DOCSLIB.ORG

2. Gut Microbiota

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
2. Gut Microbiota Research Collection Doctoral Thesis Towards understanding the modulation potential of dietary fibers on intestinal microbiota using human and a novel murine intestinal fermentation model Author(s): Poeker, Sophie Annick Thérèse Marie Publication Date: 2019 Permanent Link: https://doi.org/10.3929/ethz-b-000361486 Rights / License: In Copyright - Non-Commercial Use Permitted This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library DISS. ETH NO 25786 Towards understanding the modulation potential of dietary fibers on intestinal microbiota using human and a novel murine intestinal fermentation model A thesis submitted to attain the degree of DOCTOR OF SCIENCES of ETH ZURICH (Dr. sc. ETH Zurich) Presented by SOPHIE ANNICK THERESE MARIE POEKER Master of Science ETH in Biology, ETH Zurich, Zurich, Switzerland born on July 7, 1988 citizen of Luxembourg on the recommendation of Prof. Dr. Christophe Lacroix, examiner Prof. Dr. med. Michael Scharl, co-examiner Dr. Annelies Geirnaert, co-examiner 2019 Content Content 1 Abbreviations 4 Summary 7 Zusammenfassung 13 Chapter 1 19 General introduction 19 The gastrointestinal tract in humans and mice 20 Gut microbiota 24 Inflammatory Bowel Disease 39 Strategies to modulate the gut microbiota and to improve health 52 Models in gut microbiota research 61 Objectives of this thesis 67 Chapter 2 69 Understanding the prebiotic potential of different dietary fibers using an in vitro continuous adult fermentation model (PolyFermS) 69 Chapter 3 97 Stepwise development of an in vitro continuous fermentation model for the murine caecal microbiota. 97 Chapter 4 128 In vitro modulation of intestinal microbiota towards eubiosis and dysbiosis by dietary fibers, oxidative stress and antibiotic treatment 129 Chapter 5 171 General conclusion and perspectives 171 References 177 Acknowledgements 208 Curriculum vitae 209 3 Abbreviations Abbreviations AIEC Adherent-invasive E.coli AMPs Antimicrobial peptides ATG Autophagy gene ATP Adenosine triphosphate BCFA Branched chain fatty acid ButCoA ButyrylCoA CAT Catalase CD Crohn’s Disease CH4 Methane CO2 Carbon dioxide COX Cyclooxygenase Cu Copper DF Dietary fiber DNA Deoxyribonucleic acid DP Degree of polymerization DSS Dextran sodium sulfate FA Fatty acids FAD Flavin adenine dinucleotide Fe Iron FMT Fecal microbiota transplant FOS Fructooligosaccharide FUT Fucosyltransferase gene GALT Gut associated lymphoid tissue GIT Gastrointestinal tract GOS Galactooligosaccharide GPR G Protein-coupled receptor GPX Glutathione peroxidase H2 Hydrogen HCl Hydrochloric acid HLA Human leukocyte antigen HMA Human microbiota associated HO·¯ Hydroxyl radical HO2· Hydroperoxyl HOCl Hydrochlorus HPLC High performance liquid chromatography H2O2 Hydrogen peroxide H2S Hydrogen sulfide IBD Inflammatory bowel disease IFN Interferone Ig Immunoglobulin IL- Interleukin 4 Abbreviations IRGM Immunity-related GTPase family M protein MLN Mesenteric lymph nodes NADPH Nicotinamide adenine dinucleotide phosphate NF-КB Necrosis factor КB NH3 Ammonia NOD Nitric oxide deoxygenase NOX NADPH oxidase NSAID Nonsteroidal anti-inflammatory drugs OTU Operational taxonomic unit O2 Oxygen O2·¯ Superoxide O3 Ozone PEP Phosphoenolpyruvate PP Peyer’s Patch PRR Pattern recognition receptor PTPN Protein tyrosine phosphatase non-receptor type PUFA Polyunsaturated fatty acids qPCR Quantitative polymerase chain reaction rDNA Ribosomal deoxyribonucleic acid RNA Ribonucleic acid rRNA Ribosomal ribonucleic acid RNHCl Chloramine RNS Reactive nitrogen sepcies RO· Alcoxyl RO2· Peroxyl ROS Reactive oxygen species RT Retention time SCFA Short chain fatty acid SOD Superoxide dismutase spp. Species SRB Sulphate-reducing