No distinct microbiome signature of irritable bowel syndrome found in a Swedish random population

ObjectiveThe ethiopathogenesis of irritable bowel syndrome (IBS) is unknown. While a link to the gut microbiome is postulated, the heterogeneity of the healthy gut makes it difficult to draw definitive conclusions. We aimed to describe the faecal and mucosa-associated microbiome (MAM) and health correlates on a community cohort of healthy and IBS individuals with no colonoscopic findings.DesignThe PopCol study recruited a random sample of 3556 adults; 745 underwent colonoscopy. IBS was defined by Rome IV criteria and organic disease excluded. 16S rRNA gene sequencing was conducted on sigmoid biopsy samples from 376 representative individuals (63 IBS cases) and faecal samples from 185 individuals (32 IBS cases).ResultsWhile sigmoid MAM was dominated by Lachnospiraceae, faeces presented a higher relative abundance of Ruminococcaceae. Microbial richness in MAM was linearly correlated to that in faeces from the same individual (R²=0.255, p<3E-11) as was diversity (R²=0.06, p=0.0022). MAM diversity decreased with increasing body mass index (BMI; Pearson’s r=−0.1, p=0.08) and poorer self-rated health (r=−0.15, p=0.007), but no other health correlates. Faecal microbiome diversity was correlated to stool consistency (r=−0.16, p=0.043). Several taxonomic groups were correlated to age, BMI, depression and self-reported health, including Coprococcus catus associated with lower levels of depression (r=−0.003, p=0.00017). The degree of heterogeneity observed between IBS patients is higher than that observed between healthy individuals.ConclusionsNo distinct microbial signature was observed in IBS. Individuals presenting with low self-rated health or high BMI have lower gut microbiome richness.

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Integrative analysis of the gut microbiome and metabolome in a rat model with stress induced irritable bowel syndrome

Scientific Reports ◽

10.1038/s41598-021-97083-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Yue Hu ◽

Fang Chen ◽

Haiyong Ye ◽

Bin Lu

Keyword(s):

Irritable Bowel Syndrome ◽

Gut Microbiota ◽

Rat Model ◽

Gut Microbiome ◽

16S Rrna Gene Sequencing ◽

Metabolic Phenotype ◽

Control Group ◽

Rrna Gene ◽

Microbial Dysbiosis ◽

Irritable Bowel

AbstractStress is one of the major causes of irritable bowel syndrome (IBS), which is well-known for perturbing the microbiome and exacerbating IBS-associated symptoms. However, changes in the gut microbiome and metabolome in response to colorectal distention (CRD), combined with restraint stress (RS) administration, remains unclear. In this study, CRD and RS stress were used to construct an IBS rat model. The 16S rRNA gene sequencing was used to characterize the microbiota in ileocecal contents. UHPLC-QTOF-MS/MS assay was used to characterize the metabolome of gut microbiota. As a result, significant gut microbial dysbiosis was observed in stress-induced IBS rats, with the obvious enrichment of three and depletion of 11 bacterial taxa in IBS rats, when compared with those in the control group (q < 0.05). Meanwhile, distinct changes in the fecal metabolic phenotype of stress-induced IBS rats were also found, including five increased and 19 decreased metabolites. Furthermore, phenylalanine, tyrosine and tryptophan biosynthesis were the main metabolic pathways induced by IBS stress. Moreover, the altered gut microbiota had a strong correlation with the changes in metabolism of stress-induced IBS rats. Prevotella bacteria are correlated with the metabolism of 1-Naphthol and Arg.Thr. In conclusion, the gut microbiome, metabolome and their interaction were altered. This may be critical for the development of stress-induced IBS.

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A novel stepwise integrative analysis pipeline reveals distinct microbiota-host interactions and link to symptoms in irritable bowel syndrome

Scientific Reports ◽

10.1038/s41598-021-84686-9 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Annikka Polster ◽

Lena Öhman ◽

Julien Tap ◽

Muriel Derrien ◽

Boris Le Nevé ◽

...

