Metagenome

Publication Title: 
PloS One

The aging phenotype in humans has been thoroughly studied but a detailed metabolic profiling capable of shading light on the underpinning biological processes of longevity is still missing. Here using a combined metabonomics approach compromising holistic (1)H-NMR profiling and targeted MS approaches, we report for the first time the metabolic phenotype of longevity in a well characterized human aging cohort compromising mostly female centenarians, elderly, and young individuals.

Author(s): 
Collino, Sebastiano
Montoliu, Ivan
Martin, FranÁois-Pierre J.
Scherer, Max
Mari, Daniela
Salvioli, Stefano
Bucci, Laura
Ostan, Rita
Monti, Daniela
Biagi, Elena
Brigidi, Patrizia
Franceschi, Claudio
Rezzi, Serge
Publication Title: 
PloS One

The aging phenotype in humans has been thoroughly studied but a detailed metabolic profiling capable of shading light on the underpinning biological processes of longevity is still missing. Here using a combined metabonomics approach compromising holistic (1)H-NMR profiling and targeted MS approaches, we report for the first time the metabolic phenotype of longevity in a well characterized human aging cohort compromising mostly female centenarians, elderly, and young individuals.

Author(s): 
Collino, Sebastiano
Montoliu, Ivan
Martin, FranÁois-Pierre J.
Scherer, Max
Mari, Daniela
Salvioli, Stefano
Bucci, Laura
Ostan, Rita
Monti, Daniela
Biagi, Elena
Brigidi, Patrizia
Franceschi, Claudio
Rezzi, Serge
Publication Title: 
Gastroenterology

Little was known about the development of the gastrointestinal (GI) tract microbiota, until recently, because of difficulties in obtaining sufficient sequence information from enough people or time points. Now, with decreased costs of DNA sequencing and improved bioinformatic tools, we can compare GI tract bacterial communities among individuals, of all ages from infancy to adulthood.

Author(s): 
Dominguez-Bello, Maria Gloria
Blaser, Martin J.
Ley, Ruth E.
Knight, Rob
Publication Title: 
Nutrition Journal

Historically, in the 1950s, the chemist Linus Pauling established a relationship between decreased longevity and obesity. At this time, with the advent of studies involving the mechanisms that modulate appetite control, some researchers observed that the hypothalamus is the "appetite centre" and that peripheral tissues have important roles in the modulation of gut inflammatory processes and levels of hormones that control food intake.

Author(s): 
Pimentel, Gustavo D.
Micheletti, Thayana O.
Pace, Fernanda
Rosa, JosÈ C.
Santos, Ronaldo V. T.
Lira, Fabio S.
Publication Title: 
Cell

The biguanide drug metformin is widely prescribed to treat type 2 diabetes and metabolic syndrome, but its mode of action remains uncertain. Metformin also increases lifespan in Caenorhabditis elegans cocultured with Escherichia coli. This bacterium exerts complex nutritional and pathogenic effects on its nematode predator/host that impact health and aging. We report that metformin increases lifespan by altering microbial folate and methionine metabolism.

Author(s): 
Cabreiro, Filipe
Au, Catherine
Leung, Kit-Yi
Vergara-Irigaray, Nuria
CochemÈ, Helena M.
Noori, Tahereh
Weinkove, David
Schuster, Eugene
Greene, Nicholas D. E.
Gems, David
Publication Title: 
Journal of Neurovirology

Research on the microbiome and its interaction with various host organs, including the brain, is increasingly gaining momentum. With more evidence establishing a comprehensive microbiota-gut-brain axis, questions have been raised as to the extent to which microbes influence brain physiology and behaviour. In parallel, there is a growing literature showing active behavioural manipulation in favour of the microbe for certain parasites. However, it seems unclear where the hidden majority of microbes are localised on the parasitism-mutualism spectrum.

Author(s): 
Stilling, Roman M.
Dinan, Timothy G.
Cryan, John F.
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: 
Gastroenterology

Studies of metagenomics and the human microbiome will tremendously expand our knowledge of the composition of microbial communities in the human body. As our understanding of microbial variation and corresponding genetic parameters is refined, this information can be applied to rational remodeling or "tailoring" of human-associated microbial communities and their associated functions.

Author(s): 
Preidis, Geoffrey A.
Versalovic, James
Publication Title: 
Gut Microbes

The intestinal microbiota includes a diverse group of functional microorganisms, including candidate probiotics or viable microorganisms that benefit the host. Beneficial effects of probiotics include enhancing intestinal epithelial cell function, protecting against physiologic stress, modulating cytokine secretion profiles, influencing T lymphocyte populations, and enhancing antibody secretion. Probiotics have demonstrated significant potential as therapeutic options for a variety of diseases, but the mechanisms responsible for these effects remain to be fully elucidated.

Author(s): 
Thomas, Carissa M.
Versalovic, James
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.

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