bacteria Th cell T helper cell TGF Transforming growth factor TLR Toll-like receptor TNF Tumor necrosis factor Cu Copper UC Ulcerative colitis WT Wild type XOS Xylooligosaccharide 5 Abbreviations 6 Summary Summary The mammalian gastrointestinal tract harbors a complex and diverse community of bacteria, called gut microbiota that exerts elemental physiological functions in health and disease. Diet shapes the gut microbiota composition and activity, which in turn modulates host metabolism and homeostasis. Non-digestible dietary fibers (DFs) for example, have beneficial effects on intestinal wellbeing by acting as a carbon source for growth and functionality of selective commensal bacteria within the gut. In the colon, microbial fermentation of complex carbohydrates generates short chain fatty acids (SCFAs), such as acetate, propionate and butyrate, which are absorbed by the intestinal epithelium conferring systemic health effects. The intake of DFs can lead to increased SCFA production due to promoted bacterial cross-feeding activities, a subsequent acidification of the lumen and thus homeostasis. An adverse disruption of the structure or functionality of the gut microbiota, called microbial dysbiosis, induces significant alternations in the delicate microbe-host synergy and is associated with chronic inflammatory disorders, such as inflammatory bowel disease (IBD). There has been a rapid increase in IBD incidence, especially in Western style countries. Therefore, a Western-diet characterized by low DF intake might be a potential trigger for IBD. Besides diet, other environmental factors influence the intestinal microbiota and its activity and may induce microbial dysbiosis and trigger IBD. For example, oxidative stress caused by excessive reactive oxygen species and antibiotics are potential inducers of microbial dysbiosis. The immediate impact of microbiota modulatory factors promoting health (dietary factors) or disease (oxidative stress and antibiotics) on intestinal microbial activity and structure is difficult to assess due to inaccessibility of human colon samples or end-point samples in mouse models. In vitro fermentation models mimicking the intestinal conditions offer the possibility of investigating the microbe-microbe interactions independent of the host. The main objective of this thesis was to investigate the potential modulating effects of different dietary fibers and direct adverse effects of oxidative and antibiotic stress on gut microbiota composition and functionality using an in vitro continuous fermentation model of the human colon and mouse cecum. Study 1 In a first part, continuous in vitro colonic fermentation models using immobilized human faecal gut microbiota were set-up mimicking proximal colon condition to study the modulatory potential of four different dietary fibers. We immobilized two distinct faecal microbiota (D3 and D4) differing within the Bacteroidetes phylum with higher levels of Bacteroidaceae in D3 and higher levels of Prevotellaceae in D4, and we successfully maintained the two distinct microbiota, both on metabolic and phylogenetic levels in the PolyFermS model. We used three continuous in vitro fermentation PolyFermS models to study the modulating effects of inulin, β-glucan, xylo-oligosaccharide (XOS) and α-galacto-oligosaccharide (α-GOS) on two distinct gut microbiota, independently from host factors. The four dietary fibers (DF) were supplemented at a physiologic 8 Summary concentration, equivalent to 9 g daily intake. DF treatments resulted in increased short-chain fatty acid production, evidencing fermentability of all tested fibers by the two microbiota, and led to consistent metabolic responses depending on the donor microbiota. Irrespectively of the DF, D3 in vitro