scholarly journals Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine

2017 ◽  
Author(s):  
Jacoline Gerritsen ◽  
Bastian Hornung ◽  
Bernadette Renckens ◽  
Sacha A.F.T. van Hijum ◽  
Vitor A.P. Martins dos Santos ◽  
...  
Keyword(s):  
Amino Acids ◽  
Small Intestine ◽  
Short Chain Fatty Acids ◽  
Limited Capacity ◽  
Illumina Hiseq ◽  
Circular Chromosome ◽  
Protein Coding ◽  
Mate Pair ◽  
Simple Carbohydrates

Background. The microbiota in the small intestine relies on their capacity to rapidly import and ferment available carbohydrates to survive in a complex and highly competitive ecosystem. Understanding how these communities function requires elucidating the role of its key players, the interactions among them and with their environment/host. Methods. The genome of the gut bacterium Romboutsia ilealis CRIBT was sequenced with multiple technologies (Illumina paired end, mate pair and PacBio). The transcriptome was sequenced (Illumina HiSeq) while growing on three different carbohydrate sources and short chain fatty acids were measured via HPLC. Results. Hence, we present the complete genome of Romboutsia ilealis CRIBT, a natural inhabitant and key player of the small intestine of rats. R. ilealis CRIBT possesses a circular chromosome of 2,581,778 bp and a plasmid of 6,145 bp, carrying 2,351 and eight predicted protein coding sequences, respectively. Analysis of the genome revealed limited capacity to synthesize amino acids and vitamins, whereas multiple and partially redundant pathways for the utilization of different relatively simple carbohydrates are present. Transcriptome analysis allowed pinpointing the key components in the degradation of glucose, L-fucose and fructo-oligosaccharides. Discussion. This revealed that R. ilealis CRIBT is adapted to a nutrient-rich environment where carbohydrates, amino acids and vitamins are abundantly available and uncovered potential mechanisms for competition with mucus-degrading microbes.

scholarly journals Genomic and functional analysis ofRomboutsia ilealisCRIBTreveals adaptation to the small intestine

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3698 ◽  
Author(s):  
Jacoline Gerritsen ◽  
Bastian Hornung ◽  
Bernadette Renckens ◽  
Sacha A.F.T. van Hijum ◽  
Vitor A.P. Martins dos Santos ◽  
...  
Keyword(s):  
Amino Acids ◽  
Small Intestine ◽  
Short Chain Fatty Acids ◽  
Limited Capacity ◽  
Illumina Hiseq ◽  
Circular Chromosome ◽  
Protein Coding ◽  
Mate Pair ◽  
Simple Carbohydrates

BackgroundThe microbiota in the small intestine relies on their capacity to rapidly import and ferment available carbohydrates to survive in a complex and highly competitive ecosystem. Understanding how these communities function requires elucidating the role of its key players, the interactions among them and with their environment/host.MethodsThe genome of the gut bacteriumRomboutsia ilealisCRIBTwas sequenced with multiple technologies (Illumina paired-end, mate-pair and PacBio). The transcriptome was sequenced (Illumina HiSeq) after growth on three different carbohydrate sources, and short chain fatty acids were measured via HPLC.ResultsWe present the complete genome ofRomboutsia ilealisCRIBT, a natural inhabitant and key player of the small intestine of rats.R. ilealisCRIBTpossesses a circular chromosome of 2,581,778 bp and a plasmid of 6,145 bp, carrying 2,351 and eight predicted protein coding sequences, respectively. Analysis of the genome revealed limited capacity to synthesize amino acids and vitamins, whereas multiple and partially redundant pathways for the utilization of different relatively simple carbohydrates are present. Transcriptome analysis allowed identification of the key components in the degradation of glucose, L-fucose and fructo-oligosaccharides.DiscussionThis revealed thatR. ilealisCRIBTis adapted to a nutrient-rich environment where carbohydrates, amino acids and vitamins are abundantly available.

scholarly journals Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine

2017 ◽  
Author(s):  
Jacoline Gerritsen ◽  
Bastian Hornung ◽  
Bernadette Renckens ◽  
Sacha A.F.T. van Hijum ◽  
Vitor A.P. Martins dos Santos ◽  
...  
Keyword(s):  
Amino Acids ◽  
Small Intestine ◽  
Short Chain Fatty Acids ◽  
Limited Capacity ◽  
Illumina Hiseq ◽  
Circular Chromosome ◽  
Protein Coding ◽  
Mate Pair ◽  
Simple Carbohydrates

