Genetic and functional analysis of the bovine uterine microbiota. Part II: Purulent vaginal discharge versus healthy cows.

Bicalho MLS, Lima S, Higgins CH, Machado VS, Lima FS, Bicalho RC J Dairy Sci. May 2017 The aim of this study was to characterize, using metagenomic shotgun DNA sequencing, the intrauterine microbial population and its predicted functional diversity...

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Genetic and functional analysis of the bovine uterine microbiota. Part I: Metritis versus healthy cows.

Bicalho MLS, Machado VS, Higgins CH, Lima FS, Bicalho RC J Dairy Sci. May 2017 Metritis is a uterine disease that affects 10 to 30% of all lactating dairy cows and has detrimental effects on reproductive performance, milk production, and survival....

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The Structural and Functional Capacity of Ruminal and Cecal Microbiota in Growing Cattle Was Unaffected by Dietary Supplementation of Linseed Oil and Nitrate.

Popova M, McGovern E, McCabe MS, Martin C, Doreau M, Arbre M, Meale SJ, Morgavi DP, Waters SM Front Microbiol. 2017. doi: 10.3389/fmicb.2017.00937 Microorganisms in the digestive tract of ruminants differ in their functionality and ability to use...

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Variability, stability, and resilience of fecal microbiota in dairy cows fed whole crop corn silage.

Tang MT, Han H, Yu Z, Tsuruta T, Nishino N Appl Microbiol Biotechnol. Jun 2017. doi: 10.1007/s00253-017-8348-8 The microbiota of whole crop corn silage and feces of silage-fed dairy cows were examined. A total of 18 dairy cow feces were collected...

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Illumina MiSeq 16S amplicon sequence analysis of bovine respiratory disease associated bacteria in lung and mediastinal lymph node tissue.

Johnston D, Earley B, Cormican P, Murray G, Kenny DA, Waters SM, McGee M, Kelly AK, McCabe MS BMC Vet Res. May 2017. doi: 10.1186/s12917-017-1035-2 Bovine respiratory disease (BRD) is caused by growth of single or multiple species of pathogenic...

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Hot topic: 16S rRNA gene sequencing reveals the microbiome of the virgin and pregnant bovine uterus.

Moore SG, Ericsson AC, Poock SE, Melendez P, Lucy MC J Dairy Sci. Jun 2017 We tested the hypothesis that the uterus of virgin heifers and pregnant cows possessed a resident microbiome by 16S rRNA gene sequencing of the virgin and pregnant bovine...

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Effect of high-fat diet and growth stage on the diversity and composition of intestinal microbiota in healthy bovine livestock.

Jiao S, Cao H, Dai Y, Wu J, Lv J, Du R, Han B J Sci Food Agric. Apr 2017. doi: 10.1002/jsfa.8380 This study aimed to investigate the composition of bacteria in the bovine rectum and their functions during growth, in relation to different diets....

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Microbial population analysis of the salivary glands of ticks; a possible strategy for the surveillance of bacterial pathogens.

Qiu Y, Nakao R, Ohnuma A, Kawamori F, Sugimoto C

PLoS One. 2014. doi: 10.1371/journal.pone.0103961

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Characterization of the bacterial communities of life stages of free living lone star ticks (Amblyomma americanum).

Williams-Newkirk AJ, Rowe LA, Mixson-Hayden TR, Dasch GA

PLoS One. 2014. doi: 10.1371/journal.pone.0102130

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Dynamics of the microbiota in response to host infection.

Belzer C, Gerber GK, Roeselers G, Delaney M, DuBois A, Liu Q, Belavusava V, Yeliseyev V, Houseman A, Onderdonk A, Cavanaugh C, Bry L

PLoS One. 2014. doi: 10.1371/journal.pone.0095534

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Deep sequencing analysis reveals temporal microbiota changes associated with development of bovine digital dermatitis.

Krull AC, Shearer JK, Gorden PJ, Cooper VL, Phillips GJ, Plummer PJ

Infect Immun. Aug 2014. doi: 10.1128/IAI.02077-14

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Characterization of cellulolytic activity in the gut of the terrestrial land slug Arion ater: Biochemical identification of targets for intensive study.

Joynson R, Swamy A, Bou PA, Chapuis A, Ferry N

Comp Biochem Physiol B Biochem Mol Biol. . doi: 10.1016/j.cbpb.2014.08.003S1096-4959(14)00110-9

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A polyphenol-rich cranberry extract protects from diet-induced obesity, insulin resistance and intestinal inflammation in association with increased Akkermansia spp. population in the gut microbiota of mice.

Anhê FF, Roy D, Pilon G, Dudonné S, Matamoros S, Varin TV, Garofalo C, Moine Q, Desjardins Y, Levy E, Marette A

Gut. Jun 2015. doi: 10.1136/gutjnl-2014-307142

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The murine appendiceal microbiome is altered in spontaneous colitis and its pathological progression.