microbiota responded by increased butyrate production, whereas D4 in vitro microbiota displayed higher propionate production. Moreover, supplementation of the two short-chain carbohydrates XOS and α-GOS resulted in high acetate production in all treatments for both microbiota. Interestingly, metabolic cross-feeding of butyrate- producers on acetate within both PolyFermS microbiota was microbiota-dependent and particularly observed upon inulin supplementation, with either increase in butyrate or acetate levels. At phylogenetic level, we also observed changes in abundance of specific bacterial taxa within one depending on the microbiota, which could explain the observed short-chain fatty acid profiles and possible cross-feeding interactions between the different functional bacterial populations. Study 2 Next, a novel continuous fermentation model based on the PolyFermS platform inoculated with immobilized murine caecal microbiota was developed and validated. Murine models are the model of choice for studying the role of gut microbiota in health and disease. However, mice and human microbiota differ in species composition, and further investigation of the murine gut microbiota is important to improve current murine models and mechanistic understanding of the gut microbiota. Continuous in vitro fermentation models are powerful tools to investigate microbe-microbe interactions while circumventing animal testing and host factors. There is no model developed yet for murine intestinal microbiota fermentation. In a first step, we determined the pH, bacterial composition and the metabolic profile in the caeca of C57BL/6 mice. To support growth and activity of the murine caecal bacterial populations, a complex murine nutritive growth medium was developed to mimic substrate conditions encountered in chyme entering the mouse caecum. Different factors of the fermentation model, including caecum sampling, fermentation starting mode, pH, retention time and growth medium composition were investigated in a sequential
Load more

Recommended publications
  • Fatty Acid Diets: Regulation of Gut Microbiota Composition and Obesity and Its Related Metabolic Dysbiosis
    International Journal of Molecular Sciences Review Fatty Acid Diets: Regulation of Gut Microbiota Composition and Obesity and Its Related Metabolic Dysbiosis David Johane Machate 1, Priscila Silva Figueiredo 2 , Gabriela Marcelino 2 , Rita de Cássia Avellaneda Guimarães 2,*, Priscila Aiko Hiane 2 , Danielle Bogo 2, Verônica Assalin Zorgetto Pinheiro 2, Lincoln Carlos Silva de Oliveira 3 and Arnildo Pott 1 1 Graduate Program in Biotechnology and Biodiversity in the Central-West Region of Brazil, Federal University of Mato Grosso do Sul, Campo Grande 79079-900, Brazil; [email protected] (D.J.M.); [email protected] (A.P.) 2 Graduate Program in Health and Development in the Central-West Region of Brazil, Federal University of Mato Grosso do Sul, Campo Grande 79079-900, Brazil; pri.fi[email protected] (P.S.F.); [email protected] (G.M.); [email protected] (P.A.H.); [email protected] (D.B.); [email protected] (V.A.Z.P.) 3 Chemistry Institute, Federal University of Mato Grosso do Sul, Campo Grande 79079-900, Brazil; [email protected] * Correspondence: [email protected]; Tel.: +55-67-3345-7416 Received: 9 March 2020; Accepted: 27 March 2020; Published: 8 June 2020 Abstract: Long-term high-fat dietary intake plays a crucial role in the composition of gut microbiota in animal models and human subjects, which affect directly short-chain fatty acid (SCFA) production and host health. This review aims to highlight the interplay of fatty acid (FA) intake and gut microbiota composition and its interaction with hosts in health promotion and obesity prevention and its related metabolic dysbiosis.