Background. The microbiota in the small intestine relies on their capacity to rapidly import and ferment available carbohydrates to survive in a complex and highly competitive ecosystem. Understanding how these communities function requires elucidating the role of its key players, the interactions among them and with their environment/host. Methods. The genome of the gut bacterium Romboutsia ilealis CRIBT was sequenced with multiple technologies (Illumina paired end, mate pair and PacBio). The transcriptome was sequenced (Illumina HiSeq) while growing on three different carbohydrate sources and short chain fatty acids were measured via HPLC. Results. Hence, we present the complete genome of Romboutsia ilealis CRIBT, a natural inhabitant and key player of the small intestine of rats. R. ilealis CRIBT possesses a circular chromosome of 2,581,778 bp and a plasmid of 6,145 bp, carrying 2,351 and eight predicted protein coding sequences, respectively. Analysis of the genome revealed limited capacity to synthesize amino acids and vitamins, whereas multiple and partially redundant pathways for the utilization of different relatively simple carbohydrates are present. Transcriptome analysis allowed pinpointing the key components in the degradation of glucose, L-fucose and fructo-oligosaccharides. Discussion. This revealed that R. ilealis CRIBT is adapted to a nutrient-rich environment where carbohydrates, amino acids and vitamins are abundantly available and uncovered potential mechanisms for competition with mucus-degrading microbes.

scholarly journals Gut Microbiota-Derived Metabolites in Irritable Bowel Syndrome

2021 ◽  
Vol 11 ◽  
Author(s):  
Lin Xiao ◽  
Qin Liu ◽  
Mei Luo ◽  
Lishou Xiong
Keyword(s):  
Amino Acids ◽  
Fatty Acids ◽  
Irritable Bowel Syndrome ◽  
Gut Microbiota ◽  
Short Chain Fatty Acids ◽  
Functional Bowel Disorder ◽  
Irritable Bowel ◽  
The Brain ◽  
Bowel Disorder

Irritable bowel syndrome (IBS) is the most common functional bowel disorder worldwide and is associated with visceral hypersensitivity, gut motility, immunomodulation, gut microbiota alterations, and dysfunction of the brain-gut axis; however, its pathophysiology remains poorly understood. Gut microbiota and its metabolites are proposed as possible etiological factors of IBS. The aim of our study was to investigate specific types of microbiota-derived metabolites, especially bile acids, short-chain fatty acids, vitamins, amino acids, serotonin and hypoxanthine, which are all implicated in the pathogenesis of IBS. Metabolites-focused research has identified multiple microbial targets relevant to IBS patients, important roles of microbiota-derived metabolites in the development of IBS symptoms have been established. Thus, we provide an overview of gut microbiota and their metabolites on the different subtypes of IBS (constipation-predominant IBS-C, diarrhea-predominant IBS-D) and present controversial views regarding the role of microbiota in IBS.

scholarly journals Whole Genome Sequence of Sphingobacterium sp. G1-14, a Strain With Effective Paichongding Biodegradation

2019 ◽  
Vol 10 (1) ◽  
pp. 58
Author(s):  
Peng Yin ◽  
Suyu Liu ◽  
Xingke Wu
Keyword(s):  
Mutant Strain ◽  
Genome Sequence ◽  
Whole Genome Sequence ◽  
Original Strain ◽  
Illumina Hiseq ◽  
Circular Chromosome ◽  
Protein Coding ◽  
Sequencing Platform ◽  
Third Generation Sequencing ◽  
Phylogenomic Analyses

In this study, we obtained a Paichongding (RR/SS-IPP) degrading Sphingobacterium sp. G1-14 by UV irradiation of the original strain G1-13. This new mutant strain showed excellent RR/SS-IPP degradation performance, and the degradation of ratio was up to 30 per cent after 7 days. Subsequently, we determined the mutant strain G 1-14 as Sphingobacterium based on the phylogenomic analyses. The circular chromosome of Sphingobacterium sp. G1-14 was presented in this paper by Illumina Hiseq platform combined with a third-generation sequencing platform. 5583 protein-coding sequences of the complete genome sequence were obtained, which is beneficial to deduced genes related to RR/SS-IPP degradation.

Procedures for determining digestibility of amino acids, lipids, starch, fibre, phosphorus, and calcium in feed ingredients fed to pigs

2017 ◽  
Vol 57 (11) ◽  
pp. 2317 ◽  
Author(s):  
H. H. Stein
Keyword(s):  
Amino Acids ◽  
Fatty Acids ◽  
Small Intestine ◽  
Large Intestine ◽  
Intestinal Tract ◽  
Short Chain Fatty Acids ◽  
Practical Reasons ◽  
Feed Ingredients ◽  
Ileal Digestibility ◽  
Diet Formulation

