RNA, Ribosomal, 16S

Publication Title: 
Systematic and Applied Microbiology

Five Gram-negative, rod-shaped, non-spore-forming bacteria were isolated from galls on different plant species in Hungary: strain 39/7(T) from Prunus cerasifera Myrobalan, strain 0 from grapevine var. Ezerjó, strain 7/1 from raspberry var. Findus and in Poland, strain C3.4.1 from Colt rootstock (Prunus avium × Prunus pseudocerasus) and strain CP17.2.2 from Prunus avium. Only one of these isolates, strain 0, is able to cause crown gall on different plant species.

Author(s): 
Pu?awska, Joanna
Willems, Anne
De Meyer, Sofie E.
Süle, Sandor
Publication Title: 
Environmental Microbiology

Mycoplasms are known as pathogens of economic and medical interest in plants, animals and man. Here, we show a positive correlation between the presence of Mycoplasma-like symbionts in their isopod hosts and survivorship on low-quality food. Most isopods that survived feeding on a cellulose-based low-quality diet for 90 days harboured 'Candidatus Hepatoplasma' in their midgut glands, while those that died within 90 days mostly either harboured no or other bacterial symbionts.

Author(s): 
Fraune, Sebastian
Zimmer, Martin
Publication Title: 
Journal of Applied Microbiology

AIMS: To purify and characterize an antimicrobial protein (bacteriocin) isolated from the dairy product-derived Bacillus amyloliquefaciens. METHODS AND RESULTS: An unknown bacterial species cultured from the Yogu Farm probiotic dairy beverage was identified through 16S ribosomal RNA analysis as B. amyloliquefaciens, a phylogenetically close relative of Bacillus subtilis. The cell-free supernatant (CFS) of overnight cultures was active against Listeria monocytogenes and also against clinical isolates of Gardnerella vaginalis and Streptococcus agalactiae.

Author(s): 
Sutyak, K. E.
Wirawan, R. E.
Aroutcheva, A. A.
Chikindas, M. L.
Publication Title: 
Clinical Chemistry

BACKGROUND: The Human Microbiome Project has ushered in a new era for human metagenomics and high-throughput next-generation sequencing strategies. CONTENT: This review describes evolving strategies in metagenomics, with a special emphasis on the core technology of DNA pyrosequencing. The challenges of microbial identification in the context of microbial populations are discussed. The development of next-generation pyrosequencing strategies and the technical hurdles confronting these methodologies are addressed.

Author(s): 
Petrosino, Joseph F.
Highlander, Sarah
Luna, Ruth Ann
Gibbs, Richard A.
Versalovic, James
Publication Title: 
The ISME journal

Neonatal necrotizing enterocolitis (NEC) is an inflammatory intestinal disorder affecting preterm infants. Intestinal bacteria have an important function; however no causative pathogen has been identified. The purpose of this study was to determine if there are differences in microbial patterns that may be critical to the development of this disease. Fecal samples from 20 preterm infants, 10 with NEC and 10 matched controls (including 4 twin pairs) were obtained from patients in a single site level III neonatal intensive care unit.

Author(s): 
Wang, Yunwei
Hoenig, Jeanette D.
Malin, Kathryn J.
Qamar, Sanaa
Petrof, Elaine O.
Sun, Jun
Antonopoulos, Dionysios A.
Chang, Eugene B.
Claud, Erika C.
Publication Title: 
PloS One

Many colonic mucosal genes that are highly regulated by microbial signals are differentially expressed along the rostral-caudal axis. This would suggest that differences in regional microbiota exist, particularly mucosa-associated microbes that are less likely to be transient. We therefore explored this possibility by examining the bacterial populations associated with the normal proximal and distal colonic mucosa in context of host Toll-like receptors (TLR) expression in C57BL/6J mice housed in specific pathogen-free (SPF) and germ-free (GF) environments.

Author(s): 
Wang, Yunwei
Devkota, Suzanne
Musch, Mark W.
Jabri, Bana
Nagler, Cathryn
Antonopoulos, Dionysios A.
Chervonsky, Alexander
Chang, Eugene B.
Publication Title: 
FEMS microbiology ecology

Phylogenetic microarrays present an attractive strategy to high-throughput interrogation of complex microbial communities. In this work, we present several approaches to optimize the analysis of intestinal microbiota with the recently developed Microbiota Array. First, we determined how 16S rDNA-specific PCR amplification influenced bacterial detection and the consistency of measured abundance values. Bacterial detection improved with an increase in the number of PCR amplification cycles, but 25 cycles were sufficient to achieve the maximum possible detection.

Author(s): 
Rigsbee, Laura
Agans, Richard
Foy, Brent D.
Paliy, Oleg
Publication Title: 
FASEB journal: official publication of the Federation of American Societies for Experimental Biology

The connection between intestinal microbiota and host physiology is increasingly becoming recognized. The details of this dynamic interaction, however, remain to be explored. Toll-like receptor 2 (Tlr2) is important for its role in bacterial recognition, intestinal inflammation, and obesity-related metabolic changes. Therefore, we sought to determine the epigenomic and metagenomic consequences of Tlr2 deficiency in the colonic mucosa of mice to gain insights into biological pathways that shape the interface between the gut microbiota and the mammalian host.

Author(s): 
Kellermayer, Richard
Dowd, Scot E.
Harris, R. Alan
Balasa, Alfred
Schaible, Tiffany D.
Wolcott, Randy D.
Tatevian, Nina
Szigeti, Reka
Li, Zhijie
Versalovic, James
Smith, C. Wayne
Publication Title: 
Bioinformatics (Oxford, England)

MOTIVATION: Many current studies of complex microbial communities rely on the isolation of community genomic DNA, amplification of 16S ribosomal RNA genes (rDNA) and subsequent examination of community structure through interrogation of the amplified 16S rDNA pool by high-throughput sequencing, phylogenetic microarrays or quantitative PCR. RESULTS: Here we describe the development of a mathematical model aimed to simulate multitemplate amplification of 16S ribosomal DNA sample and subsequent detection of these amplified 16S rDNA species by phylogenetic microarray.

Author(s): 
Paliy, Oleg
Foy, Brent D.
Publication Title: 
Gastroenterology

BACKGROUND & AIMS: The intestinal microbiomes of healthy children and pediatric patients with irritable bowel syndrome (IBS) are not well defined. Studies in adults have indicated that the gastrointestinal microbiota could be involved in IBS. METHODS: We analyzed 71 samples from 22 children with IBS (pediatric Rome III criteria) and 22 healthy children, ages 7-12 years, by 16S ribosomal RNA gene sequencing, with an average of 54,287 reads/stool sample (average 454 read length = 503 bases).

Author(s): 
Saulnier, Delphine M.
Riehle, Kevin
Mistretta, Toni-Ann
Diaz, Maria-Alejandra
Mandal, Debasmita
Raza, Sabeen
Weidler, Erica M.
Qin, Xiang
Coarfa, Cristian
Milosavljevic, Aleksandar
Petrosino, Joseph F.
Highlander, Sarah
Gibbs, Richard
Lynch, Susan V.
Shulman, Robert J.
Versalovic, James

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