    [Show full text]
  • British Journal of Nutrition (2014), 111, 2135–2145 Doi:10.1017/S000711451400021X Q the Authors 2014
    Downloaded from British Journal of Nutrition (2014), 111, 2135–2145 doi:10.1017/S000711451400021X q The Authors 2014 https://www.cambridge.org/core Iron supplementation promotes gut microbiota metabolic activity but not colitis markers in human gut microbiota-associated rats Alexandra Dostal1, Christophe Lacroix1*, Van T. Pham1, Michael B. Zimmermann2, . IP address: Christophe Del’homme3, Annick Bernalier-Donadille3 and Christophe Chassard1 1Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Switzerland 170.106.202.8 2Laboratory of Human Nutrition, Institute of Food, Nutrition and Health, ETH Zurich, Switzerland 3UR454 Microbiology Unit, INRA, Clermont-Ferrand Research Centre, St Gene`s-Champanelle, France (Submitted 17 June 2013 – Final revision received 14 November 2013 – Accepted 14 January 2014 – First published online 21 February 2014) , on 01 Oct 2021 at 15:56:07 Abstract The global prevalence of Fe deficiency is high and a common corrective strategy is oral Fe supplementation, which may affect the commensal gut microbiota and gastrointestinal health. The aim of the present study was to investigate the impact of different dietary Fe concentrations on the gut microbiota and gut health of rats inoculated with human faecal microbiota. Rats (8 weeks old, n 40) were divided into five (n 8 each) groups and fed diets differing only in Fe concentration during an Fe-depletion period (12 weeks) and an , subject to the Cambridge Core terms of use, available at Fe-repletion period (4 weeks) as follows: (1) Fe-sufficient diet throughout the study period; (2) Fe-sufficient diet followed by 70 mg Fe/kg diet; (3) Fe-depleted diet throughout the study period; (4) Fe-depleted diet followed by 35 mg Fe/kg diet; (5) Fe-depleted diet followed by 70 mg Fe/kg diet.
    [Show full text]
  • Modulation of the Gut Microbiota Alters the Tumour-Suppressive Efficacy of Tim-3 Pathway Blockade in a Bacterial Species- and Host Factor-Dependent Manner
    microorganisms Article Modulation of the Gut Microbiota Alters the Tumour-Suppressive Efficacy of Tim-3 Pathway Blockade in a Bacterial Species- and Host Factor-Dependent Manner Bokyoung Lee 1,2, Jieun Lee 1,2, Min-Yeong Woo 1,2, Mi Jin Lee 1, Ho-Joon Shin 1,2, Kyongmin Kim 1,2 and Sun Park 1,2,* 1 Department of Microbiology, Ajou University School of Medicine, Youngtongku Wonchondong San 5, Suwon 442-749, Korea; [email protected] (B.L.); [email protected] (J.L.); [email protected] (M.-Y.W.); [email protected] (M.J.L.); [email protected] (H.-J.S.); [email protected] (K.K.) 2 Department of Biomedical Sciences, The Graduate School, Ajou University, Youngtongku Wonchondong San 5, Suwon 442-749, Korea * Correspondence: [email protected]; Tel.: +82-31-219-5070 Received: 22 August 2020; Accepted: 9 September 2020; Published: 11 September 2020 Abstract: T cell immunoglobulin and mucin domain-containing protein-3 (Tim-3) is an immune checkpoint molecule and a target for anti-cancer therapy. In this study, we examined whether gut microbiota manipulation altered the anti-tumour efficacy of Tim-3 blockade. The gut microbiota of mice was manipulated through the administration of antibiotics and oral gavage of bacteria. Alterations in the gut microbiome were analysed by 16S rRNA gene sequencing. Gut dysbiosis triggered by antibiotics attenuated the anti-tumour efficacy of Tim-3 blockade in both C57BL/6 and BALB/c mice. Anti-tumour efficacy was restored following oral gavage of faecal bacteria even as antibiotic administration continued. In the case of oral gavage of Enterococcus hirae or Lactobacillus johnsonii, transferred bacterial species and host mouse strain were critical determinants of the anti-tumour efficacy of Tim-3 blockade.