The proportion of nutrients that is absorbed from the intestinal tract of the pig differs among dietary ingredients; therefore, it would be desirable to determine the proportion of nutrients that is absorbed for each ingredient, but, for practical reasons, values for the digestibility of nutrients in each ingredient are used as predictors of absorption. For amino acids, starch and lipids, ileal digestibility must be determined because nutrients not absorbed in the small intestine will be fermented or changed in the large intestine, which invalidates data for total tract digestibility of these nutrients. For starch, apparent ileal digestibility is a reasonable predictor of its disappearance from the small intestine, but because of endogenous secretions of amino acids and lipids into the small intestine, standardised ileal digestibility of amino acids and true ileal digestibility of fat must be determined. For fibre, total tract digestibility is used to estimate fermentation and subsequent absorption of short-chain fatty acids, but it must be corrected for endogenous secretions. Likewise, for phosphorus and calcium, values for apparent total tract digestibility must be corrected for basal endogenous losses; consequently, standardised total tract digestibility of phosphorus and calcium is calculated and used in diet formulation. These procedures for determining the digestibility of nutrients in feed ingredients make it possible to formulate diets in which concentrations of digestible nutrients can be predicted from values for individual feed ingredients.

scholarly journals Amino acid transporters in the regulation of insulin secretion and signalling

2019 ◽  
Vol 47 (2) ◽  
pp. 571-590 ◽  
Author(s):  
Kiran Javed ◽  
Stephen J. Fairweather
Keyword(s):  
Amino Acids ◽  
Small Intestine ◽  
Insulin Secretion ◽  
Amino Acid ◽  
Insulin Signalling ◽  
Amino Acid Transporter ◽  
Fibroblast Growth Factor 21 ◽  
Amino Acid Transporters ◽  
Acid Transporter

Abstract Amino acids are increasingly recognised as modulators of nutrient disposal, including their role in regulating blood glucose through interactions with insulin signalling. More recently, cellular membrane transporters of amino acids have been shown to form a pivotal part of this regulation as they are primarily responsible for controlling cellular and circulating amino acid concentrations. The availability of amino acids regulated by transporters can amplify insulin secretion and modulate insulin signalling in various tissues. In addition, insulin itself can regulate the expression of numerous amino acid transporters. This review focuses on amino acid transporters linked to the regulation of insulin secretion and signalling with a focus on those of the small intestine, pancreatic β-islet cells and insulin-responsive tissues, liver and skeletal muscle. We summarise the role of the amino acid transporter B0AT1 (SLC6A19) and peptide transporter PEPT1 (SLC15A1) in the modulation of global insulin signalling via the liver-secreted hormone fibroblast growth factor 21 (FGF21). The role of vesicular vGLUT (SLC17) and mitochondrial SLC25 transporters in providing glutamate for the potentiation of insulin secretion is covered. We also survey the roles SNAT (SLC38) family and LAT1 (SLC7A5) amino acid transporters play in the regulation of and by insulin in numerous affective tissues. We hypothesise the small intestine amino acid transporter B0AT1 represents a crucial nexus between insulin, FGF21 and incretin hormone signalling pathways. The aim is to give an integrated overview of the important role amino acid transporters have been found to play in insulin-regulated nutrient signalling.

scholarly journals 253 Glutamate and glutamine are the major metabolic fuels in enterocytes of suckling piglets

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 68-68 ◽  
Author(s):  
Wenliang He ◽  
Yongqing Hou ◽  
Guoyao Wu
Keyword(s):  
Amino Acids ◽  
Fatty Acids ◽  
Small Intestine ◽  
Age Groups ◽  
Relative Role ◽  
Bicarbonate Buffer ◽  
Atp Production ◽  
Suckling Piglets ◽  
And Function

Abstract Glutamate and glutamine are known to be important energy substrates in pig enterocytes, and aspartate has also been reported to be extensively catabolized by the rat small intestine. However, little is known about the relative role of amino acids, glucose and fatty acids in ATP production by enterocytes. In the present study, enterocytes isolated from 0-, 7-, 14- and 21-day-old piglets were used to determine the rates of oxidation of amino acids, fatty acids and glucose. Enterocytes were incubated at 37oC for 30 min in Krebs-Henseleit bicarbonate buffer (pH 7.4) containing 5 mM D-glucose and one of the following: 0.5–5 mM L-[U-14C]glutamate, 0.5–5 mM L-[U-14C]glutamine, 0.5–5 mM L-[U-14C]aspartate, 0.5–5 mM L-[U-14C]alanine, 0.5–2 mM L-[U-14C]palmitate, D-[U-14C]glucose, 0.5–5 mM [U-14C]propionate, or 0.5–5 mM [1-14C]butyrate. At the end of the incubation, 14CO2 produced from each 14C-labeled substrate was collected. Rates of oxidation of each substrate in enterocytes from all age groups of piglets increased (P < 0.01) progressively with increasing its extracellular concentrations. The rates of oxidation of glutamate, glutamine, aspartate, glucose by enterocytes from 0- to 21-day-old pigs were much greater (P < 0.01) than those for the same concentrations of alanine, palmitate, propionate, and butyrate. In cells from all age groups of piglets, rates of oxidation of, and ATP production from 5 mM glutamate or 5 mM glutamine were greater (P < 0.01) than those from 5 mM glucose and aspartate. Oxidation of alanine, propionate, butyrate and palmitate by enterocytes was limited. At each postnatal age, the oxidation of glutamate and glutamine produced more ATP than any other substrates. Our results indicated that glutamate and glutamine are the major metabolic fuels in enterocytes of 0- to 21-day-old pigs. Because of limited uptake of arterial glutamate by enterocytes, dietary glutamate is essential to the integrity and function of the pig small intestine.

