scholarly journals P053 Overabundance of Lactobacillus species in gut microbiota of IBD patients

2021 ◽  
Vol 15 (Supplement_1) ◽  
pp. S160-S161
Author(s):  
D Khusnutdinova ◽  
M Markelova ◽  
M Siniagina ◽  
E Boulygina ◽  
S Abdulkhakov ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Intestinal Microbiota ◽  
Active Phase ◽  
Bioinformatic Analysis ◽  
Lactobacillus Species ◽  
Control Group ◽  
Metagenomic Sequencing ◽  
Shotgun Metagenomic Sequencing ◽  
Inflammatory Bowel ◽  
Stool Samples

Abstract Background Changes in the composition of gut microbiota, and their metabolic pathways, are important factors in the pathogenesis of inflammatory bowel disease (IBD). Many clinical trials have shown that taking probiotics based on Lactobacillus has a positive effect on patients with IBD. However, Lactobacillus should be used more carefully during the active phase of IBD, since some strains can negatively affect the pathogenesis of the disease1,2. The aim of this study was to assess the diversity of Lactobacillus species in the gut microbiome of IBD patients and healthy volunteers. Methods In the study, 62 stool samples from healthy people, 31 from patients with Crohn’s disease (CD), and 34 - ulcerative colitis (UC) in active phase were analyzed. DNA was isolated using the QIAamp Fast DNA Stool Mini Kit (Qiagen, USA) following with shotgun metagenomic sequencing the NextSeq 500 (project #0671-2020-0058). Bioinformatic analysis was performed with the MetaPhlAn2 package. Results An increased relative abundance of Lactobacillus was found in patients with IBD (3.2% ± 6.6% in CD and 1.6% ± 2.8 in UC) compared to healthy individuals (0.3% ± 1.2%, p<0.05). In the control group, Lactobacillus were absent in 41% of samples and 1–5 species were found in 58% of samples. Most CD and UC patients are characterized by the presence of 3 to 5 species of Lactobacillus (38% and 31%, respectively). For 23% of CD patients and 26% of UC patients, 6 to 9 types of Lactobacillus were found. Some patients with IBD have more than 10 different types of Lactobacillus in the gut microbiota (Fig.1). The intestinal microbiota in IBD patients is characterized by an increased abundance of several species: L. salivarius, L. gasseri, L. mucosae, as well as L. casei paracasei in patients with CD and L. vaginalis in patients with UC (Fig.2). Conclusion The composition of the intestinal microbiota of IBD patients differs significantly in terms of Lactobacillus proportion and species diversity. Overabundance of five Lactobacillus species could be associated with the active phase of IBD. References

scholarly journals Associations of the gut microbiome and clinical factors with acute GVHD in allogeneic HSCT recipients

2020 ◽  
Vol 4 (22) ◽  
pp. 5797-5809
Author(s):  
Emma E. Ilett ◽  
Mette Jørgensen ◽  
Marc Noguera-Julian ◽  
Jens Christian Nørgaard ◽  
Gedske Daugaard ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Bacterial Diversity ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Clinical Factors ◽  
Hematopoietic Stem ◽  
Lower Abundance ◽  
Shotgun Metagenomic Sequencing ◽  
Stool Samples ◽  
Gene Richness