Keyword(s):

Irritable Bowel Syndrome ◽

Complex Variable ◽

16S Rrna Gene Sequencing ◽

Integrative Analysis ◽

Rrna Gene ◽

Analysis Pipeline ◽

Host Interactions ◽

Functional Relationships ◽

Irritable Bowel ◽

Host Genes

AbstractAlthough incompletely understood, microbiota-host interactions are assumed to be altered in irritable bowel syndrome (IBS). We, therefore, aimed to develop a novel analysis pipeline tailored for the integrative analysis of microbiota-host interactions and association to symptoms and prove its utility in a pilot cohort. A multilayer stepwise integrative analysis pipeline was developed to visualize complex variable associations. Application of the pipeline was demonstrated on a dataset of IBS patients and healthy controls (HC), using the R software package to analyze colonic host mRNA and mucosal microbiota (16S rRNA gene sequencing), as well as gastrointestinal (GI) and psychological symptoms. In total, 42 IBS patients (57% female, mean age 33.6 (range 18–58)) and 20 HC (60% female, mean age 26.8 (range 23–41)) were included. Only in IBS patients, mRNA expression of Toll-like receptor 4 and genes associated with barrier function (PAR2, OCLN, TJP1) intercorrelated closely, suggesting potential functional relationships. This host genes-based “permeability cluster” was associated to mucosa-adjacent Chlamydiae and Lentisphaerae, and furthermore associated to satiety as well as to anxiety, depression and fatigue. In both IBS patients and HC, chromogranins, secretogranins and TLRs clustered together. In IBS patients, this host genes-based “immune-enteroendocrine cluster” was associated to specific members of Firmicutes, and to depression and fatigue, whereas in HC no significant association to microbiota was identified. We have developed a stepwise integrative analysis pipeline that allowed identification of unique host-microbiota intercorrelation patterns and association to symptoms in IBS patients. This analysis pipeline may aid in advancing the understanding of complex variable associations in health and disease.

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Gut microbiome is affected by inter-sexual and inter-seasonal variation in diet for thick-billed murres (Uria lomvia)

Scientific Reports ◽

10.1038/s41598-020-80557-x ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Esteban Góngora ◽

Kyle H. Elliott ◽

Lyle Whyte

Keyword(s):

Gut Microbiome ◽

Sulfur Isotopes ◽

Trophic Position ◽

Isotope Analysis ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Uria Lomvia ◽

Fecal Microbiome ◽

Prey Specialization ◽

Rrna Gene Sequencing

AbstractThe role of the gut microbiome is increasingly being recognized by health scientists and veterinarians, yet its role in wild animals remains understudied. Variations in the gut microbiome could be the result of differential diets among individuals, such as variation between sexes, across seasons, or across reproductive stages. We evaluated the hypothesis that diet alters the avian gut microbiome using stable isotope analysis (SIA) and 16S rRNA gene sequencing. We present the first description of the thick-billed murre (Uria lomvia) fecal microbiome. The murre microbiome was dominated by bacteria from the genus Catellicoccus, ubiquitous in the guts of many seabirds. Microbiome variation was explained by murre diet in terms of proportion of littoral carbon, trophic position, and sulfur isotopes, especially for the classes Actinobacteria, Bacilli, Bacteroidia, Clostridia, Alphaproteobacteria, and Gammaproteobacteria. We also observed differences in the abundance of bacterial genera such as Catellicoccus and Cetobacterium between sexes and reproductive stages. These results are in accordance with behavioural observations of changes in diet between sexes and across the reproductive season. We concluded that the observed variation in the gut microbiome may be caused by individual prey specialization and may also be reinforced by sexual and reproductive stage differences in diet.