    [Show full text]
  • Individuality in Gut Microbiota Composition Is a Complex Polygenic Trait Shaped by Multiple Environmental and Host Genetic Factors
    Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors Andrew K. Bensona,1, Scott A. Kellyb, Ryan Leggea, Fangrui Maa, Soo Jen Lowa, Jaehyoung Kima, Min Zhanga, Phaik Lyn Oha, Derrick Nehrenbergb, Kunjie Huab, Stephen D. Kachmanc, Etsuko N. Moriyamad, Jens Waltera, Daniel A. Petersona, and Daniel Pompb,e aDepartment of Food Science and Technology and Core for Applied Genomics and Ecology, University of Nebraska, Lincoln, NE 68583-0919; bDepartment of Genetics, Carolina Center for Genome Science, University of North Carolina, Chapel Hill, NC 27599-7545; cDepartment of Statistics, University of Nebraska, Lincoln, NE 68583-0963; dSchool of Biological Sciences and Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588-0118; and eDepartment of Nutrition, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599-7461 Edited by Trudy F. C. Mackay, North Carolina State University, Raleigh, NC, and approved September 8, 2010 (received for review June 10, 2010) In vertebrates, including humans, individuals harbor gut microbial to be multifactorial, with both environmental and genetic compo- communities whose species composition and relative proportions nents (11–13), and the contribution of the gut microbiota is cur- of dominant microbial groups are tremendously varied. Although rently viewed as an environmental factor (14). Although a number external and stochastic factors clearly contribute to the individu- of studies have suggested that composition of the gut microbiota ality of the microbiota, the fundamental principles dictating how may be subject to host genetic forces, existing evidence is conflicting environmental factors and host genetic factors combine to shape and confounded by the genetic diversity of vertebrate (especially this complex ecosystem are largely unknown and require system- human) populations and strong environmental effects (15–19).
    [Show full text]
  • Gut Microbiota Predicts Healthy Late-Life Aging in Male Mice
    bioRxiv preprint doi: https://doi.org/10.1101/2021.06.22.449472; this version posted June 22, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Gut Microbiota predicts Healthy Late-life Aging in Male Mice 2 Shanlin Ke1,2, Sarah J. Mitchell3,4, Michael R. MacArthur3,4, Alice E. Kane5, David A. 3 Sinclair5, Emily M. Venable6, Katia S. Chadaideh6, Rachel N. Carmody6, Francine 4 Grodstein1,7, James R. Mitchell4, Yang-Yu Liu1 5 6 1Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical 7 School, Boston, Massachusetts 02115, USA. 8 2State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural 9 University 330045, China. 10 3Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, 11 02115, USA. 12 4Department of Health Sciences and Technology, ETH Zurich, Zurich 8005 Switzerland. 13 5Blavatnik Institute, Dept. of Genetics, Paul F. Glenn Center for Biology of Aging Research at 14 Harvard Medical School, Boston, MA 02115 USA. 15 6Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA. 16 7Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA. 17 18 #To whom correspondence should be addressed: Y.-Y.L. ([email protected]) and 19 S.J.M. ([email protected]) 20 21 Calorie restriction (CR) extends lifespan and retards age-related chronic diseases in most 22 species. There is growing evidence that the gut microbiota has a pivotal role in host health 23 and age-related pathological conditions.
    [Show full text]
  • Human Microbiota Reveals Novel Taxa and Extensive Sporulation Hilary P
    OPEN LETTER doi:10.1038/nature17645 Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation Hilary P. Browne1*, Samuel C. Forster1,2,3*, Blessing O. Anonye1, Nitin Kumar1, B. Anne Neville1, Mark D. Stares1, David Goulding4 & Trevor D. Lawley1 Our intestinal microbiota harbours a diverse bacterial community original faecal sample and the cultured bacterial community shared required for our health, sustenance and wellbeing1,2. Intestinal an average of 93% of raw reads across the six donors. This overlap was colonization begins at birth and climaxes with the acquisition of 72% after de novo assembly (Extended Data Fig. 2). Comparison to a two dominant groups of strict anaerobic bacteria belonging to the comprehensive gene catalogue that was derived by culture-independent Firmicutes and Bacteroidetes phyla2. Culture-independent, genomic means from the intestinal microbiota of 318 individuals4 found that approaches have transformed our understanding of the role of the 39.4% of the genes in the larger database were represented in our cohort human microbiome in health and many diseases1. However, owing and 73.5% of the 741 computationally derived metagenomic species to the prevailing perception that our indigenous bacteria are largely identified through this analysis were also detectable in the cultured recalcitrant to culture, many of their functions and phenotypes samples. remain unknown3. Here we describe a novel workflow based on Together, these results demonstrate that a considerable proportion of targeted phenotypic culturing linked to large-scale whole-genome the bacteria within the faecal microbiota can be cultured with a single sequencing, phylogenetic analysis and computational modelling that growth medium.
