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  1. Bacterial biocatalysts play a key role in our transition to a bio-based, post-petroleum economy. However, the discovery of new biocatalysts is currently limited by our ability to analyze genomic information an...

    Authors: Premankur Sukul, Sina Schäkermann, Julia E. Bandow, Anna Kusnezowa, Minou Nowrousian and Lars I. Leichert
    Citation: Microbiome 2017 5:28
  2. Data from 16S ribosomal RNA (rRNA) amplicon sequencing present challenges to ecological and statistical interpretation. In particular, library sizes often vary over several ranges of magnitude, and the data co...

    Authors: Sophie Weiss, Zhenjiang Zech Xu, Shyamal Peddada, Amnon Amir, Kyle Bittinger, Antonio Gonzalez, Catherine Lozupone, Jesse R. Zaneveld, Yoshiki Vázquez-Baeza, Amanda Birmingham, Embriette R. Hyde and Rob Knight
    Citation: Microbiome 2017 5:27
  3. Children with high body mass index (BMI) at preschool age are at risk of developing obesity. Early identification of factors that increase the risk of excessive weight gain could help direct preventive actions...

    Authors: K. Korpela, M. A. C. Zijlmans, M. Kuitunen, K. Kukkonen, E. Savilahti, A. Salonen, C. de Weerth and W. M. de Vos
    Citation: Microbiome 2017 5:26
  4. The plant microbiome represents one of the key determinants of plant health and productivity by providing a plethora of functional capacities such as access to low-abundance nutrients, suppression of phytopath...

    Authors: Bram Beckers, Michiel Op De Beeck, Nele Weyens, Wout Boerjan and Jaco Vangronsveld
    Citation: Microbiome 2017 5:25
  5. Autism spectrum disorders (ASDs) are neurodevelopmental conditions characterized by social and behavioural impairments. In addition to neurological symptoms, ASD subjects frequently suffer from gastrointestina...

    Authors: Francesco Strati, Duccio Cavalieri, Davide Albanese, Claudio De Felice, Claudio Donati, Joussef Hayek, Olivier Jousson, Silvia Leoncini, Daniela Renzi, Antonio Calabrò and Carlotta De Filippo
    Citation: Microbiome 2017 5:24
  6. There is a paucity of data regarding the microbial constituents of tobacco products and their impacts on public health. Moreover, there has been no comparative characterization performed on the bacterial micro...

    Authors: Jessica Chopyk, Suhana Chattopadhyay, Prachi Kulkarni, Emma Claye, Kelsey R. Babik, Molly C. Reid, Eoghan M. Smyth, Lauren E. Hittle, Joseph N. Paulson, Raul Cruz-Cano, Mihai Pop, Stephanie S. Buehler, Pamela I. Clark, Amy R. Sapkota and Emmanuel F. Mongodin
    Citation: Microbiome 2017 5:22
  7. Authors: Cian J. Hill, Denise B. Lynch, Kiera Murphy, Marynka Ulaszewska, Ian B. Jeffery, Carol Anne O’Shea, Claire Watkins, Eugene Dempsey, Fulvio Mattivi, Kieran Tuohy, R. Paul Ross, C. Anthony Ryan, Paul W. O’Toole and Catherine Stanton
    Citation: Microbiome 2017 5:21

    The original article was published in Microbiome 2017 5:4

  8. Cystic fibrosis (CF) is a life-threatening genetic disorder, characterized by chronic microbial lung infections due to abnormally viscous mucus secretions within airways. The clinical management of CF typicall...

    Authors: Rounak Feigelman, Christian R. Kahlert, Florent Baty, Frank Rassouli, Rebekka L. Kleiner, Philipp Kohler, Martin H. Brutsche and Christian von Mering
    Citation: Microbiome 2017 5:20
  9. Community-level analysis of the human microbiota has culminated in the discovery of relationships between overall shifts in the microbiota and a wide range of diseases and conditions. However, existing work ha...