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Correction: 16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome

PLoS ONE ◽

10.1371/journal.pone.0212474 ◽

2019 ◽

Vol 14 (2) ◽

pp. e0212474 ◽

Cited By ~ 1

Author(s):

Daniel E. Almonacid ◽

Laurens Kraal ◽

Francisco J. Ossandon ◽

Yelena V. Budovskaya ◽

Juan Pablo Cardenas ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Gut Microbiome ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Reference Ranges ◽

Human Gut ◽

Human Gut Microbiome ◽

Rrna Gene Sequencing

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The Effect of Xuebijing on the Gut Microbiota and Metabolic of Heat 1 Stroke Rat 2

10.21203/rs.3.rs-142370/v1 ◽

2021 ◽

Author(s):

Qiang wen ◽

Xuan He ◽

Yu Shao ◽

Lun Peng ◽

Li Zhao ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Gut Microbiome ◽

Heat Stroke ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Control Group ◽

Rrna Gene ◽

Metabolism Pathway ◽

Rrna Gene Sequencing

Abstract The goal of the present study was to evaluate the fecal microbiome and serum metabolites in 16 Xuebijing (XBJ)-injected rats after heat stroke using 16S rRNA gene sequencing and gas chromatography-mass spectrometry (GC-MS) metabolomics. Eighteen rats were divided into the control group (CON), heat stroke group (HS), and XBJ group. The 16S rRNA gene sequencing results revealed that the abundance of Bacteroidetes was overrepresented in the XBJ group compared to the HS group, while Actinobacteria was underrepresented. Metabolomic profiling showed that the pyrimidine metabolism pathway, pentose phosphate pathway, and glycerophospholipid metabolism pathway were upregulated in the XBJ group compared to the HS group. Taken together, these results demonstrated that heat stroke not only altered the gut microbiome community structure of rats but also greatly affected metabolic functions, leading to gut microbiome toxicity.

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Dietary sphinganine is selectively assimilated by members of the gut microbiome

10.1101/2020.06.08.140665 ◽

2020 ◽

Author(s):

Min-Ting Lee ◽

Henry H. Le ◽

Elizabeth L. Johnson

Keyword(s):

Gut Microbiome ◽

16S Rrna Gene Sequencing ◽

Dietary Lipids ◽

Rrna Gene ◽

Bioactive Components ◽

Microbiome Composition ◽

Metabolic Products ◽

Comparative Metabolomics ◽

Rrna Gene Sequencing ◽

Gut Microbial Community

AbstractFunctions of the gut microbiome have a growing number of implications for host metabolic health, with diet being one of the most significant influences on microbiome composition. Compelling links between diet and the gut microbiome suggest key roles for various macronutrients, including lipids, yet how individual classes of dietary lipids interact with the microbiome remain largely unknown. A class of lipids known as sphingolipids are bioactive components of most foods and are produced by prominent gut microbes. This makes sphingolipids intriguing candidates for shaping diet-microbiome interactions. Here, we use a click-chemistry based approach to track the incorporation of bioorthogonal dietary omega-alkynyl sphinganine (sphinganine alkyne – SAA) into the gut microbial community (Click). Identification of microbe and SAA-specific metabolic products was achieved by fluorescence-based sorting of SAA containing microbes (Sort), 16S rRNA gene sequencing to identify the sphingolipid-interacting microbes (Seq), and comparative metabolomics to identify products of SAA assimilation by the microbiome (Spec). Together this approach, Click-Sort-Seq-Spec (ClickSSS), revealed that SAA-assimilation was nearly exclusively performed by gut Bacteroides, indicating that sphingolipid-producing bacteria play a major role in processing dietary sphinganine. Comparative metabolomics of cecal microbiota from SAA-treated mice showed conversion of SAA to a suite of dihydroceramides, consistent with metabolic activity via Bacteroides and Bifidobacterium. Additionally, other sphingolipid-interacting microbes were identified with a focus on an uncharacterized ability of Bacteroides and Bifidobacterium to metabolize dietary sphingolipids. Therefore, ClickSSS provides a platform to study the flux of virtually any alkyne-labeled metabolite in diet-microbiome interactions.