    [Show full text]
  • Schistosoma Mansoni Infection Is Associated with Quantitative and Qualitative Modifications of the Mammalian Intestinal Microbio
    www.nature.com/scientificreports OPEN Schistosoma mansoni infection is associated with quantitative and qualitative modifcations of the Received: 4 April 2018 Accepted: 20 July 2018 mammalian intestinal microbiota Published: xx xx xxxx Timothy P. Jenkins1, Laura E. Peachey1, Nadim J. Ajami 2, Andrew S. MacDonald 3, Michael H. Hsieh4,5,6, Paul J. Brindley7, Cinzia Cantacessi 1 & Gabriel Rinaldi7,8 In spite of the extensive contribution of intestinal pathology to the pathophysiology of schistosomiasis, little is known of the impact of schistosome infection on the composition of the gut microbiota of its mammalian host. Here, we characterised the fuctuations in the composition of the gut microbial fora of the small and large intestine, as well as the changes in abundance of individual microbial species, of mice experimentally infected with Schistosoma mansoni with the goal of identifying microbial taxa with potential roles in the pathophysiology of infection and disease. Bioinformatic analyses of bacterial 16S rRNA gene data revealed an overall reduction in gut microbial alpha diversity, alongside a signifcant increase in microbial beta diversity characterised by expanded populations of Akkermansia muciniphila (phylum Verrucomicrobia) and lactobacilli, in the gut microbiota of S. mansoni-infected mice when compared to uninfected control animals. These data support a role of the mammalian gut microbiota in the pathogenesis of hepato-intestinal schistosomiasis and serves as a foundation for the design of mechanistic studies to unravel the complex relationships amongst parasitic helminths, gut microbiota, pathophysiology of infection and host immunity. Schistosomiasis, a major neglected tropical disease, is considered the most problematic of the human helmin- thiases in terms of morbidity and mortality1.
    [Show full text]
  • Ketogenic Diet Enhances Neurovascular Function with Altered
    www.nature.com/scientificreports OPEN Ketogenic diet enhances neurovascular function with altered gut microbiome in young healthy Received: 14 September 2017 Accepted: 17 April 2018 mice Published: xx xx xxxx David Ma1, Amy C. Wang1, Ishita Parikh1, Stefan J. Green 2, Jared D. Hofman1,3, George Chlipala2, M. Paul Murphy1,4, Brent S. Sokola5, Björn Bauer5, Anika M. S. Hartz1,3 & Ai-Ling Lin1,3,6 Neurovascular integrity, including cerebral blood fow (CBF) and blood-brain barrier (BBB) function, plays a major role in determining cognitive capability. Recent studies suggest that neurovascular integrity could be regulated by the gut microbiome. The purpose of the study was to identify if ketogenic diet (KD) intervention would alter gut microbiome and enhance neurovascular functions, and thus reduce risk for neurodegeneration in young healthy mice (12–14 weeks old). Here we show that with 16 weeks of KD, mice had signifcant increases in CBF and P-glycoprotein transports on BBB to facilitate clearance of amyloid-beta, a hallmark of Alzheimer’s disease (AD). These neurovascular enhancements were associated with reduced mechanistic target of rapamycin (mTOR) and increased endothelial nitric oxide synthase (eNOS) protein expressions. KD also increased the relative abundance of putatively benefcial gut microbiota (Akkermansia muciniphila and Lactobacillus), and reduced that of putatively pro-infammatory taxa (Desulfovibrio and Turicibacter). We also observed that KD reduced blood glucose levels and body weight, and increased blood ketone levels, which might be associated with gut microbiome alteration. Our fndings suggest that KD intervention started in the early stage may enhance brain vascular function, increase benefcial gut microbiota, improve metabolic profle, and reduce risk for AD.
