Different Drugs in Modulating Gut Microbiome of Colitis Mice
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Effects of Long-Acting, Broad Spectra Anthelmintic Treatments on The
www.nature.com/scientificreports OPEN Efects of long‑acting, broad spectra anthelmintic treatments on the rumen microbial community compositions of grazing sheep Christina D. Moon1*, Luis Carvalho1, Michelle R. Kirk1, Alan F. McCulloch2, Sandra Kittelmann3, Wayne Young1, Peter H. Janssen1 & Dave M. Leathwick1 Anthelmintic treatment of adult ewes is widely practiced to remove parasite burdens in the expectation of increased ruminant productivity. However, the broad activity spectra of many anthelmintic compounds raises the possibility of impacts on the rumen microbiota. To investigate this, 300 grazing ewes were allocated to treatment groups that included a 100‑day controlled release capsule (CRC) containing albendazole and abamectin, a long‑acting moxidectin injection (LAI), and a non‑treated control group (CON). Rumen bacterial, archaeal and protozoal communities at day 0 were analysed to identify 36 sheep per treatment with similar starting compositions. Microbiota profles, including those for the rumen fungi, were then generated for the selected sheep at days 0, 35 and 77. The CRC treatment signifcantly impacted the archaeal community, and was associated with increased relative abundances of Methanobrevibacter ruminantium, Methanosphaera sp. ISO3‑F5, and Methanomassiliicoccaceae Group 12 sp. ISO4‑H5 compared to the control group. In contrast, the LAI treatment increased the relative abundances of members of the Veillonellaceae and resulted in minor changes to the bacterial and fungal communities by day 77. Overall, the anthelmintic treatments resulted in few, but highly signifcant, changes to the rumen microbiota composition. Anthelmintic treatment of adult ewes is practiced by about 80% of sheep farmers in New Zealand1, and many of these treatments use active compounds with broad-spectrum persistent activity. -
The Gut Microbiota in Young and Middle-Aged Rats Showed Different
Zhu et al. BMC Microbiology (2016) 16:281 DOI 10.1186/s12866-016-0895-0 RESEARCH ARTICLE Open Access The gut microbiota in young and middle-aged rats showed different responses to chicken protein in their diet Yingying Zhu1,2,HeLi1, Xinglian Xu1, Chunbao Li1* and Guanghong Zhou1* Abstract Background: Meat protein in the diet has been shown to be beneficial for the growth of Lactobacillus in the caecum of growing rats; however, it is unknown whether gut microbiota in middle-aged animals have the same responses to meat protein diets. This study compared the composition of the gut microbiota between young and middle-aged rats after being fed 17.7% chicken protein diet for 14 days. Methods: Feces were collected on day 0 and day 14 from young rats (4 weeks old) and middle-aged rats (64 weeks old) fed with 17.7% chicken protein diets. The composition of the gut bacteria was analyzed by sequencing the V4-V5 region of the 16S ribosomal RNA gene. Results: The results showed that the composition of the gut microbiota was significantly different between young and middle-aged rats on both day 0 and day 14. The percentage of Firmicutes decreased for middle-aged rats (72.1% versus 58.1% for day 0 and day 14, respectively) but increased for young rats (41.5 versus 57.7% for day 0 and day 14, respectively). The percentage of Bacteroidetes increased to 31.2% (20.5% on day 0) for middle-aged rats and decreased to 29.6% (41.3% on day 0) for young rats. -
Determining the Culturability of the Rumen Bacterial Microbiome
bs_bs_banner Determining the culturability of the rumen bacterial microbiome Christopher J. Creevey,1,2 William J. Kelly,3,4* list of cultured rumen isolates that are representative Gemma Henderson3,4 and Sinead C. Leahy3,4 of abundant, novel and core bacterial species in the 1Animal and Bioscience Research Department, Animal rumen. In addition, we have identified taxa, particu- and Grassland Research and Innovation Centre, larly within the phylum Bacteroidetes, where further Teagasc, Grange, Dunsany, Co. Meath, Ireland. cultivation efforts are clearly required. 2Institute of Biological, Environmental and Rural This information is being used to guide the isola- Sciences, Aberystwyth University, Aberystwyth, tion efforts and selection of bacteria from the rumen Ceredigion, UK. microbiota for sequencing through the Hungate1000. 