Abstract Acute graft-versus-host disease (aGVHD) is a leading cause of transplantation-related mortality after allogeneic hematopoietic stem cell transplantation (aHSCT). 16S ribosomal RNA (16S rRNA) gene-based studies have reported that lower gut bacterial diversity and the relative abundance of certain bacteria after aHSCT are associated with aGVHD. Using shotgun metagenomic sequencing and a large cohort, we aimed to confirm and extend these observations. Adult aHSCT recipients with stool samples collected from day −30 to day 100 relative to aHSCT were included. One sample was selected per patient per period (pre-aHSCT (day −30 to day 0), early post-aHSCT (day 1 to day 28), and late post-aHSCT (day 29 to day 100)), resulting in 150 aHSCT recipients and 259 samples. Microbial and clinical factors were tested for differences between time periods and an association with subsequent aGVHD. Patients showed a decline in gut bacterial diversity posttransplant, with several patients developing a dominance of Enterococcus. A total of 36 recipients developed aGVHD at a median of 34 days (interquartile range, 26-50 days) post-aHSCT. Lower microbial gene richness (P = .02), a lower abundance of the genus Blautia (P = .05), and a lower abundance of Akkermansia muciniphila (P = .01) early post-aHSCT was observed in those who developed aGVHD. Myeloablative conditioning was associated with aGVHD along with a reduction in gene richness and abundance of Blautia and A muciniphila. These results confirm low diversity and Blautia being associated with aGVHD. Crucially, we add that pretransplant conditioning is associated with changes in gut microbiota. Investigations are warranted to determine the interplay of gut microbiota and conditioning in the development of aGVHD.

scholarly journals Lower Level of Bacteroides in the Gut Microbiota Is Associated with Inflammatory Bowel Disease: A Meta-Analysis

2016 ◽  
Vol 2016 ◽  
pp. 1-9 ◽  
Author(s):  
Yingting Zhou ◽  
Fachao Zhi
Keyword(s):  
Inflammatory Bowel Disease ◽  
Gut Microbiota ◽  
Bowel Disease ◽  
Meta Analysis ◽  
Active Phase ◽  
Cochrane Library ◽  
Control Group ◽  
Inflammatory Bowel ◽  
Normal Controls

Background and Aims. Multiple studies have reported associations between inflammatory bowel disease (IBD) and the flora disequilibrium of Bacteroides. We performed a meta-analysis of the available data to provide a more precise estimate of the association between Bacteroides level in the gut and IBD. Methods. We searched PubMed/MEDLINE, EMBASE, Cochrane Library, Wiley Library, BIOSIS previews, Web of Science, CNKI, and ScienceDirect databases for published literature on IBD and gut microbiota from 1990 to 2016. Quality of all eligible studies was assessed using the Newcastle-Ottawa Quality Assessment Scale (NOS). We compared the level of Bacteroides in IBD patients with that in a control group without IBD, different types of IBD patients, and IBD patients with active phase and in remission. Results. We identified 63 articles, 9 of which contained sufficient data for evaluation. The mean level of Bacteroides was significantly lower in Crohn’s disease (CD) and ulcerative colitis (UC) patients in active phase than in normal controls. The level of Bacteroides in remission CD and UC patients was much lower than patients in the control group. Bacteroides level was even lower in patients with CD and UC in active phase than in remission. Conclusions. This analysis suggests that lower levels of Bacteroides are associated with IBD, especially in active phase.

scholarly journals Gut microbiota differs between children with Inflammatory Bowel Disease and healthy siblings in taxonomic and functional composition: a metagenomic analysis

2017 ◽  
Vol 312 (4) ◽  
pp. G327-G339 ◽  
Author(s):  
Rebecca L. Knoll ◽  
Kristoffer Forslund ◽  
Jens Roat Kultima ◽  
Claudius U. Meyer ◽  
Ulrike Kullmer ◽  
...  
Keyword(s):  
Inflammatory Bowel Disease ◽  
Gut Microbiota ◽  
Bowel Disease ◽  
Virulence Genes ◽  
Metagenomic Sequencing ◽  
Fecal Microbiome ◽  
Microbial Dysbiosis ◽  
Healthy Siblings ◽  
Inflammatory Bowel ◽  
Sibling Study