    Authors: Anna Plantinga, Xiang Zhan, Ni Zhao, Jun Chen, Robert R. Jenq and Michael C. Wu
    Citation: Microbiome 2017 5:17
  10. Obesity-related diseases, including type 2 diabetes and cardiovascular disease, have reached epidemic proportions in industrialized nations, and dietary interventions for their prevention are therefore importa...

    Authors: Laure B. Bindels, Rafael R. Segura Munoz, João Carlos Gomes-Neto, Valentin Mutemberezi, Inés Martínez, Nuria Salazar, Elizabeth A. Cody, Maria I. Quintero-Villegas, Hatem Kittana, Clara G de los Reyes-Gavilán, Robert J. Schmaltz, Giulio G. Muccioli, Jens Walter and Amanda E. Ramer-Tait
    Citation: Microbiome 2017 5:12
  11. The degree to which host genetic variation can modulate microbial communities in humans remains an open question. Here, we performed a genetic mapping study of the microbiome in two accessible upper airway sit...

    Authors: Catherine Igartua, Emily R. Davenport, Yoav Gilad, Dan L. Nicolae, Jayant Pinto and Carole Ober
    Citation: Microbiome 2017 5:16
  12. Gut microbes play a critical role in human health and disease, and researchers have begun to characterize their genomes, the so-called gut metagenome. Thus far, metagenomics studies have focused on genus- or s...

    Authors: Yaowen Chen, Zongcheng Li, Shuofeng Hu, Jian Zhang, Jiaqi Wu, Ningsheng Shao, Xiaochen Bo, Ming Ni and Xiaomin Ying
    Citation: Microbiome 2017 5:15
  13. Recently, the potential role of gut microbiome in metabolic diseases has been revealed, especially in cardiovascular diseases. Hypertension is one of the most prevalent cardiovascular diseases worldwide, yet w...

    Authors: Jing Li, Fangqing Zhao, Yidan Wang, Junru Chen, Jie Tao, Gang Tian, Shouling Wu, Wenbin Liu, Qinghua Cui, Bin Geng, Weili Zhang, Ryan Weldon, Kelda Auguste, Lei Yang, Xiaoyan Liu, Li Chen…
    Citation: Microbiome 2017 5:14
  14. Symbiotic bacteria affect insect physiology and ecology. They may also mediate insecticide resistance within their hosts and thereby impact pest and vector control practices. Here, we document a novel mechanis...

    Authors: Daifeng Cheng, Zijun Guo, Markus Riegler, Zhiyong Xi, Guangwen Liang and Yijuan Xu
    Citation: Microbiome 2017 5:13
  15. Microbiome sequencing projects typically collect tens of millions of short reads per sample. Depending on the goals of the project, the short reads can either be subjected to direct sequence analysis or be ass...

    Authors: Daniel H. Huson, Rewati Tappu, Adam L Bazinet, Chao Xie, Michael P. Cummings, Kay Nieselt and Rohan Williams
    Citation: Microbiome 2017 5:11
  16. A variety of bacteria are known to influence carcinogenesis. Therefore, we sought to investigate if publicly available whole genome and whole transcriptome sequencing data generated by large public cancer geno...

    Authors: Kelly M. Robinson, Jonathan Crabtree, John S. A. Mattick, Kathleen E. Anderson and Julie C. Dunning Hotopp
    Citation: Microbiome 2017 5:9
  17. Autism spectrum disorders (ASD) are complex neurobiological disorders that impair social interactions and communication and lead to restricted, repetitive, and stereotyped patterns of behavior, interests, and ...

    Authors: Dae-Wook Kang, James B. Adams, Ann C. Gregory, Thomas Borody, Lauren Chittick, Alessio Fasano, Alexander Khoruts, Elizabeth Geis, Juan Maldonado, Sharon McDonough-Means, Elena L. Pollard, Simon Roux, Michael J. Sadowsky, Karen Schwarzberg Lipson, Matthew B. Sullivan, J. Gregory Caporaso…
    Citation: Microbiome 2017 5:10
  18. The vaginal microbiome is an important site of bacterial-mammalian symbiosis. This symbiosis is currently best characterized for humans, where lactobacilli dominate the microbial community and may help defend ...

