Works in Microbiome, 2016, Vol 4

Results: 72

The gut microbiota in conventional and serrated precursors of colorectal cancer.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0218-6

By:

Peters, Brandilyn A.;
Dominianni, Christine;
Shapiro, Jean A.;
Church, Timothy R.;
Jing Wu;
Miller, George;
Yuen, Elizabeth;
Freiman, Hal;
Lustbader, Ian;
Salik, James;
Friedlander, Charles;
Hayes, Richard B.;
Jiyoung Ahn

Publication type:

Article

The developing hypopharyngeal microbiota in early life.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0215-9

By:

Mortensen, Martin Steen;
Brejnrod, Asker Daniel;
Roggenbuck, Michael;
Al-Soud, Waleed Abu;
Balle, Christina;
Krogfelt, Karen Angeliki;
Stokholm, Jakob;
Thorsen, Jonathan;
Waage, Johannes;
Rasmussen, Morten Arendt;
Bisgaard, Hans;
Sørensen, Søren Johannes

Publication type:

Article

Influence of maternal breast milk ingestion on acquisition of the intestinal microbiome in preterm infants.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0214-x

By:

Gregory, Katherine E.;
Samuel, Buck S.;
Houghteling, Pearl;
Shan, Guru;
Ausubel, Frederick M.;
Sadreyev, Ruslan I.;
Walker, W. Allan

Publication type:

Article

Temporal bacterial and metabolic development of the preterm gut reveals specific signatures in health and disease.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0216-8

By:

Stewart, Christopher J.;
Embleton, Nicholas D.;
Marrs, Emma C. L.;
Smith, Daniel P.;
Nelson, Andrew;
Abdulkadir, Bashir;
Skeath, Tom;
Petrosino, Joseph F.;
Perry, John D.;
Berrington, Janet E.;
Cummings, Stephen P.

Publication type:

Article

Disruption of the microbiota across multiple body sites in critically ill children.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0211-0

By:

Rogers, Matthew B.;
Firek, Brian;
Min Shi;
Yeh, Andrew;
Brower-Sinning, Rachel;
Aveson, Victoria;
Kohl, Brittany L.;
Fabio, Anthony;
Carcillo, Joseph A.;
Morowitz, Michael J.

Publication type:

Article

Resilient microorganisms in dust samples of the International Space Station--survival of the adaptation specialists.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0217-7

By:

Mora, Maximilian;
Perras, Alexandra;
Alekhova, Tatiana A.;
Wink, Lisa;
Krause, Robert;
Aleksandrova, Alina;
Novozhilova, Tatiana;
Moissl-Eichinger, Christine

Publication type:

Article

Transmission of viruses via our microbiomes.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0212-z

By:

Ly, Melissa;
Jones, Marcus B.;
Abeles, Shira R.;
Santiago-Rodriguez, Tasha M.;
Gao, Jonathan;
Chan, Ivan C.;
Ghose, Chandrabali;
Pride, David T.

Publication type:

Article

Staphylococcal species heterogeneity in the nasal microbiome following antibiotic prophylaxis revealed by tuf gene deep sequencing.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0210-1

By:

McMurray, Claire L.;
Hardy, Katherine J.;
Calus, Szymon T.;
Loman, Nicholas J.;
Hawkey, Peter M.

Publication type:

Article

Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0208-8

By:

Thorsen, Jonathan;
Brejnrod, Asker;
Mortensen, Martin;
Rasmussen, Morten A.;
Stokholm, Jakob;
Al-Soud, Waleed Abu;
Sørensen, Søren;
Bisgaard, Hans;
Waage, Johannes

Publication type:

Article

Extending colonic mucosal microbiome analysis—assessment of colonic lavage as a proxy for endoscopic colonic biopsies.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0207-9

By:

Watt, Euan;
Gemmell, Matthew R.;
Berry, Susan;
Glaire, Mark;
Farquharson, Freda;
Louis, Petra;
Murray, Graeme I.;
El-Omar, Emad;
Hold, Georgina L.

Publication type:

Article

The lung microbiota in early rheumatoid arthritis and autoimmunity.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0206-x

By:

Scher, Jose U.;
Joshua, Vijay;
Artacho, Alejandro;
Abdollahi-Roodsaz, Shahla;
Öckinger, Johan;
Kullberg, Susanna;
Sköld, Magnus;
Eklund, Anders;
Grunewald, Johan;
Clemente, Jose C.;
Ubeda, Carles;
Segal, Leopoldo N.;
Catrina, Anca I.