3Grasslands Research Centre, AgResearch Limited, Palmerston North, New Zealand. Introduction 4New Zealand Agricultural Greenhouse Gas Research Ruminants have evolved a symbiotic relationship with a Centre, Palmerston North, New Zealand. complex microbiome consisting of bacteria, archaea, fungi, protozoa, and viruses located in their fore-stomach Summary (reticulorumen) that allows these animals to utilize the lignocellulose component of plant material as their main The goal of the Hungate1000 project is to generate a energy source. The microbial degradation of lignocellu- reference set of rumen microbial genome sequences. lose, and fermentation of the released soluble sugars, Toward this goal we have carried out a meta-analysis produces short-chain fatty acids that are absorbed across using information from culture collections, scientific the rumen epithelium and utilized by the ruminant for literature, and the NCBI and RDP databases and growth, while the microbial cells pass from the rumen to linked this with a comparative study of several rumen the digestive tract where they become the main source of 16S rRNA gene-based surveys. -
Characterization of the Rumen Microbiota and Volatile Fatty Acid Profiles of Weaned Goat Kids Under Shrub-Grassland Grazing and Indoor Feeding
animals Article Characterization of the Rumen Microbiota and Volatile Fatty Acid Profiles of Weaned Goat Kids under Shrub-Grassland Grazing and Indoor Feeding 1, 1, 1, 2 1,3 1 1,3 Jiazhong Guo y, Pengfei Li y, Shuai Liu y, Bin Miao , Bo Zeng , Yahui Jiang , Li Li , Linjie Wang 1,3 , Yu Chen 2 and Hongping Zhang 1,* 1 College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; [email protected] (J.G.); [email protected] (P.L.); [email protected] (S.L.); [email protected] (B.Z.); [email protected] (Y.J.); [email protected] (L.L.); [email protected] (L.W.) 2 Nanjiang Yellow Goat Scientific Research Institute, Nanjiang 635600, China; [email protected] (B.M.); [email protected] (Y.C.) 3 Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China * Correspondence: [email protected] These authors contributed equally to this work. y Received: 17 December 2019; Accepted: 20 January 2020; Published: 21 January 2020 Simple Summary: Although grazing and indoor feeding are both major production systems in the goat industry worldwide, the impacts of different feeding systems on rumen fermentation remain poorly understood. In this study, we observed large differences in microbial community compositions and volatile fatty acid profiles in the rumen of weaned goats among three feeding systems, which provides an in-depth understanding of rumen fermentation in response to changes in feeding systems. Abstract: In this study, we conducted comparative analyses to characterize the rumen microbiota and volatile fatty acid (VFA) profiles of weaned Nanjiang Yellow goat kids under shrub-grassland grazing (GR), shrub-grassland grazing and supplementary feeding (SF), and indoor feeding (IF) systems. -
CGM-18-001 Perseus Report Update Bacterial Taxonomy Final Errata
report Update of the bacterial taxonomy in the classification lists of COGEM July 2018 COGEM Report CGM 2018-04 Patrick L.J. RÜDELSHEIM & Pascale VAN ROOIJ PERSEUS BVBA Ordering information COGEM report No CGM 2018-04 E-mail: [email protected] Phone: +31-30-274 2777 Postal address: Netherlands Commission on Genetic Modification (COGEM), P.O. Box 578, 3720 AN Bilthoven, The Netherlands Internet Download as pdf-file: http://www.cogem.net → publications → research reports When ordering this report (free of charge), please mention title and number. Advisory Committee The authors gratefully acknowledge the members of the Advisory Committee for the valuable discussions and patience. Chair: Prof. dr. J.P.M. van Putten (Chair of the Medical Veterinary subcommittee of COGEM, Utrecht University) Members: Prof. dr. J.E. Degener (Member of the Medical Veterinary subcommittee of COGEM, University Medical Centre Groningen) Prof. dr. ir. J.D. van Elsas (Member of the Agriculture subcommittee of COGEM, University of Groningen) Dr. Lisette van der Knaap (COGEM-secretariat) Astrid Schulting (COGEM-secretariat) Disclaimer This report was commissioned by COGEM. The contents of this publication are the sole responsibility of the authors and may in no way be taken to represent the views of COGEM. Dit rapport is samengesteld in opdracht van de COGEM. De meningen die in het rapport worden weergegeven, zijn die van de auteurs en weerspiegelen niet noodzakelijkerwijs de mening van de COGEM. 2 | 24 Foreword COGEM advises the Dutch government on classifications of bacteria, and publishes listings of pathogenic and non-pathogenic bacteria that are updated regularly. These lists of bacteria originate from 2011, when COGEM petitioned a research project to evaluate the classifications of bacteria in the former GMO regulation and to supplement this list with bacteria that have been classified by other governmental organizations. -