Current treatment for pediatric inflammatory bowel disease (IBD) patients is often ineffective, with serious side effects. Manipulating the gut microbiota via fecal microbiota transplantation (FMT) is an emerging treatment approach but remains controversial. We aimed to assess the composition of the fecal microbiome through a comparison of pediatric IBD patients to their healthy siblings, evaluating risks and prospects for FMT in this setting. A case-control (sibling) study was conducted analyzing fecal samples of six children with Crohn’s disease (CD), six children with ulcerative colitis (UC) and 12 healthy siblings by metagenomic sequencing. In addition, lifetime antibiotic intake was retrospectively determined. Species richness and diversity were significantly reduced in UC patients compared with control [Mann-Whitney U-test false discovery rate (MWU FDR) = 0.011]. In UC, bacteria positively influencing gut homeostasis, e.g., Eubacterium rectale and Faecalibacterium prausnitzii, were significantly reduced in abundance (MWU FDR = 0.05). Known pathobionts like Escherichia coli were enriched in UC patients (MWU FDR = 0.084). Moreover, E. coli abundance correlated positively with that of several virulence genes (SCC > 0.65, FDR < 0.1). A shift toward antibiotic-resistant taxa in both IBD groups distinguished them from controls [MWU Benjamini-Hochberg-Yekutieli procedure (BY) FDR = 0.062 in UC, MWU BY FDR = 0.019 in CD). The collected results confirm a microbial dysbiosis in pediatric UC, and to a lesser extent in CD patients, replicating associations found previously using different methods. Taken together, these observations suggest microbiotal remodeling therapy from family donors, at least for children with UC, as a viable option. NEW & NOTEWORTHY In this sibling study, prior reports of microbial dysbiosis in IBD patients from 16S rRNA sequencing was verified using deep shotgun sequencing and augmented with insights into the abundance of bacterial virulence genes and bacterial antibiotic resistance determinants, seen against the background of data on the specific antibiotic intake of each of the study participants. The observed dysbiosis, which distinguishes patients from siblings, highlights such siblings as potential donors for microbiotal remodeling therapy in IBD.

scholarly journals Characteristics of Gut Microbiota in Children With Biliary Atresia After Liver Transplantation

2021 ◽  
Vol 12 ◽  
Author(s):  
Wei Song ◽  
Li-Ying Sun ◽  
Zhi-Jun Zhu ◽  
Lin Wei ◽  
Wei Qu ◽  
...  
Keyword(s):  
Liver Transplantation ◽  
Gut Microbiota ◽  
Biliary Atresia ◽  
Control Level ◽  
Control Group ◽  
Metagenomic Sequencing ◽  
Polyamine Biosynthesis ◽  
Fecal Samples ◽  
Linear Discriminant ◽  
Significant Difference

Background and AimsBiliary atresia (BA) is an idiopathic neonatal cholestasis and is the most common indication in pediatric liver transplantation (LT). Previous studies have suggested that the gut microbiota (GM) in BA is disordered. However, the effect of LT on gut dysbiosis in patients with BA has not yet been elucidated.MethodsPatients with BA (n = 16) and healthy controls (n = 10) were recruited. In the early life of children with BA, Kasai surgery is a typical procedure for restoring bile flow. According to whether BA patients had previously undergone Kasai surgery, we divided the post-LT patients into the with-Kasai group (n = 8) and non-Kasai group (n = 8). Fecal samples were collected in both the BA and the control group; among BA patients, samples were obtained again 6 months after LT. A total of 40 fecal samples were collected, of which 16 were pre-LT, 14 were post-LT (8 were with-Kasai, 6 were non-Kasai), and 10 were from the control group. Metagenomic sequencing was performed to evaluate the GM.ResultsThe Kruskal-Wallis test showed a statistically significant difference in the number of genes between the pre-LT and the control group, the pre-LT and the post-LT group (P &lt; 0.05), but no statistical difference between the post-LT and the control group. Principal coordinate analysis also showed that the microbiome structure was similar between the post-LT and control group (P &gt; 0.05). Analysis of the GM composition showed a significant decrease in Serratia, Enterobacter, Morganella, Skunalikevirus, and Phifllikevirus while short chain fatty acid (SCFA)-producing bacteria such as Roseburia, Blautia, Clostridium, Akkermansia, and Ruminococcus were increased after LT (linear discriminant analysis &gt; 2, P &lt; 0.05). However, they still did not reach the normal control level. Concerning functional profiles, lipopolysaccharide metabolism, multidrug resistance, polyamine biosynthesis, GABA biosynthesis, and EHEC/EPEC pathogenicity signature were more enriched in the post-LT group compared with the control group. Prior Kasai surgery had a specific influence on the postoperative GM.ConclusionLT partly improved the GM in patients with BA, which provided new insight into understanding the role of LT in BA.