Publication type:

Article

DNA from fecal immunochemical test can replace stool for detection of colonic lesions using a microbiota-based model.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0205-y

By:

Baxter, Nielson T.;
Koumpouras, Charles C.;
Rogersv, Mary A. M.;
Ruffin IV, Mack T.;
Schloss, Patrick D.

Publication type:

Article

The vaginal microbiota, human papillomavirus infection and cervical intraepithelial neoplasia: what do we know and where are we going next?

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0203-0

By:

Mitra, Anita;
MacIntyre, David A.;
Marchesi, Julian R.;
Lee, Yun S.;
Bennett, Phillip R.;
Kyrgiou, Maria

Publication type:

Article

Unusual sub-genus associations of faecal Prevotella and Bacteroides with specific dietary patterns.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0202-1

By:

De Filippis, Francesca;
Pellegrini, Nicoletta;
Laghi, Luca;
Gobbetti, Marco;
Ercolini, Danilo

Publication type:

Article

Rumen metagenome and metatranscriptome analyses of low methane yield sheep reveals a Sharpeaenriched microbiome characterised by lactic acid formation and utilisation.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0201-2

By:

Kamke, Janine;
Kittelmann, Sandra;
Soni, Priya;
Yang Li;
Tavendale, Michael;
Ganesh, Siva;
Janssen, Peter H.;
Weibing Shi;
Froula, Jeff;
Rubin, Edward M.;
Attwood, Graeme T.

Publication type:

Article

Fat and vitamin intakes during pregnancy have stronger relations with a proinflammatory maternal microbiota than does carbohydrate intake.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0200-3

By:

Mandal, Siddhartha;
Godfrey, Keith M.;
McDonald, Daniel;
Treuren, Will V.;
Bjørnholt, Jørgen V.;
Midtvedt, Tore;
Moen, Birgitte;
Rudi, Knut;
Knight, Rob;
Brantsæter, Anne Lise;
Peddada, Shyamal D.;
Eggesbø, Merete

Publication type:

Article

The structure and diversity of human, animal and environmental resistomes.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0199-5

By:

Pal, Chandan;
Bengtsson-Palme, Johan;
Kristiansson, Erik;
Larsson, D. G. Joakim

Publication type:

Article

Rapid change of fecal microbiome and disappearance of Clostridium difficile in a colonized infant after transition from breast milk to cow milk.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0198-6

By:

Davis, Manli Y.;
Husen Zhang;
Brannan, Lera E.;
Carman, Robert J.;
Boone, James H.

Publication type:

Article

Picodroplet partitioned whole genome amplification of low biomass samples preserves genomic diversity for metagenomic analysis.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0197-7

By:

Hammond, Maria;
Homa, Felix;
Andersson-Svahn, Helene;
Ettema, Thijs J. G.;
Joensson, Haakan N.

Publication type:

Article

The impact of sequence database choice on metaproteomic results in gut microbiota studies.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0196-8

By:

Tanca, Alessandro;
Palomba, Antonio;
Fraumene, Cristina;
Pagnozzi, Daniela;
Manghina, Valeria;
Deligios, Massimo;
Muth, Thilo;
Rapp, Erdmann;
Martens, Lennart;
Addis, Maria Filippa;
Uzzau, Sergio

Publication type:

Article

Intestinal microbiota in pediatric patients with end stage renal disease: a Midwest Pediatric Nephrology Consortium study.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0195-9

By:

Crespo-Salgado, Janice;
Vehaskari, V. Matti;
Stewart, Tyrus;
Ferris, Michael;
Qiang Zhang;
Guangdi Wang;
Blanchard, Eugene E.;
Taylor, Christopher M.;
Kallash, Mahmoud;
Greenbaum, Larry A.;
Aviles, Diego H.

Publication type:

Article

Post-translational modifications are enriched within protein functional groups important to bacterial adaptation within a deep-sea hydrothermal vent environment.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0194-x

By:

Weipeng Zhang;
Jin Sun;
Huiluo Cao;
Renmao Tian;
Lin Cai;
Wei Ding;
Pei-Yuan Qian

Publication type:

Article

Mungo bean sprout microbiome and changes associated with culture based enrichment protocols used in detection of Gram-negative foodborne pathogens.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0193-y

By:

Margot, Heike;
Stephan, Roger;
Tasara, Taurai

Publication type:

Article

Comparison of faecal microbiota in Blastocystis-positive and Blastocystis-negative irritable bowel syndrome patients.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0191-0

By:

Nagel, Robyn;
Traub, Rebecca J.;
Allcock, Richard J. N.;
Kwan, Marcella M. S.;
Bielefeldt-Ohmann, Helle

Publication type:

Article

Skin fungal community and its correlation with bacterial community of urban Chinese individuals.