Alkadhi S, Kunde D, Cheluvappa R, Randall-Demllo S, Eri R

Gut Pathog. 2014. doi: 10.1186/1757-4749-6-25

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Coupling genetic and chemical microbiome profiling reveals heterogeneity of archaeome and bacteriome in subsurface biofilms that are dominated by the same archaeal species.

Probst AJ, Birarda G, Holman HY, DeSantis TZ, Wanner G, Andersen GL, Perras AK, Meck S, Völkel J, Bechtel HA, Wirth R, Moissl-Eichinger C

PLoS One. 2014. doi: 10.1371/journal.pone.0099801

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[Taxonomic composition of metagenomic community in the larval gut of mosquito Anopheles sinensis (Diptera: Culicidae)].

Nan CY, Ma YJ, Xu JN, Liang J

Zhongguo Ji Sheng Chong Xue Yu Ji Sheng Chong Bing Za Zhi. Apr 2013

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Metaproteomics analysis reveals the adaptation process for the chicken gut microbiota.

Tang Y, Underwood A, Gielbert A, Woodward MJ, Petrovska L

Appl Environ Microbiol. Jan 2014. doi: 10.1128/AEM.02472-13

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Convergence of gut microbiomes in myrmecophagous mammals.

Delsuc F, Metcalf JL, Wegener Parfrey L, Song SJ, González A, Knight R

Mol Ecol. Mar 2014. doi: 10.1111/mec.12501

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Characterization of prepartum and postpartum rumen fluid microbiomes and its correlation with production traits in dairy cows.

Lima FS, Oikonomou G, Lima SF, Bicalho ML, Ganda EK, Oliveira Filho JC, Lorenzo G, Trojacanec P, Bicalho RC

Appl Environ Microbiol. Dec 2014

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Purifying the impure: sequencing metagenomes and metatranscriptomes from complex animal-associated samples.

Lim YW, Haynes M, Furlan M, Robertson CE, Harris JK, Rohwer F

J Vis Exp. 2014. doi: 10.3791/52117

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Revisiting bovine pyometra--new insights into the disease using a culture-independent deep sequencing approach.

Knudsen LR, Karstrup CC, Pedersen HG, Agerholm JS, Jensen TK, Klitgaard K

Vet Microbiol. Feb 2015. doi: 10.1016/j.vetmic.2014.12.006S0378-1135(14)00579-3

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Effect of polybrominated diphenyl ether (PBDE) treatment on the composition and function of the bacterial community in the sponge Haliclona cymaeformis.

Tian RM, Lee OO, Wang Y, Cai L, Bougouffa S, Chiu JM, Wu RS, Qian PY

Front Microbiol. 2014. doi: 10.3389/fmicb.2014.00799

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Age and microenvironment outweigh genetic influence on the Zucker rat microbiome.

Lees H, Swann J, Poucher SM, Nicholson JK, Holmes E, Wilson ID, Marchesi JR

PLoS One. 2014. doi: 10.1371/journal.pone.0100916

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Characterization of the rat oral microbiome and the effects of dietary nitrate.

Hyde ER, Luk B, Cron S, Kusic L, McCue T, Bauch T, Kaplan H, Tribble G, Petrosino JF, Bryan NS

Free Radic Biol Med. Dec 2014. doi: 10.1016/j.freeradbiomed.2014.09.017S0891-5849(14)00436-5

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Variation in koala microbiomes within and between individuals: effect of body region and captivity status.

Alfano N, Courtiol A, Vielgrader H, Timms P, Roca AL, Greenwood AD

Sci Rep. 2015. doi: 10.1038/srep10189

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Composition of Anopheles coluzzii and Anopheles gambiae microbiota from larval to adult stages

Gimonneau G1, Tchioffo MT2, Abate L3, Boissière A4, Awono-Ambene PH5, Nsango SE6, Christen R7, Morlais I8. Infect Genet Evol. 2014 Dec;28:715-24. doi: 10.1016/j.meegid.2014.09.029. Epub 2014 Oct 2.  ...

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Faecal microbiota of cats with insulin-treated diabetes mellitus

Bell ET1, Suchodolski JS2, Isaiah A2, Fleeman LM3, Cook AK4, Steiner JM2, Mansfield CS1.

PLoS One. 2014 Oct 3;9(10):e108729. doi: 10.1371/journal.pone.0108729. eCollection 2014.


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Assessment of fecal bacterial diversity among healthy piglets during the weaning transition.

Alain B Pajarillo E1, Chae JP, P Balolong M, Bum Kim H, Kang DK.

J Gen Appl Microbiol. 2014;60(4):140-6.