    [Show full text]
  • Characterization of the Fecal Microbiome in Cats with Inflammatory Bowel Disease Or Alimentary Small Cell Lymphoma
    www.nature.com/scientificreports OPEN Characterization of the fecal microbiome in cats with infammatory bowel disease or alimentary small cell lymphoma Sina Marsilio1,2*, Rachel Pilla1, Benjamin Sarawichitr1, Betty Chow 3,6, Steve L. Hill3,7, Mark R. Ackermann4, J. Scot Estep5, Jonathan A. Lidbury1, Joerg M. Steiner1 & Jan S. Suchodolski1 Feline chronic enteropathy (CE) is a common gastrointestinal disorder in cats and mainly comprises infammatory bowel disease (IBD) and small cell lymphoma (SCL). Both IBD and SCL in cats share features with chronic enteropathies such as IBD and monomorphic epitheliotropic intestinal T-cell lymphoma in humans. The aim of this study was to characterize the fecal microbiome of 38 healthy cats and 27 cats with CE (13 cats with IBD and 14 cats with SCL). Alpha diversity indices were signifcantly decreased in cats with CE (OTU p = 0.003, Shannon Index p = 0.008, Phylogenetic Diversity p = 0.019). ANOSIM showed a signifcant diference in bacterial communities, albeit with a small efect size (P = 0.023, R = 0.073). Univariate analysis and LEfSE showed a lower abundance of facultative anaerobic taxa of the phyla Firmicutes (families Ruminococcaceae and Turicibacteraceae), Actinobacteria (genus Bifdobacterium) and Bacteroidetes (i.a. Bacteroides plebeius) in cats with CE. The facultative anaerobic taxa Enterobacteriaceae and Streptococcaceae were increased in cats with CE. No signifcant diference between the microbiome of cats with IBD and those with SCL was found. Cats with CE showed patterns of dysbiosis similar to those in found people with IBD. Feline chronic enteropathy (CE) is common in elderly cats and is defned as the presence of clinical signs of gastrointestinal disease for more than 3 weeks in the absence of infectious intestinal diseases (e.g., parasites) and extraintestinal causes (e.g., renal disease, hyperthyroidism)1.
    [Show full text]
  • A Synthetic Probiotic Engineered for Colorectal Cancer Therapy Modulates Gut Microbiota
    A Synthetic Probiotic Engineered for Colorectal Cancer Therapy Modulates Gut Microbiota Yusook Chung Cell Biotech, Co., Ltd. Yongku Ryu Cell Biotech, Co., Ltd. Byung Chull An Cell Biotech, Co., Ltd. Yeo-Sang Yoon Cell Biotech, Co., Ltd. Oksik Choi Cell Biotech, Co., Ltd. Tai Yeub Kim Cell Biotech, Co., Ltd. Jae Kyung Yoon Yonsei University Jun Young Ahn Cell Biotech, Co., Ltd. Ho Jin Park Cell Biotech, Co., Ltd. Soon-Kyeong Kwon Yonsei University Jihyun F. Kim ( [email protected] ) Yonsei University https://orcid.org/0000-0001-7715-6992 Myung Jun Chung ( [email protected] ) Cell Biotech, Co., Ltd. Research Keywords: Lactobacillus rhamnosus CBT LR5 (KCTC 12202BP), alanine racemase, DLD-1 xenograft, AOM/DSS model of colitis-associated cancer, microbiome, Akkermansia, Turicibacter Posted Date: August 13th, 2020 DOI: https://doi.org/10.21203/rs.3.rs-56674/v1 Page 1/26 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 2/26 Abstract Background: Successful chemoprevention or chemotherapy is achieved through targeted delivery of prophylactic agents during initial phases of carcinogenesis or therapeutic agents to malignant tumors. Bacteria can be used as anticancer agents, but efforts to utilize attenuated pathogenic bacteria suffer from the risk of toxicity or infection. Lactic acid bacteria are safe to eat and often confer health benets, making them ideal candidates for live vehicles engineered to deliver anticancer drugs. Results: In this study, we developed an effective bacterial drug delivery system for colorectal cancer (CRC) therapy using the lactic acid bacterium Pediococcus pentosaceus. It is equipped with dual gene cassettes driven by a strong inducible promoter that encode the therapeutic protein P8 fused to a secretion signal peptide and a complementation system.
