title: Analysis of gut microbiota - An ever changing landscape.
abstract: In the last two decades, the field of metagenomics has greatly expanded due to improvement in sequencing technologies allowing for a more comprehensive characterization of microbial communities. The use of these technologies has led to an unprecedented understanding of human, animal, and environmental microbiomes and have shown that the gut microbiota are comparable to an organ that is intrinsically linked with a variety of diseases. Characterization of microbial communities using next-generation sequencing-by-synthesis approaches have revealed important shifts in microbiota associated with debilitating diseases such as Clostridium difficile infection. But due to limitations in sequence read length, primer biases, and the quality of databases, genus- and species-level classification have been difficult. Third-generation technologies, such as Pacific Biosciences' single molecule, real-time (SMRT) approach, allow for unbiased, more specific identification of species that are likely clinically relevant. Comparison of Illumina next-generation characterization and SMRT sequencing of samples from patients treated for C. difficile infection revealed similarities in community composition at the phylum and family levels, but SMRT sequencing further allowed for species-level characterization - permitting a better understanding of the microbial ecology of this disease. Thus, as sequencing technologies continue to advance, new species-level insights can be gained in the study of complex and clinically-relevant microbial communities.
authors.affiliation: a BioTechnology Institute , University of Minnesota , St. Paul , Minnesota , USA.|b Department of Soil, Water & Climate , University of Minnesota , St. Paul , Minnesota , USA.
authors.forename: Michael J
authors.identifier: 0000-0001-8779-2781
authors.initials: MJ
authors.lastname: Sadowsky
authors.affiliation: a BioTechnology Institute , University of Minnesota , St. Paul , Minnesota , USA.
authors.forename: Christopher
authors.initials: C
authors.lastname: Staley
authors.affiliation: c Pacific Biosciences , Menlo Park , CA USA.
authors.forename: Cheryl
authors.initials: C
authors.lastname: Heiner
authors.affiliation: c Pacific Biosciences , Menlo Park , CA USA.
authors.forename: Richard
authors.initials: R
authors.lastname: Hall
authors.affiliation: d Department of Medicine , The Warren Alpert Medical School of Brown University , Providence , Rhode Island , USA.|e Women's Medicine Collaborative, The Miriam Hospital , Providence , Rhode Island , USA.
authors.forename: Colleen R
authors.initials: CR
authors.lastname: Kelly
authors.affiliation: f Department of Medicine, Division of Gastroenterology, Albert Einstein College of Medicine , Montefiore Medical Center , Bronx , NY ; USA.
authors.forename: Lawrence
authors.initials: L
authors.lastname: Brandt
authors.affiliation: g Department of Medicine, Division of Gastroenterology , University of Minnesota , Minneapolis , Minnesota , USA.|h Center for Immunology , University of Minnesota , Minneapolis , Minnesota , USA.
authors.forename: Alexander
authors.initials: A
authors.lastname: Khoruts
mesh_terms: D000818:Animals; D003015:Clostridium Infections / Q000628:therapy; D005243:Feces / Q000382:microbiology*; D000069196:Gastrointestinal Microbiome; D041981:Gastrointestinal Tract / Q000382:microbiology*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D056186:Metagenomics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D012336:RNA, Ribosomal, 16S
keywords: Clostridium difficile; PacBio; SMRT sequencing; fecal microbial transplant; gut microbiota; next-generation sequencing