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Commensal Bifidobacterium Strains Enhance the Efficacy of Neo-Epitope Based Cancer Vaccines

Vaccines ◽

10.3390/vaccines9111356 ◽

2021 ◽

Vol 9 (11) ◽

pp. 1356

Author(s):

Michele Tomasi ◽

Mattia Dalsass ◽

Francesco Beghini ◽

Ilaria Zanella ◽

Elena Caproni ◽

...

Keyword(s):

Gut Microbiome ◽

Cancer Vaccines ◽

Molecular Mimicry ◽

Large Body ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Shotgun Metagenomics ◽

Cancer Immunity ◽

Rrna Gene Sequencing

A large body of data both in animals and humans demonstrates that the gut microbiome plays a fundamental role in cancer immunity and in determining the efficacy of cancer immunotherapy. In this work, we have investigated whether and to what extent the gut microbiome can influence the antitumor activity of neo-epitope-based cancer vaccines in a BALB/c-CT26 cancer mouse model. Similarly to that observed in the C57BL/6-B16 model, Bifidobacterium administration per se has a beneficial effect on CT26 tumor inhibition. Furthermore, the combination of Bifidobacterium administration and vaccination resulted in a protection which was superior to vaccination alone and to Bifidobacterium administration alone, and correlated with an increase in the frequency of vaccine-specific T cells. The gut microbiome analysis by 16S rRNA gene sequencing and shotgun metagenomics showed that tumor challenge rapidly altered the microbiome population, with Muribaculaceae being enriched and Lachnospiraceae being reduced. Over time, the population of Muribaculaceae progressively reduced while the Lachnospiraceae population increased—a trend that appeared to be retarded by the oral administration of Bifidobacterium. Interestingly, in some Bacteroidales, Prevotella and Muribaculacee species we identified sequences highly homologous to immunogenic neo-epitopes of CT26 cells, supporting the possible role of “molecular mimicry” in anticancer immunity. Our data strengthen the importance of the microbiome in cancer immunity and suggests a microbiome-based strategy to potentiate neo-epitope-based cancer vaccines.

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Molecular and Microbial Signatures Predictive of Prebiotic Action of Neoagarotetraose in a Dextran Sulfate Sodium-Induced Murine Colitis Model

Microorganisms ◽

10.3390/microorganisms8070995 ◽

2020 ◽

Vol 8 (7) ◽

pp. 995

Author(s):

Fang Liu ◽

Jianan Liu ◽

Thomas T.Y. Wang ◽

Zhen Liu ◽

Changhu Xue ◽

...

Keyword(s):

Gut Microbiome ◽

Dextran Sulfate ◽

Dextran Sulfate Sodium ◽

Intestinal Inflammation ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Murine Colitis ◽

Bioactive Properties ◽

Rrna Gene Sequencing ◽

Colitis Model

Neoagarotetraose (NT), a hydrolytic product of agar by β-agarase, is known to possess bioactive properties. However, the mechanisms via which NT alleviates intestinal inflammation remain unknown. In this study, a dextran sulfate sodium (DSS)-induced murine model was developed to evaluate the effect of NT on gut microbiome and microbial metabolism using 16S rRNA gene sequencing and untargeted metabolomics. Our data demonstrate that NT ingestion improved gut integrity and inflammation scores. NT reversed the abundance of Proteobacteria from an elevated level induced by DSS and significantly increased the abundance of Verrucomicrobia. Further, NT significantly increased the abundance of Akkermansia and Lactobacillus and concomitantly decreased that of Sutterella, which were among the important features identified by random forests analysis contributing to classification accuracy for NT supplementation. A microbial signature consisting of Adlercreutzia (denominator) and Turicibacter (numerator) predicted the NT supplementation status. Moreover, NT significantly modulated multiple gut metabolites, particularly those related to histidine, polyamine and tocopherol metabolism. Together, our findings provided novel insights into the mechanisms by which NT modulated the gut microbiome and metabolome and should facilitate the development of NT as a potent prebiotic for colitis management.