    [Show full text]
  • Maturation of the Gut Microbiome During the First Year of Life
    1 Maturation of the gut microbiome during the first year of life 2 contributes to the protective farm effect on childhood asthma 3 4 Martin Depner, PhD,1 Diana Hazard Taft, PhD,2 Pirkka V. Kirjavainen, PhD,3,4 Karen M. Kalanetra, 5 PhD,2 Anne M. Karvonen, PhD,3 Stefanie Peschel, MSc,1 Elisabeth Schmausser-Hechfellner, BSc,1 6 Caroline Roduit, MD, PhD,5,6,7 Remo Frei, PhD,5,8 Roger Lauener, MD,5,7,9,10 Amandine Divaret- 7 Chauveau, MD,11,12,13 Jean-Charles Dalphin, MD,13† Josef Riedler, MD,14 Marjut Roponen, PhD,15 8 Michael Kabesch MD,16 Harald Renz, MD, PhD,17,18 Juha Pekkanen, MD, PhD,3,19 Freda M. 9 Farquharson,20 Petra Louis, PhD,20 David Mills, PhD2, Erika von Mutius, MD,1,18,21 PASTURE study 10 group,* Markus J. Ege, MD18,21 11 12 Affiliations 13 1 Institute for Asthma and Allergy Prevention, Helmholtz Zentrum München, German Research 14 Center for Environmental Health, Neuherberg, Germany 15 2 Viticulture and Enology, University of California, Davis, USA 16 3 Department of Health Security, Finnish Institute for Health and Welfare, Kuopio, Finland 17 4 Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland 18 5 Christine Kühne Center for Allergy Research and Education (CK-CARE), Davos, Switzerland 19 6 Children's Hospital, University of Zürich, Zürich, Switzerland 20 7 Childrens Hospital of Eastern Switzerland, St. Gallen, Switzerland 21 8 Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland 22 9 University of Zurich, Zurich, Switzerland 23 10
    [Show full text]
  • Dakotella Fusiforme Gen. Nov., Sp. Nov., Isolated from Healthy Human Feces
    Description of a new member of the family Erysipelotrichaceae: Dakotella fusiforme gen. nov., sp. nov., isolated from healthy human feces Sudeep Ghimire, Supapit Wongkuna and Joy Scaria Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, United States of America ABSTRACT A Gram-positive, non-motile, rod-shaped facultative anaerobic bacterial strain SG502T was isolated from healthy human fecal samples in Brookings, SD, USA. The comparison of the 16S rRNA gene placed the strain within the family Erysipelotrichaceae. Within this family, Clostridium innocuum ATCC 14501T, Longicatena caecimuris strain PG- 426-CC-2, Eubacterium dolichum DSM 3991T and E. tortuosum DSM 3987T (=ATCC 25548T) were its closest taxa with 95.28%, 94.17%, 93.25%, and 92.75% 16S rRNA sequence identities respectively. The strain SG502T placed itself close to C. innocuum in the 16S rRNA phylogeny. The members of genus Clostridium within family Erysipelotrichaceae was proposed to be reassigned to genus Erysipelatoclostridium to resolve the misclassification of genus Clostridium. Therefore, C. innocuum was also classified into this genus temporarily with the need to reclassify it in the future because of its difference in genomic properties. Similarly, genome sequencing of the strain and comparison with its 16S phylogenetic members and proposed members of the genus Erysipelatoclostridium, SG502T warranted a separate genus even though its 16S rRNA similarity was >95% when comapred to C. innocuum. The strain was 71.8% similar at ANI, 19.8% [17.4–22.2%] at dDDH and 69.65% similar at AAI to its closest neighbor C. innocuum. The genome size was nearly 2,683,792 bp with 32.88 mol% G+C content, Submitted 19 November 2019 which is about half the size of C.
    [Show full text]