System ◽  
Human Gut ◽  
Human Host ◽  
Inflammatory Bowel

ABSTRACT Many commensal bacteria antagonize each other or their host by producing syringe-like secretion systems called contractile injection systems (CIS). Members of the Bacteroidales family have been shown to produce only one type of CIS—a contact-dependent type 6 secretion system that mediates bacterium-bacterium interactions. Here, we show that a second distinct cluster of genes from Bacteroidales bacteria from the human microbiome may encode yet-uncharacterized injection systems that we term Bacteroidales injection systems (BIS). We found that BIS genes are present in the gut microbiomes of 99% of individuals from the United States and Europe and that BIS genes are more prevalent in the gut microbiomes of healthy individuals than in those individuals suffering from inflammatory bowel disease. Gene clusters similar to that of the BIS mediate interactions between bacteria and diverse eukaryotes, like amoeba, insects, and tubeworms. Our findings highlight the ubiquity of the BIS gene cluster in the human gut and emphasize the relevance of the gut microbiome to the human host. These results warrant investigations into the structure and function of the BIS and how they might mediate interactions between Bacteroidales bacteria and the human host or microbiome. IMPORTANCE To engage with host cells, diverse pathogenic bacteria produce syringe-like structures called contractile injection systems (CIS). CIS are evolutionarily related to the contractile tails of bacteriophages and are specialized to puncture membranes, often delivering effectors to target cells. Although CIS are key for pathogens to cause disease, paradoxically, similar injection systems have been identified within healthy human microbiome bacteria. Here, we show that gene clusters encoding a predicted CIS, which we term Bacteroidales injection systems (BIS), are present in the microbiomes of nearly all adult humans tested from Western countries. BIS genes are enriched within human gut microbiomes and are expressed both in vitro and in vivo. Further, a greater abundance of BIS genes is present within healthy gut microbiomes than in those humans with with inflammatory bowel disease (IBD). Our discovery provides a potentially distinct means by which our microbiome interacts with the human host or its microbiome.

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