    Authors: Elizabeth A. Miller, Joshua A. Livermore, Susan C. Alberts, Jenny Tung and Elizabeth A. Archie
    Citation: Microbiome 2017 5:8
  19. Metagenomics is a rapidly emerging field aimed to analyze microbial diversity and dynamics by studying the genomic content of the microbiota. Metataxonomics tools analyze high-throughput sequencing data, prima...

    Authors: Jeremy W. Cox, Richard A. Ballweg, Diana H. Taft, Prakash Velayutham, David B. Haslam and Aleksey Porollo
    Citation: Microbiome 2017 5:7
  20. Preterm birth is the primary cause of infant death worldwide. A short cervix in the second trimester of pregnancy is a risk factor for preterm birth. In specific patient cohorts, vaginal progesterone reduces t...

    Authors: Lindsay M. Kindinger, Phillip R. Bennett, Yun S Lee, Julian R. Marchesi, Ann Smith, Stefano Cacciatore, Elaine Holmes, Jeremy K. Nicholson, T. G. Teoh and David A. MacIntyre
    Citation: Microbiome 2017 5:6
  21. Ancient microbiota information represents an important resource to evaluate bacterial evolution and to explore the biological spread of infectious diseases in history. The soft tissue of frozen mummified human...

    Authors: Gabriele Andrea Lugli, Christian Milani, Leonardo Mancabelli, Francesca Turroni, Chiara Ferrario, Sabrina Duranti, Douwe van Sinderen and Marco Ventura
    Citation: Microbiome 2017 5:5

    The Erratum to this article has been published in Microbiome 2017 5:23

  22. The gut is the most extensively studied niche of the human microbiome. The aim of this study was to characterise the initial gut microbiota development of a cohort of breastfed infants (n = 192) from 1 to 24 wee...

    Authors: Cian J. Hill, Denise B. Lynch, Kiera Murphy, Marynka Ulaszewska, Ian B. Jeffery, Carol Anne O’Shea, Claire Watkins, Eugene Dempsey, Fulvio Mattivi, Kieran Tuohy, R. Paul Ross, C. Anthony Ryan, Paul W. O’ Toole and Catherine Stanton
    Citation: Microbiome 2017 5:4

    The Erratum to this article has been published in Microbiome 2017 5:21

  23. The goal of the study was to investigate whether cigarette smoking alters oral and nasal microbial diversity, composition, and structure. Twenty-three current smokers and 20 never smokers were recruited. From ...

    Authors: Guoqin Yu, Stephen Phillips, Mitchell H. Gail, James J. Goedert, Michael S. Humphrys, Jacques Ravel, Yanfang Ren and Neil E. Caporaso
    Citation: Microbiome 2017 5:3
  24. Diverse assemblages of microbes colonize plant roots and collectively function as a microbiome. Earlier work has characterized the root microbiomes of numerous plant species, but little information is availabl...

    Authors: Kyle Hartman, Marcel GA van der Heijden, Valexia Roussely-Provent, Jean-Claude Walser and Klaus Schlaeppi
    Citation: Microbiome 2017 5:2
  25. The airways of healthy humans harbor a distinct microbial community. Perturbations in the microbial community have been associated with disease, yet little is known about the formation and development of a hea...

    Authors: Martin Steen Mortensen, Asker Daniel Brejnrod, Michael Roggenbuck, Waleed Abu Al-Soud, Christina Balle, Karen Angeliki Krogfelt, Jakob Stokholm, Jonathan Thorsen, Johannes Waage, Morten Arendt Rasmussen, Hans Bisgaard and Søren Johannes Sørensen
    Citation: Microbiome 2016 4:70
  26. Colorectal cancer is a heterogeneous disease arising from at least two precursors—the conventional adenoma (CA) and the serrated polyp. We and others have previously shown a relationship between the human gut ...