scholarly journals Yoghurt Consumption is Associated With Transient Changes in the Composition of the Human Gut Microbiome

2020 ◽  
Author(s):  
Caroline Ivanne Le Roy ◽  
Alexander Kurilshikov ◽  
Emily Leeming ◽  
Alessia Visconti ◽  
Ruth Bowyer ◽  
...  
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
Visceral Fat ◽  
Gut Microbiome ◽  
Body Weight Gain ◽  
Healthy Eating Index ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Shotgun Metagenomic Sequencing

Abstract Background: Yoghurt contains live bacteria that could contribute via modulation of the gut microbiota to its reported beneficial effects such as reduced body weight gain and lower incidence of type 2 diabetes. To date, the association between yoghurt consumption and the composition of the gut microbiota is underexplored. Here we used clinical variables, metabolomics, 16S rRNA and shotgun metagenomic sequencing data collected on over 1000 predominantly female UK twins to define the link between the gut microbiota and yoghurt-associated health benefits. Results: According to food frequency questionnaires (FFQ), 73% of subjects consumed yoghurt. Consumers presented a healthier diet pattern (healthy eating index: beta = 2.17±0.34; P = 2.72x10-10) and improved metabolic health characterised by reduced visceral fat (beta = -28.18±11.71 g; P = 0.01). According to 16S rRNA gene analyses and whole shotgun metagenomic sequencing approach consistent taxonomic variations were observed with yoghurt consumption. More specifically, we identified higher abundance of species used as yoghurt starters Streptococcus thermophilus (beta = 0.41±0.051; P = 6.14x10-12) and sometimes added Bifidobacterium animalis subsp. lactis (beta = 0.30±0.052; P = 1.49x10-8) in the gut of yoghurt consumers. Replication in 1103 volunteers from the LifeLines-DEEP cohort confirmed the increase of S. thermophilus among yoghurt consumers. Using food records collected the day prior to faecal sampling we showed that increase in these two yoghurt bacteria could be transient. Metabolomics analysis revealed that B. animalis subsp. lactis was associated with 13 faecal metabolites including a 3-hydroxyoctanoic acid, known to be involved in the regulation of gut inflammation.Conclusions: Yoghurt consumption is associated with reduced visceral fat mass and changes in gut microbiome including transient increase of yoghurt-contained species (i.e. S. thermophilus and B. lactis).

Abstract P174: Adiposity Mediates the Association Between Gut Microbial Diversity and Hypertension: Cardia Study

Circulation ◽  
2020 ◽  
Vol 141 (Suppl_1) ◽  
Author(s):  
Yuichiro Yano ◽  
Anju Lulla ◽  
Annie Green Howard ◽  
Samuel Gidding ◽  
Paul Muntner ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Antihypertensive Medication ◽  
Diversity Index ◽  
Metagenomic Sequencing ◽  
Mediation Analyses ◽  
Shotgun Metagenomic Sequencing ◽  
Stool Samples ◽  
Microbiota Diversity ◽  
Microbial Effects

Introduction: We have shown that gut microbial diversity is associated with hypertension in the Coronary Artery Risk Development in Young Adults (CARDIA) Study. Animal models have documented gut microbial effects on adiposity, a known risk factor for hypertension. The extent to which adiposity may mediate the association between the gut microbiome and hypertension has not been studied. Hypothesis: We hypothesize that adiposity is a mediator of the association between gut microbial diversity and hypertension. Methods: We analyzed data from the CARDIA Study (480 participants). Shotgun metagenomic sequencing was performed on DNA extracted from stool samples collected at the Year 30 exam (2015-2016). Taxonomic classification of sequenced reads was performed using Kraken2. Within-person gut microbial diversity was assessed at the genus level using the Shannon Diversity Index and richness (number of distinct genera); lower values indicate less diversity. Hypertension was defined as systolic BP ≥140, diastolic BP ≥90 mm Hg, or taking antihypertensive medication. We performed mediation analyses to quantify the percentage of the total estimated effect of gut microbial diversity on hypertension that is mediated by adiposity as assessed using body mass index (BMI). Results: Mean age of the participants was 55.1 (3.4) years, 47% were African American, and 53% were female. In multivariable-adjusted mediation analysis, BMI explained on average 26-34% of the association between gut microbiota diversity and hypertension (Table). Results were robust to adjustment for sociodemographic variables (Model 2) and health behaviors (Model 3). Conclusions: Approximately one-third of the total effect of gut microbial diversity on hypertension is mediated through adiposity.