Phylogenetic Analysis of 16S Rdna Sequences Manifest Rumen Bacterial Diversity in Gayals (Bos Frontalis) Fed Fresh Bamboo Leaves and Twigs (Sinarumdinaria)
1057 Asian-Aust. J. Anim. Sci. Vol. 20, No. 7 : 1057 - 1066 July 2007 www.ajas.info Phylogenetic Analysis of 16S rDNA Sequences Manifest Rumen Bacterial Diversity in Gayals (Bos frontalis) Fed Fresh Bamboo Leaves and Twigs (Sinarumdinaria) Weidong Deng1, 2, 3, Metha Wanapat2, *, Songcheng Ma3, Jing Chen3, Dongmei Xi3, Tianbao He4 Zhifang Yang4 and Huaming Mao1, 3 1 Yunnan Provincial Laboratory of Animal Nutrition and Feed Science Yunnan Agricultural University, Kunming 650201, P. R. China ABSTRACT : Six male Gayal (Bos frontalis), approximately two years of age and with a mean live weight of 203±17 kg (mean±standard deviation), were housed indoors in metabolism cages and fed bamboo (Sinarundinaria) leaves and twigs. After an adjustment period of 24 days of feeding the diet, samples of rumen liquor were obtained for analyses of bacteria in the liquor. The diversity of rumen bacteria was investigated by constructing a 16S rDNA clone library. A total of 147 clones, comprising nearly full length sequences (with a mean length of 1.5 kb) were sequenced and submitted to an on-line similarity search and phylogenetic analysis. Using the criterion of 97% or greater similarity with the sequences of known bacteria, 17 clones were identified as Ruminococcus albus, Butyrivibrio fibrosolvens, Quinella ovalis, Clostridium symbiosium, Succiniclasticum ruminis, Selenomonas ruminantium and Allisonella histaminiformans, respectively. A further 22 clones shared similarity ranging from 90-97% with known bacteria but the similarity in sequences for the remaining 109 clones was less than 90% of those of known bacteria. Using a phylogenetic analysis it was found that the majority of the clones identified (57.1%) were located in the low G+C subdivision, with most of the remainder (42.2% of clones) located in the Cytophage-Flexibacter-Bacteroides (CFB) phylum and one clone (0.7%) was identified as a Spirochaete. -
Relationship Between the True Digestibility of Dietary Calcium and Gastrointestinal Microorganisms in Goats
animals Article Relationship between the True Digestibility of Dietary Calcium and Gastrointestinal Microorganisms in Goats 1, 1,2, 1, 1 1 1 Yuehui Liu y, Ali Mujtaba Shah y , Lizhi Wang *, Lei Jin , Zhisheng Wang , Bai Xue and Quanhui Peng 1 1 Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; [email protected] (Y.L.); [email protected] (A.M.S.); [email protected] (L.J.); [email protected] (Z.W.); [email protected] (B.X.); [email protected] (Q.P.) 2 Department of Livestock Production, Shaheed Benazir Bhutto University of Veterinary and Animal Science, Sakrand 67210, Pakistan * Correspondence: [email protected]; Tel./Fax: +86-28-86290922 These authors contributed equally in this work. y Received: 29 March 2020; Accepted: 13 May 2020; Published: 18 May 2020 Simple Summary: The specific enzymes secreted by microorganisms in the gastrointestinal tract (GIT) of ruminants, such as phytase, can catalyze the decomposition of calcium compounds (e.g., phytic acid) and release bound calcium for the absorption of animals. Therefore, we speculate that gastrointestinal microbes could be a factor affecting digestion and absorption of dietary calcium. However, little related research has been reported. In the present study, we found that the true digestibility of calcium (TDC) in goats is related to gastrointestinal bacteria. Some gastro-intestinal bacteria, such as ruminal Prevotella, were beneficial for true host digestibility of dietary calcium. Abstract: The current study was performed to examine the relationship between the true digestibility of calcium (TDC) in the diet and bacterial community structure in the gastrointestinal tract (GIT) of goats. -
The Ruminal Microbiome Associated with Methane Emissions from Ruminant Livestock Ilma Tapio1, Timothy J