    Authors: Brandilyn A. Peters, Christine Dominianni, Jean A. Shapiro, Timothy R. Church, Jing Wu, George Miller, Elizabeth Yuen, Hal Freiman, Ian Lustbader, James Salik, Charles Friedlander, Richard B. Hayes and Jiyoung Ahn
    Citation: Microbiome 2016 4:69

    The Erratum to this article has been published in Microbiome 2017 5:29

  27. The initial acquisition and early development of the intestinal microbiome during infancy are important to human health across the lifespan. Mode of birth, antibiotic administration, environment of care, and n...

    Authors: Katherine E. Gregory, Buck S. Samuel, Pearl Houghteling, Guru Shan, Frederick M. Ausubel, Ruslan I. Sadreyev and W. Allan Walker
    Citation: Microbiome 2016 4:68
  28. The preterm microbiome is crucial to gut health and may contribute to necrotising enterocolitis (NEC), which represents the most significant pathology affecting preterm infants. From a cohort of 318 infants, <...

    Authors: Christopher J. Stewart, Nicholas D. Embleton, Emma C. L. Marrs, Daniel P. Smith, Andrew Nelson, Bashir Abdulkadir, Tom Skeath, Joseph F. Petrosino, John D. Perry, Janet E. Berrington and Stephen P. Cummings
    Citation: Microbiome 2016 4:67
  29. Despite intense interest in the links between the microbiome and human health, little has been written about dysbiosis among ICU patients. We characterized microbial diversity in samples from 37 children in a ...

    Authors: Matthew B. Rogers, Brian Firek, Min Shi, Andrew Yeh, Rachel Brower-Sinning, Victoria Aveson, Brittany L. Kohl, Anthony Fabio, Joseph A. Carcillo and Michael J. Morowitz
    Citation: Microbiome 2016 4:66
  30. The International Space Station (ISS) represents a unique biotope for the human crew but also for introduced microorganisms. Microbes experience selective pressures such as microgravity, desiccation, poor nutr...

    Authors: Maximilian Mora, Alexandra Perras, Tatiana A. Alekhova, Lisa Wink, Robert Krause, Alina Aleksandrova, Tatiana Novozhilova and Christine Moissl-Eichinger
    Citation: Microbiome 2016 4:65
  31. Bacteria inhabiting the human body have important roles in a number of physiological processes and are known to be shared amongst genetically-related individuals. Far less is known about viruses inhabiting the...

    Authors: Melissa Ly, Marcus B. Jones, Shira R. Abeles, Tasha M. Santiago-Rodriguez, Jonathan Gao, Ivan C. Chan, Chandrabali Ghose and David T. Pride
    Citation: Microbiome 2016 4:64
  32. Staphylococci are a major constituent of the nasal microbiome and a frequent cause of hospital-acquired infection. Antibiotic surgical prophylaxis is administered prior to surgery to reduce a patient’s risk of...

    Authors: Claire L. McMurray, Katherine J. Hardy, Szymon T. Calus, Nicholas J. Loman and Peter M. Hawkey
    Citation: Microbiome 2016 4:63
  33. There is an immense scientific interest in the human microbiome and its effects on human physiology, health, and disease. A common approach for examining bacterial communities is high-throughput sequencing of ...

    Authors: Jonathan Thorsen, Asker Brejnrod, Martin Mortensen, Morten A. Rasmussen, Jakob Stokholm, Waleed Abu Al-Soud, Søren Sørensen, Hans Bisgaard and Johannes Waage
    Citation: Microbiome 2016 4:62
  34. Sequencing-based analysis has become a well-established approach to deciphering the composition of the gut microbiota. However, due to the complexity of accessing sufficient material from colonoscopic biopsy s...

    Authors: Euan Watt, Matthew R. Gemmell, Susan Berry, Mark Glaire, Freda Farquharson, Petra Louis, Graeme I. Murray, Emad El-Omar and Georgina L. Hold
    Citation: Microbiome 2016 4:61
  35. Airway abnormalities and lung tissue citrullination are found in both rheumatoid arthritis (RA) patients and individuals at-risk for disease development. This suggests the possibility that the lung could be a ...