scholarly journals Diversity and Function of Wolf Spider Gut Microbiota Revealed by Shotgun Metagenomics

2021 ◽  
Vol 12 ◽  
Author(s):  
Runbiao Wu ◽  
Luyu Wang ◽  
Jianping Xie ◽  
Zhisheng Zhang
Keyword(s):  
Gut Microbiota ◽  
Wolf Spider ◽  
Metagenomic Sequencing ◽  
Wolf Spiders ◽  
Shotgun Metagenomics ◽  
Microbial Genomes ◽  
Shotgun Metagenomic Sequencing ◽  
Crucial Component ◽  
Genes Encoding ◽  
And Function

Wolf spiders (Lycosidae) are crucial component of integrated pest management programs and the characteristics of their gut microbiota are known to play important roles in improving fitness and survival of the host. However, there are only few studies of the gut microbiota among closely related species of wolf spider. Whether wolf spiders gut microbiota vary with habitats remains unknown. Here, we used shotgun metagenomic sequencing to compare the gut microbiota of two wolf spider species, Pardosa agraria and P. laura from farmland and woodland ecosystems, respectively. The results show that the gut microbiota of Pardosa spiders is similar in richness and abundance. Approximately 27.3% of the gut microbiota of P. agraria comprises Proteobacteria, and approximately 34.5% of the gut microbiota of P. laura comprises Firmicutes. We assembled microbial genomes and found that the gut microbiota of P. laura are enriched in genes for carbohydrate metabolism. In contrast, those of P. agraria showed a higher proportion of genes encoding acetyltransferase, an enzyme involved in resistance to antibiotics. We reconstructed three high-quality and species-level microbial genomes: Vulcaniibacterium thermophilum, Anoxybacillus flavithermus and an unknown bacterium belonging to the family Simkaniaceae. Our results contribute to an understanding of the diversity and function of gut microbiota in closely related spiders.

The Nursing Home Older Adult Gut Microbiome Composition Shows Time-dependent Dysbiosis and is Influenced by Medication Exposures, Age, Environment, and Frailty

2021 ◽  
Author(s):  
John P Haran ◽  
Abigail Zeamer ◽  
Doyle V Ward ◽  
Protiva Dutta ◽  
Vanni Bucci ◽  
...  
Keyword(s):  
Older Adults ◽  
Gut Microbiota ◽  
Older Adult ◽  
Gut Microbiome ◽  
Assessment Tool ◽  
Mini Nutritional Assessment ◽  
Metagenomic Sequencing ◽  
Mixed Effect ◽  
Stool Samples ◽  
Over Time

Abstract Older adults in nursing homes (NHs) have increased frailty, medication, and antimicrobial exposures, all factors that are known to affect the composition of gut microbiota. Our objective was to define which factors have the greatest association with the NH resident gut microbiota, explore patterns of dysbiosis and compositional changes in gut microbiota over time in this environment. We collected serial stool samples from NH residents. Residents were assessed using the Mini Nutritional Assessment tool and Clinical Frailty Scale. Bacterial composition of resident stool samples was determined by metagenomic sequencing. We used mixed-effect random forest modeling to identify clinical covariates that associate with microbiota. We enrolled and followed 166 residents from 5 NHs collecting 512 stool samples and following 15 residents for &gt; 1 year. Medications, particularly psychoactive and anti-hypertensive medications, had the greatest effect on the microbiota. Age and frailty also contributed, and were associated with increased and decreased diversity, respectively. The microbiota of residents who had lived in the NH for &gt; 1 year were enriched in inflammatory and pathogenic species and reduced in anti-inflammatory and symbiotic species. We observed intra-individual stability of the microbiome among older adults who had lived in the NH already for &gt;1 year followed with sample collections 1 year apart. Older adult NH gut microbiome is heavily influenced by medications, age, and frailty. This microbiome is influenced by length of NH residence with dysbiosis becoming evident at 12 months, however after this point there is demonstrated relative stability over time.