Tapio et al. Journal of Animal Science and Biotechnology (2017) 8:7 DOI 10.1186/s40104-017-0141-0 REVIEW Open Access The ruminal microbiome associated with methane emissions from ruminant livestock Ilma Tapio1, Timothy J. Snelling2, Francesco Strozzi3 and R. John Wallace2* Abstract Methane emissions from ruminant livestock contribute significantly to the large environmental footprint of agriculture. The rumen is the principal source of methane, and certain features of the microbiome are associated with low/high methane phenotypes. Despite their primary role in methanogenesis, the abundance of archaea has only a weak correlation with methane emissions from individual animals. The composition of the archaeal community appears to have a stronger effect, with animals harbouring the Methanobrevibacter gottschalkii clade tending to be associated with greater methane emissions. Ciliate protozoa produce abundant H2, the main substrate for methanogenesis in the rumen, and their removal (defaunation) results in an average 11% lower methane emissions in vivo, but the results are not consistent. Different protozoal genera seem to result in greater methane emissions, though community types (A, AB, B and O) did not differ. Within the bacteria, three different ‘ruminotypes’ have been identified, two of which predispose animals to have lower methane emissions. The two low-methane ruminotypes are generally characterized by less abundant H2-producing bacteria. A lower abundance of Proteobacteria and differences in certain Bacteroidetes and anaerobic fungi seem to be associated with high methane emissions. Rumen anaerobic fungi produce abundant H2 and formate, and their abundance generally corresponds to the level of methane emissions. Thus, microbiome analysis is consistent with known pathways for H2 production and methanogenesis, but not yet in a predictive manner. -
Liraglutide Attenuates Nonalcoholic Fatty Liver Disease by Modulating Gut Microbiota in Rats Administered a High-Fat Diet
Hindawi BioMed Research International Volume 2020, Article ID 2947549, 10 pages https://doi.org/10.1155/2020/2947549 Research Article Liraglutide Attenuates Nonalcoholic Fatty Liver Disease by Modulating Gut Microbiota in Rats Administered a High-Fat Diet Ningjing Zhang ,1 Junxian Tao ,2 Lijun Gao ,1 Yan Bi ,2 Ping Li ,2 Hongdong Wang ,2 Dalong Zhu ,2 and Wenhuan Feng 1,2 1Medical School of Southeast University Nanjing Drum Tower Hospital, Nanjing, China 2Department of Endocrinology, Drum Tower Hospital Affiliated to Nanjing University Medical School, Nanjing, China Correspondence should be addressed to Dalong Zhu; [email protected] and Wenhuan Feng; [email protected] Received 4 September 2019; Revised 15 December 2019; Accepted 4 January 2020; Published 18 February 2020 Academic Editor: Yoshifumi Saisho Copyright © 2020 Ningjing Zhang et al. 1is is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 1is study aimed to determine whether modulation of the gut microbiota structure by liraglutide helps improve nonalcoholic fatty liver disease (NAFLD) in rats on a high-fat diet (HFD). Rats were administered an HFD for 12 weeks to induce NAFLD and then administered liraglutide for 4 additional weeks. Next-generation sequencing and multivariate analysis were performed to assess structural changes in the gut microbiota. Liraglutide attenuated excessive hepatic ectopic fat deposition, maintained intestinal barrier integrity, and alleviated metabolic endotoxemia in HFD rats. Liraglutide significantly altered the overall structure of the HFD-disrupted gut microbiota and gut microbial composition in HFD rats in comparison to those on a normal diet. -
Universidade De Lisboa Faculdade De Medicina Veterinária
UNIVERSIDADE DE LISBOA FACULDADE DE MEDICINA VETERINÁRIA MODULATION OF RUMINAL BIOHYDROGENATION IN SHEEP THROUGH DIETARY TANNINS OR ENERGY SOURCES MÓNICA MENDES DA COSTA Orientador: Professor Doutor Rui José Branquinho de Bessa Tese especialmente elaborada para obtenção do grau de Doutor em Ciências Veterinárias na Especialidade de Produção Animal 2017 UNIVERSIDADE DE LISBOA FACULDADE DE MEDICINA VETERINÁRIA MODULATION OF RUMINAL BIOHYDROGENATION IN SHEEP THROUGH DIETARY TANNINS OR ENERGY SOURCES MÓNICA MENDES DA COSTA Orientador: Professor Doutor Rui José Branquinho De Bessa Tese especialmente elaborada para obtenção do grau de Doutor em Ciências Veterinárias na Especialidade de Produção Animal Júri: Presidente: Doutor Rui Manuel Vasconcelos e Horta Caldeira Vogais: - Doutor Carlos Mendes Godinho de