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Metagenome-Wide Association of Microbial Determinants of Host Phenotype in Drosophila melanogaster

Chaston JM1, Newell PD2, Douglas AE.

MBio. 2014 Sep 30;5(5):e01631-14. doi: 10.1128/mBio.01631-14.

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Temporal analysis of the effect of extruded flaxseed on the swine gut microbiota

Holman DB1, Baurhoo B, Chénier MR.

Can J Microbiol. 2014 Oct;60(10):649-59. doi: 10.1139/cjm-2014-0317. Epub 2014 Sep 3.

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Changes in the faecal microbiota of mares precede the development of postpartum colic

Weese JS1, Holcombe SJ, Embertson RM, Kurtz KA, Roessner HA, Jalali M, Wismer SE.

Equine Vet J. 2014 Sep 25. doi: 10.1111/evj.12361.

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Routes of acquisition of the gut microbiota of Apis mellifera

Powell JE1, Martinson VG2, Urban-Mead K2, Moran NA3.

Appl Environ Microbiol. 2014 Sep 19. pii: AEM.01861-14.


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Utilization of rye as energy source affects bacterial translocation, intestinal viscosity, microbiota composition, and bone mineralization in broiler chickens.

Tellez G1, Latorre JD1, Kuttappan VA1, Kogut MH2, Wolfenden A1, Hernandez-Velasco X3, Hargis BM1, Bottje WG1, Bielke LR1,Faulkner OB1. Front Genet. 2014 Sep 25;5:339. doi: 10.3389/fgene.2014.00339. eCollection...

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A metagenomic assessment of the bacteria associated with Lucilia sericata and Lucilia cuprina (Diptera: Calliphoridae).

Singh B1, Crippen TL, Zheng L, Fields AT, Yu Z, Ma Q, Wood TK, Dowd SE, Flores M, Tomberlin JK, Tarone AM. Appl Microbiol Biotechnol. 2015 Jan;99(2):869-83. doi: 10.1007/s00253-014-6115-7. Epub...

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Temporal changes and the effect of subtherapeutic concentrations of antibiotics in the gutmicrobiota of swine.

Holman DB1, Chénier MR.

FEMS Microbiol Ecol. 2014 Dec;90(3):599-608. doi: 10.1111/1574-6941.12419. Epub 2014 Oct 2.

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Small Bowel Resection Induces Long-Term Changes in the Enteric Microbiota of Mice.

Sommovilla J1, Zhou Y, Sun RC, Choi PM, Diaz-Miron J, Shaikh N, Sodergren E, Warner BB, Weinstock GM, Tarr PI, Warner BW. J Gastrointest Surg. 2015 Jan;19(1):56-64; discussion 64. doi: 10.1007/s11605-014-2631-0....

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Anterior Foregut Microbiota of the Glassy-Winged Sharpshooter Explored Using Deep 16S rRNA Gene Sequencing from Individual Insects.

Rogers EE, Backus EA.

PLoS One. 2014 Sep 3;9(9):e106215. doi: 10.1371/journal.pone.0106215. eCollection 2014.


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Characterization of Egg Laying Hen and Broiler Fecal Microbiota in Poultry Farms in Croatia, Czech Republic, Hungary and Slovenia.

Videnska P1, Rahman MM1, Faldynova M1, Babak V1, Matulova ME1, Prukner-Radovcic E2, Krizek I2, Smole-Mozina S3, Kovac J3, Szmolka A4, Nagy B4, Sedlar K5, Cejkova D1, Rychlik I1. PLoS...

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Bacterial community structure in Apis florea larvae analyzed by denaturing gradient gel electrophoresis and 16S rRNA gene sequencing.

Saraithong P1, Li Y, Saenphet K, Chen Z, Chantawannakul P.

Insect Sci. 2014 Nov 13. doi: 10.1111/1744-7917.12155.

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Gut microbiota of humans, dogs and cats: current knowledge and future opportunities and challenges.

Deng P, Swanson KS.

Br J Nutr. 2015 Jan;113 Suppl:S6-17. doi: 10.1017/S0007114514002943. Epub 2014 Nov 21.

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Metagenomics of the mucosal microbiota of European eels.

Carda-Diéguez M1, Ghai R2, Rodriguez-Valera F2, Amaro C3.

Genome Announc. 2014 Nov 6;2(6). pii: e01132-14. doi: 10.1128/genomeA.01132-14.

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Dickey AM1, Trease AJ2, Jara-Cavieres A3, Kumar V1, Christenson MK2, Potluri LP2, Morgan JK4, Shatters RG Jr4, Mckenzie CL4, Davis PH2, Osborne LS1. Fla. Entomol. 2014 Jun;97(2):362-366. ...

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Metagenomic assessment of the eastern oyster-associated microbiota.

Chauhan A1, Wafula D2, Lewis DE2, Pathak A2.