scholarly journals The Central Role of the Gut Microbiota in Chronic Inflammatory Diseases

2014 ◽  
Vol 2014 ◽  
pp. 1-12 ◽  
Author(s):  
Caroline Marcantonio Ferreira ◽  
Angélica Thomaz Vieira ◽  
Marco Aurelio Ramirez Vinolo ◽  
Fernando A. Oliveira ◽  
Rui Curi ◽  
...  
Keyword(s):  
Immune System ◽  
Gut Microbiota ◽  
Intestinal Microbiota ◽  
Immune Cell ◽  
Inflammatory Diseases ◽  
Sequencing Analysis ◽  
Metagenomic Sequencing ◽  
Microbiota Composition ◽  
Chronic Inflammatory Diseases ◽  
Commensal Microbiota

The commensal microbiota is in constant interaction with the immune system, teaching immune cells to respond to antigens. Studies in mice have demonstrated that manipulation of the intestinal microbiota alters host immune cell homeostasis. Additionally, metagenomic-sequencing analysis has revealed alterations in intestinal microbiota in patients suffering from inflammatory bowel disease, asthma, and obesity. Perturbations in the microbiota composition result in a deficient immune response and impaired tolerance to commensal microorganisms. Due to altered microbiota composition which is associated to some inflammatory diseases, several strategies, such as the administration of probiotics, diet, and antibiotic usage, have been utilized to prevent or ameliorate chronic inflammatory diseases. The purpose of this review is to present and discuss recent evidence showing that the gut microbiota controls immune system function and onset, development, and resolution of some common inflammatory diseases.

scholarly journals Gut Dysbiosis and IL-21 Response in Patients with Severe COVID-19

2021 ◽  
Vol 9 (6) ◽  
pp. 1292
Author(s):  
Mahejibin Khan ◽  
Bijina J. Mathew ◽  
Priyal Gupta ◽  
Garima Garg ◽  
Sagar Khadanga ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Disease Severity ◽  
Inflammatory Responses ◽  
Control Group ◽  
Medical Sciences ◽  
Predisposing Factor ◽  
Cross Sectional ◽  
Metagenomics Data ◽  
Stool Samples ◽  
Gut Microbiota Dysbiosis

Background: The disease severity, ranging from being asymptomatic to having acute illness, and associated inflammatory responses has suggested that alterations in the gut microbiota may play a crucial role in the development of chronic disorders due to COVID-19 infection. This study describes gut microbiota dysbiosis in COVID-19 patients and its implications relating to the disease. Design: A cross sectional prospective study was performed on thirty RT-PCR-confirmed COVID-19 patients admitted to the All India Institute of Medical Sciences, Bhopal, India, between September 10 and 20, 2020. Ten healthy volunteers were recruited as the control group. IFN, TNF, and IL-21 profiling was conducted using plasma samples, and gut bacterial analysis was performed after obtaining the metagenomics data of stool samples. Results: Patients with a variable COVID-19 severity showed distinct gut microflora and peripheral interleukin-21 levels. A low Firmicute/Bacteroidetes ratio, caused by the depletion of the fibre-utilizing bacteria, F. prausnitzii, B. Plebius, and Prevotella, and an increase in Bacteroidetes has associated gut microbiota dysbiosis with COVID-19 disease severity. Conclusions: The loss of the functional attributes of signature commensals in the gut, due to dysbiosis, is a predisposing factor of COVID-19 pathophysiology.

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