Andrade Fontes - Doutor Miguel António Machado Rodrigues - Doutor Rui José Branquinho de Bessa - Doutor José Manuel Bento Santos Silva - Doutora Margarida Rosa Garcez Maia 2017 I dedicate this thesis to My parents and my sister My grandparents Acknowledgements I want to thank to the following entities and people because without them the work presented in this thesis would not be accomplished: To Foundation for Science and Technology (FCT) for my PhD fellowship and the project that financed the work. To the Faculty of Veterinary Medicine, University of Lisbon (FMV-UL), for being the place were I spent twelve years studying and working, not only for my PhD but also for previous research and integrated master in Veterinary Medicine. To Centre for Interdisciplinary Research in Animal Health (CIISA), for all the facilities and materials necessary for my PhD work. To Professor Rui José Branquinho de Bessa, for being my supervisor during my PhD while providing me with some of his vast knowledge, mainly in experimental design and statistics, and for all his suggestions and corrections during my journey through the Animal Production research field that were indispensable for the elaboration of the thesis and research articles. -
Influence of Season and Diet on Fiber Digestion and Bacterial Community Structure in the Rumen of Muskoxen
microorganisms Article Influence of Season and Diet on Fiber Digestion and Bacterial Community Structure in the Rumen of Muskoxen (Ovibos moschatus) Emilio M. Ungerfeld 1,†, Mary Beth Leigh 2,3, Robert J. Forster 1,* and Perry S. Barboza 2,3,*,‡ 1 Lethbridge Research Centre, Agriculture and Agri-Food Canada, 5403 1st Ave S, Lethbridge, AB T1J 4B1, Canada; [email protected] 2 Department of Biology and Wildlife, Institute of Arctic Biology, Fairbanks, AK 99775-7000, USA; [email protected] 3 Department of Biology and Wildlife, University of Alaska, Fairbanks, AK 99775-7000, USA * Correspondence: [email protected] (R.J.F.); [email protected] (P.S.B.); Tel.: +1-403-317-2292 (R.J.F.); +1-979-845-3492 (P.S.B.) † Current address: Instituto de Investigaciones Agropecuarias, INIA Carillanca, Temuco 8340422, Chile ‡ Current address: Wildlife & Fisheries Sciences, Texas A&M University, TAMU 2258, College Station, TX 77843-2258, USA Received: 28 June 2018; Accepted: 14 August 2018; Published: 20 August 2018 Abstract: We studied the relationship between fiber digestion and the composition of the bacterial community in the rumen of muskoxen at the start and the end of the annual window of plant growth from spring to fall. Eight ruminally cannulated castrated males were fed brome hay or triticale straw (69.6% vs. 84.6% neutral detergent fiber, respectively) that were similar in fiber content to the sedges consumed by wild muskoxen (64.5 to 71.7% neutral detergent fiber). Muskoxen digested fiber from both forages faster and to a greater extent when straw rather than hay was consumed. -
Determining the Culturability of the Rumen Bacterial Microbiome
Determining the culturability of the rumen bacterial microbiome Creevey, C. J., Kelly, W. J., Henderson, G., & Leahy, S. C. (2014). Determining the culturability of the rumen bacterial microbiome. Microbial Biotechnology, 7(5), 467-479. https://doi.org/10.1111/1751-7915.12141 Published in: Microbial Biotechnology Document Version: Publisher's PDF, also known as Version of record Queen's University Belfast - Research Portal: Link to publication record in Queen's University Belfast Research Portal Publisher rights Copyright 2014 the authors. This is an open access article published under a Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium, provided the author and source are cited. General rights Copyright for the publications made accessible via the Queen's University Belfast Research Portal is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The Research Portal is Queen's institutional repository that provides access to Queen's research output. Every effort has been made to ensure that content in the Research Portal does not infringe any person's rights, or applicable UK laws. If you discover content in the Research Portal that you believe breaches copyright or violates any law, please contact [email protected]. Download date:06. Oct. 2021 bs_bs_banner Determining the culturability of the rumen bacterial microbiome Christopher J. Creevey,1,2 William J. Kelly,3,4* list of cultured rumen isolates that are representative Gemma Henderson3,4 and Sinead C.