scholarly journals Influence of branched chain amino acids on insulin sensitivity and the mediator roles of short chain fatty acids and gut hormones: a review

2018 ◽  
Vol 2 ◽  
Author(s):  
Akram Abolbaghaei ◽  
B. Dave Oomah ◽  
Hamed Tavakoli ◽  
Farah Hosseinian
Keyword(s):  
Insulin Resistance ◽  
Amino Acids ◽  
Fatty Acids ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Hormone Secretion ◽  
Short Chain Fatty Acids ◽  
Branched Chain Amino Acids ◽  
Branched Chain

Circulating levels of branched chain amino acids (BCAAs) correlate strongly with type 2 diabetes (T2D). The correlation may be associated with insulin-resistance factors independent of glycemic markers currently used in the diagnosis and monitoring of diabetes. This can revolutionize the thought process and methodology not only in diabetes treatment, but also in its advance screening and prevention with BCAAs used as biomarkers and targets for treatment. Whether insulin resistance is the cause or result of BCAAs imbalances requires further investigation. Although the overall diet is important, the role of specific diets targeting the gut microbiome composition and hormone secretion affecting BCAA absorption and metabolism will be explored. Generic diet modifications apparently induce only negligible changes in the intrinsic genetic make-up of the gut and BCAA levels but influence specific modulation of the gut microbiome. This genetic make-up is indeed similar among T2D patients independent of numerous variables including obesity. Short-chain fatty acids (SCFAs), the primary end-products of non-digestible carbohydrates (NDC) fermentation, mediate metabolic imbalances through gut microbiota and gut hormone secretion. This review focuses on extensive evidence gathered using diverse methodologies on the strong parallel correlation between BCAA levels and insulin resistance. Furthermore, the role of specific diets particularly SCFAs as mediators of the stubbornly fixed intrinsic genetic make-up of gut microbiota will be scrutinized to delineate BCAA levels and insulin resistance in T2D.

scholarly journals Association of Protective HLA-A With HLA-B∗27 Positive Ankylosing Spondylitis

2021 ◽  
Vol 12 ◽  
Author(s):  
Jessika Nordin ◽  
Mats Pettersson ◽  
Lina Hultin Rosenberg ◽  
Argyri Mathioudaki ◽  
Åsa Karlsson ◽  
...  
Keyword(s):  
Amino Acids ◽  
Ankylosing Spondylitis ◽  
Protein Coding ◽  
Female Population ◽  
Risk Variants ◽  
Disease Predisposition ◽  
Hla Dqa1 ◽  
Coding Variants ◽  
The Impact

ObjectivesTo further elucidate the role of the MHC in ankylosing spondylitis by typing 17 genes, searching for HLA-B∗27 independent associations and assessing the impact of sex on this male biased disease.MethodsHigh-confidence two-field resolution genotyping was performed on 310 cases and 2196 controls using an n-1 concordance method. Protein-coding variants were called from next-generation sequencing reads using up to four software programs and the consensus result recorded. Logistic regression tests were applied to the dataset as a whole, and also in stratified sets based on sex or HLA-B∗27 status. The amino acids driving association were also examined.ResultsTwenty-five HLA protein-coding variants were significantly associated to disease in the population. Three novel protective associations were found in a HLA-B∗27 positive population, HLA-A∗24:02 (OR = 0.4, CI = 0.2–0.7), and HLA-A amino acids Leu95 and Gln156. We identified a key set of seven loci that were common to both sexes, and robust to change in sample size. Stratifying by sex uncovered three novel risk variants restricted to the female population (HLA-DQA1∗04.01, -DQB1∗04:02, -DRB1∗08:01; OR = 2.4–3.1). We also uncovered a set of neutral variants in the female population, which in turn conferred strong effects in the male set, highlighting how population composition can lead to the masking of true associations.ConclusionPopulation stratification allowed for a nuanced investigation into the tightly linked MHC region, revealing novel HLA-B∗27 signals as well as replicating previous HLA-B∗27 dependent results. This dissection of signals may help to elucidate sex biased disease predisposition and clinical progression.

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