Published in:

Microbiome, 2016, v. 4, p. 2, doi. 10.1186/s40168-016-0192-z

By:

Leung, Marcus H. Y.;
Chan, Kelvin C. K.;
Lee, Patrick K. H.

Publication type:

Article

Erratum to: The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium Inaugural Meeting Report.

Published in:: Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0184-z
Publication type:: Article

Environment shapes the fecal microbiome of invasive carp species.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0190-1

By:

Eichmiller, Jessica J.;
Hamilton, Matthew J.;
Staley, Christopher;
Sadowsky, Michael J.;
Sorensen, Peter W.

Publication type:

Article

Reviewer acknowledgement 2015.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0188-8

By:

Ravel, Jacques;
Wommack, Eric

Publication type:

Article

Cardiorespiratory fitness as a predictor of intestinal microbial diversity and distinct metagenomic functions.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0189-7

By:

Estaki, Mehrbod;
Pither, Jason;
Baumeister, Peter;
Little, Jonathan P.;
Gill, Sandeep K.;
Ghosh, Sanjoy;
Ahmadi-Vand, Zahra;
Marsden, Katelyn R.;
Gibson, Deanna L.

Publication type:

Article

Microbial diversity in individuals and their household contacts following typical antibiotic courses.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0187-9

By:

Abeles, Shira R.;
Jones, Marcus B.;
Santiago-Rodriguez, Tasha M.;
Ly, Melissa;
Klitgord, Niels;
Yooseph, Shibu;
Nelson, Karen E.;
Pride, David T.

Publication type:

Article

Latitude in sample handling and storage for infant faecal microbiota studies: the elephant in the room?

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0186-x

By:

Shaw, Alexander G.;
Sim, Kathleen;
Powell, Elizabeth;
Cornwell, Emma;
Cramer, Teresa;
McClure, Zoë E.;
Li, Ming-Shi;
Kroll, J. Simon

Publication type:

Article

Altered gut microbiota in Rett syndrome.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0185-y

By:

Strati, Francesco;
Cavalieri, Duccio;
Albanese, Davide;
De Felice, Claudio;
Donati, Claudio;
Hayek, Joussef;
Jousson, Olivier;
Leoncini, Silvia;
Pindo, Massimo;
Renzi, Daniela;
Rizzetto, Lisa;
Stefanini, Irene;
Calabrò, Antonio;
De Filippo, Carlotta

Publication type:

Article

A comprehensive method for ampliconbased and metagenomic characterization of viruses, bacteria, and eukaryotes in freshwater samples.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0166-1

By:

Uyaguari-Diaz, Miguel I.;
Chan, Michael;
Chaban, Bonnie L.;
Croxen, Matthew A.;
Finke, Jan F.;
Hill, Janet E.;
Peabody, Michael A.;
Van Rossum, Thea;
Suttle, Curtis A.;
Brinkman, Fiona S. L.;
Isaac-Renton, Judith;
Prystajecky, Natalie A.;
Tang, Patrick

Publication type:

Article

Longitudinal analysis of the lung microbiota of cynomolgous macaques during long-term SHIV infection.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0183-0

By:

Morris, Alison;
Paulson, Joseph N.;
Talukder, Hisham;
Tipton, Laura;
Kling, Heather;
Lijia Cui;
Fitch, Adam;
Pop, Mihai;
Norris, Karen A.;
Ghedin, Elodie

Publication type:

Article

The microbiota in bronchoalveolar lavage from young children with chronic lung disease includes taxa present in both the oropharynx and nasopharynx.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0182-1

By:

Marsh, R. L.;
Kaestli, M.;
Chang, A. B.;
Binks, M. J.;
Pope, C. E.;
Hoffman, L. R.;
Smith-Vaughan, H. C.