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Digestive gland microbiome of Pleurobema cordatum: mesocosms induce dysbiosis

Journal of Molluscan Studies ◽

10.1093/mollus/eyaa024 ◽

2020 ◽

Vol 86 (4) ◽

pp. 280-289

Author(s):

Alison K Aceves ◽

Paul D Johnson ◽

Carla L Atkinson ◽

Brian C van Ee ◽

Stephen A Bullard ◽

...

Keyword(s):

Digestive Gland ◽

Gut Microbiome ◽

Bacterial Communities ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Artificial Rearing ◽

Tennessee River ◽

Wasting Syndrome ◽

Water And Sediment ◽

Rrna Gene Sequencing

ABSTRACT Herein, we characterized the digestive gland (‘gut’) bacterial community (microbiome) of the Ohio pigtoe, Pleurobema cordatum (Rafinesque, 1820), using 16S rRNA gene sequencing. Two populations were compared: wild P. cordatum (n = 5) from the Tennessee River and P. cordatum (n = 9) relocated to artificial mesocosms and exposed to various thermal regimes for 2 weeks. We also characterized the bacterial communities from the habitat (water and sediment) of these wild and mesocosm-held populations. The gut microbiome of wild P. cordatum was dominated by members of the bacterial phylum Tenericutes (72%). By contrast, the gut microbiome of mesocosm-held P. cordatum was dominated by members of the bacterial phylum Proteobacteria (64%). We found no temperature-associated difference in the gut microbiome of mesocosm-held P. cordatum. The bacterial communities of water and sediment from the Tennessee River were diverse and distinct from those of the studied mussels. By contrast, the bacterial communities of water and sediment in the mesocosms were dominated by Proteobacteria. These results suggest that when the studied mussels were moved into artificial rearing environments, their gut microbiome shifted to reflect that of their habitat (i.e. an increase in Proteobacteria). Moreover, the abundance of Tenericutes (also previously reported in other unionids) was reduced from 72% in wild mussels to 3% in mesocosm-held mussels. As a result, we think that mesocosm-held P. cordatum became dysbiotic, which could explain the observed wasting syndrome and associated trickling mortalities in captive P. cordatum.

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Increasing the Dose and/or Repeating Faecal Microbiota Transplantation (FMT) Increases the Response in Patients with Irritable Bowel Syndrome (IBS)

Nutrients ◽

10.3390/nu11061415 ◽

2019 ◽

Vol 11 (6) ◽

pp. 1415 ◽

Cited By ~ 7

Author(s):

Magdy El-Salhy ◽

Trygve Hausken ◽

Jan Gunnar Hatlebakk

Keyword(s):

Quality Of Life ◽

Irritable Bowel Syndrome ◽

Response Rate ◽

High Dose ◽

Faecal Microbiota ◽

Abdominal Symptoms ◽

Faecal Samples ◽

Irritable Bowel ◽

Faecal Microbiome

Background: Faecal microbiome transplantation (FMT) appears to be an effective method for treating irritable bowel syndrome (IBS) patients. However, it is not clear if a high transplant dose and/or repeating FMT are/is needed to ensure a response. The present study was undertaken to clarify this matter. Methods: Ten IBS patients who did not respond to a 30-g transplant subsequently received a 60-g transplant into the duodenum via a gastroscope. The patients provided faecal samples before and 1 month after FMT. They completed five questionnaires measuring symptoms, fatigue and quality of life at baseline and then at 2 weeks, 1 month and 3 months after FMT. The dysbiosis index (DI) was measured using the GA-map Dysbiosis Test®. Results: Seven patients (70%) responded to the 60-g transplant, with significant clinical improvements in the abdominal symptoms, fatigue and quality of life in 57%, 80% and 67% of these patients. The 60-g transplant also reduced the DI. Conclusion: FMT is an effective treatment for IBS. A high-dose transplant and/or repeated FMT increase the response rate and the intensity of the effects of FMT.

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