    Authors: Jose U. Scher, Vijay Joshua, Alejandro Artacho, Shahla Abdollahi-Roodsaz, Johan Öckinger, Susanna Kullberg, Magnus Sköld, Anders Eklund, Johan Grunewald, Jose C. Clemente, Carles Ubeda, Leopoldo N. Segal and Anca I. Catrina
    Citation: Microbiome 2016 4:60
  36. There is a significant demand for colorectal cancer (CRC) screening methods that are noninvasive, inexpensive, and capable of accurately detecting early stage tumors. It has been shown that models based on the...

    Authors: Nielson T. Baxter, Charles C. Koumpouras, Mary A. M. Rogers, Mack T. Ruffin IV and Patrick D. Schloss
    Citation: Microbiome 2016 4:59
  37. The vaginal microbiota plays a significant role in health and disease of the female reproductive tract. Next-generation sequencing techniques based upon the analysis of bacterial 16S rRNA genes permit in-depth...

    Authors: Anita Mitra, David A. MacIntyre, Julian R. Marchesi, Yun S. Lee, Phillip R. Bennett and Maria Kyrgiou
    Citation: Microbiome 2016 4:58
  38. Diet has a recognized effect in shaping gut microbiota. Many studies link an increase in Prevotella to high-fibre diet, while Bacteroides abundance is usually associated with the consumption of animal fat and pro...

    Authors: Francesca De Filippis, Nicoletta Pellegrini, Luca Laghi, Marco Gobbetti and Danilo Ercolini
    Citation: Microbiome 2016 4:57
  39. Enteric fermentation by farmed ruminant animals is a major source of methane and constitutes the second largest anthropogenic contributor to global warming. Reducing methane emissions from ruminants is needed ...

    Authors: Janine Kamke, Sandra Kittelmann, Priya Soni, Yang Li, Michael Tavendale, Siva Ganesh, Peter H. Janssen, Weibing Shi, Jeff Froula, Edward M. Rubin and Graeme T. Attwood
    Citation: Microbiome 2016 4:56
  40. Although diet is known to have a major modulatory influence on gut microbiota, knowledge of the specific roles of particular vitamins, minerals, and other nutrients is limited.

    Authors: Siddhartha Mandal, Keith M. Godfrey, Daniel McDonald, Will V. Treuren, Jørgen V. Bjørnholt, Tore Midtvedt, Birgitte Moen, Knut Rudi, Rob Knight, Anne Lise Brantsæter, Shyamal D. Peddada and Merete Eggesbø
    Citation: Microbiome 2016 4:55
  41. Clostridium difficile is the most common known cause of antibiotic-associated diarrhea. Upon the disturbance of gut microbiota by antibiotics, C. difficile establishes growth and relea...

    Authors: Manli Y. Davis, Husen Zhang, Lera E. Brannan, Robert J. Carman and James H. Boone
    Citation: Microbiome 2016 4:53
  42. Whole genome amplification (WGA) is a challenging, key step in metagenomic studies of samples containing minute amounts of DNA, such as samples from low biomass environments. It is well known that multiple dis...

    Authors: Maria Hammond, Felix Homa, Helene Andersson-Svahn, Thijs J. G. Ettema and Haakan N. Joensson
    Citation: Microbiome 2016 4:52
  43. Elucidating the role of gut microbiota in physiological and pathological processes has recently emerged as a key research aim in life sciences. In this respect, metaproteomics, the study of the whole protein c...

    Authors: Alessandro Tanca, Antonio Palomba, Cristina Fraumene, Daniela Pagnozzi, Valeria Manghina, Massimo Deligios, Thilo Muth, Erdmann Rapp, Lennart Martens, Maria Filippa Addis and Sergio Uzzau
    Citation: Microbiome 2016 4:51
  44. End-stage renal disease (ESRD) is associated with uremia and increased systemic inflammation. Alteration of the intestinal microbiota may facilitate translocation of endotoxins into the systemic circulation le...

    Authors: Janice Crespo-Salgado, V. Matti Vehaskari, Tyrus Stewart, Michael Ferris, Qiang Zhang, Guangdi Wang, Eugene E. Blanchard, Christopher M. Taylor, Mahmoud Kallash, Larry A. Greenbaum and Diego H. Aviles
    Citation: Microbiome 2016 4:50

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