Publication type:

Article

Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0181-2

By:

Ormerod, Kate L.;
Wood, David L. A.;
Lachner, Nancy;
Gellatly, Shaan L.;
Daly, Joshua N.;
Parsons, Jeremy D.;
Dal'Molin, Cristiana G. O.;
Palfreyman, Robin W.;
Nielsen, Lars K.;
Cooper, Matthew A.;
Morrison, Mark;
Hansbro, Philip M.;
Hugenholtz, Philip

Publication type:

Article

Erratum to: Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires.

Published in:: Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0180-3
Publication type:: Article

Nasopharyngeal microbiota composition of children is related to the frequency of upper respiratory infection and acute sinusitis.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0179-9

By:

Santee, Clark A.;
Nagalingam, Nabeetha A.;
Faruqi, Ali A.;
DeMuri, Gregory P.;
Gern, James E.;
Wald, Ellen R.;
Lynch, Susan V.

Publication type:

Article

Variable responses of human microbiomes to dietary supplementation with resistant starch.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0178-x

By:

Venkataraman, A.;
Sieber, J. R.;
Schmidt, A. W.;
Waldron, C.;
Theis, K. R.;
Schmidt, T. M.

Publication type:

Article

Research on the human virome: where are we and what is next.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0177-y

By:

Shimian Zou;
Caler, Lis;
Colombini-Hatch, Sandra;
Glynn, Simone;
Srinivas, Pothur

Publication type:

Article

MetaPro-IQ: a universal metaproteomic approach to studying human and mouse gut microbiota.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0176-z

By:

Xu Zhang;
Zhibin Ning;
Mayne, Janice;
Moore, Jasmine I.;
Li, Jennifer;
Butcher, James;
Deeke, Shelley Ann;
Rui Chen;
Cheng-Kang Chiang;
Ming Wen;
Mack, David;
Stintzi, Alain;
Figeys, Daniel

Publication type:

Article

Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0172-3

By:

Laude, Abigail P.;
Roche, Aoife M.;
Sherrill-Mix, Scott;
Bailey, Aubrey;
Laughlin, Alice L.;
Bittinger, Kyle;
Leite, Rita;
Elovitz, Michal A.;
Parry, Samuel;
Bushman, Frederic D.

Publication type:

Article

Reduced diversity and altered composition of the gut microbiome in individuals with myalgic encephalomyelitis/chronic fatigue syndrome.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0171-4

By:

Giloteaux, Ludovic;
Goodrich, Julia K.;
Walters, William A.;
Levine, Susan M.;
Ley, Ruth E.;
Hanson, Maureen R.

Publication type:

Article

αT-catenin in restricted brain cell types and its potential connection to autism.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40303-016-0017-9

By:

Sai Folmsbee, Stephen;
Wilcox, Douglas R.;
Tyberghein, Koen;
De Bleser, Pieter;
Tourtellotte, Warren G.;
van Hengel, Jolanda;
van Roy, Frans;
Gottardi, Cara J.

Publication type:

Article

Host species identity, site and time drive temperate tree phyllosphere bacterial community structure.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0174-1

By:

Laforest-Lapointe, Isabelle;
Messier, Christian;
Kembel, Steven W.

Publication type:

Article

Two sampling methods yield distinct microbial signatures in the nasopharynges of asthmatic children.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0170-5

By:

Pérez-Losada, Marcos;
Crandall, Keith A.;
Freishtat, Robert J.

Publication type:

Article

Effect of postnatal low-dose exposure to environmental chemicals on the gut microbiome in a rodent model.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0173-2

By:

Jianzhong Hu;
Raikhel, Vincent;
Gopalakrishnan, Kalpana;
Fernandez-Hernandez, Heriberto;
Lambertini, Luca;
Manservisi, Fabiana;
Falcioni, Laura;
Bua, Luciano;
Belpoggi, Fiorella;
Teitelbaum, Susan L.;
Jia Chen

Publication type:

Article

Diet may influence the oral microbiome composition in cats.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0169-y

By:

Adler, Christina J.;
Malik, Richard;
Browne, Gina V.;
Norris, Jacqueline M.

Publication type:

Article

The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report.

Published in:: Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0168-z
Publication type:: Article

Microbial succession in an inflated lunar/Mars analog habitat during a 30-day human occupation.

Published in:

Microbiome, 2016, v. 4, p. 1, doi. 10.1186/s40168-016-0167-0

By:

Mayer, Teresa;
Blachowicz, Adriana;
Probst, Alexander J.;
Vaishampayan, Parag;
Checinska, Aleksandra;
Swarmer, Tiffany;
de Leon, Pablo;
Venkateswaran, Kasthuri

Publication type:

Article