Genome Announc. 2014 Oct 23;2(5). pii: e01083-14. doi: 10.1128/genomeA.01083-14.

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Microbial shifts in the aging mouse gut.

Langille MG, Meehan CJ, Koenig JE, Dhanani AS, Rose RA, Howlett SE, Beiko RG

Microbiome. 2014. doi: 10.1186/s40168-014-0050-9

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Alteration of the fecal microbiota and serum metabolite profiles in dogs with idiopathic inflammatory bowel disease.

Minamoto Y, Otoni CC, Steelman SM, Büyükleblebici O, Steiner JM, Jergens AE, Suchodolski JS

Gut Microbes. Dec 2014

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Taxonomic and functional annotation of gut bacterial communities of Eisenia foetida and Perionyx excavatus.

Singh A, Singh DP, Tiwari R, Kumar K, Singh RV, Singh S, Prasanna R, Saxena AK, Nain L

Microbiol Res. Mar 2015

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Deciphering chicken gut microbial dynamics based on high-throughput 16S rRNA metagenomics analyses.

Mohd Shaufi MA, Sieo CC, Chong CW, Gan HM, Ho YW

Gut Pathog. 2015. doi: 10.1186/s13099-015-0051-7

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Rumen bacterial diversity of 80 to 110-day-old goats using 16S rRNA sequencing.

Han X, Yang Y, Yan H, Wang X, Qu L, Chen Y

PLoS One. 2015. doi: 10.1371/journal.pone.0117811

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Influence of age, reproductive cycling status, and menstruation on the vaginal microbiome in baboons (Papio anubis).

Uchihashi M, Bergin IL, Bassis CM, Hashway SA, Chai D, Bell JD

Am J Primatol. Feb 2015. doi: 10.1002/ajp.22378

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First insights into the microbial diversity in the omasum and reticulum of bovine using Illumina sequencing.

Peng S, Yin J, Liu X, Jia B, Chang Z, Lu H, Jiang N, Chen Q

J Appl Genet. Jan 2015

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Metagenomic insights into the effects of fructo-oligosaccharides (FOS) on the composition of fecal microbiota in mice.

Mao B, Li D, Zhao J, Liu X, Gu Z, Chen YQ, Zhang H, Chen W

J Agric Food Chem. Jan 2015. doi: 10.1021/jf505156h

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Directed shift of vaginal microbiota induced by vaginal application of sucrose gel in rhesus macaques.

Hu KT, Zheng JX, Yu ZJ, Chen Z, Cheng H, Pan WG, Yang WZ, Wang HY, Deng QW, Zeng ZM

Int J Infect Dis. Apr 2015. doi: 10.1016/j.ijid.2014.12.040S1201-9712(14)01758-5

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High-throughput Methods Redefine the Rumen Microbiome and Its Relationship with Nutrition and Metabolism.

McCann JC, Wickersham TA, Loor JJ

Bioinform Biol Insights. 2014. doi: 10.4137/BBI.S15389

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Salivary glands harbor more diverse microbial communities than gut in Anopheles culicifacies.

Sharma P, Sharma S, Maurya RK, Das De T, Thomas T, Lata S, Singh N, Pandey KC, Valecha N, Dixit R

Parasit Vectors. 2014. doi: 10.1186/1756-3305-7-235

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Metagenomic analysis of the medicinal leech gut microbiota.

Maltz MA, Bomar L, Lapierre P, Morrison HG, McClure EA, Sogin ML, Graf J

Front Microbiol. 2014. doi: 10.3389/fmicb.2014.00151

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Simultaneous assessment of the macrobiome and microbiome in a bulk sample of tropical arthropods through DNA metasystematics.

Gibson J, Shokralla S, Porter TM, King I, van Konynenburg S, Janzen DH, Hallwachs W, Hajibabaei M

Proc Natl Acad Sci U S A. Jun 2014. doi: 10.1073/pnas.1406468111

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Extensive microbial and functional diversity within the chicken cecal microbiome.

Sergeant MJ, Constantinidou C, Cogan TA, Bedford MR, Penn CW, Pallen MJ

PLoS One. 2014. doi: 10.1371/journal.pone.0091941

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Microbial biodiversity of the liquid fraction of rumen content from lactating cows.

Sandri M, Manfrin C, Pallavicini A, Stefanon B

Animal. Apr 2014. doi: 10.1017/S1751731114000056

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Arsenic exposure perturbs the gut microbiome and its metabolic profile in mice: an integrated metagenomics and metabolomics analysis.

Lu K, Abo RP, Schlieper KA, Graffam ME, Levine S, Wishnok JS, Swenberg JA, Tannenbaum SR, Fox JG

Environ Health Perspect. Mar 2014. doi: 10.1289/ehp.1307429

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