%0 Journal Article %J mSphere %D 2020 %T Comparison of Methods To Collect Fecal Samples for Microbiome Studies Using Whole-Genome Shotgun Metagenomic Sequencing. %A Byrd, Doratha A %A Sinha, Rashmi %A Hoffman, Kristi L %A Chen, Jun %A Hua, Xing %A Shi, Jianxin %A Chia, Nicholas %A Petrosino, Joseph %A Vogtmann, Emily %K Adult %K DNA, Bacterial %K Ethanol %K Feces %K Female %K Freezing %K Gastrointestinal Microbiome %K Healthy Volunteers %K Humans %K Male %K Metagenome %K Metagenomics %K Middle Aged %K Preservation, Biological %K RNA, Ribosomal, 16S %K Specimen Handling %K Temperature %K Whole Genome Sequencing %X

Few previous studies have assessed stability and "gold-standard" concordance of fecal sample collection methods for whole-genome shotgun metagenomic sequencing (WGSS), an increasingly popular method for studying the gut microbiome. We used WGSS data to investigate ambient temperature stability and putative gold-standard concordance of microbial profiles in fecal samples collected and stored using fecal occult blood test (FOBT) cards, fecal immunochemical test (FIT) tubes, 95% ethanol, or RNAlater. Among 15 Mayo Clinic employees, for each collection method, we calculated intraclass correlation coefficients (ICCs) to estimate stability of fecal microbial profiles after storage for 4 days at ambient temperature and concordance with immediately frozen, no-solution samples (i.e., the putative gold standard). ICCs were estimated for multiple metrics, including relative abundances of select phyla, species, KEGG k-genes (representing any coding sequence that had >70% identity and >70% query coverage with respect to a known KEGG ortholog), KEGG modules, and KEGG pathways; species and k-gene alpha diversity; and Bray-Curtis and Jaccard species beta diversity. ICCs for microbial profile stability were excellent (≥90%) for fecal samples collected via most of the collection methods, except those preserved in 95% ethanol. Concordance with the immediately frozen, no-solution samples varied for all collection methods, but the number of observed species and the beta diversity metrics tended to have higher concordance than other metrics. Our findings, taken together with previous studies and feasibility considerations, indicated that FOBT cards, FIT tubes, and RNAlater are acceptable choices for fecal sample collection methods in future WGSS studies. A major direction for future microbiome research is implementation of fecal sample collections in large-scale, prospective epidemiologic studies. Studying microbiome-disease associations likely requires microbial data to be pooled from multiple studies. Our findings suggest collection methods that are most optimal to be used standardly across future WGSS microbiome studies.

%B mSphere %V 5 %8 2020 Feb 26 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/32250964?dopt=Abstract %R 10.1128/mSphere.00827-19 %0 Journal Article %J Nature %D 2018 %T Temporal development of the gut microbiome in early childhood from the TEDDY study. %A Stewart, Christopher J %A Ajami, Nadim J %A O'Brien, Jacqueline L %A Hutchinson, Diane S %A Smith, Daniel P %A Wong, Matthew C %A Ross, Matthew C %A Lloyd, Richard E %A Harshavardhan Doddapaneni %A Ginger A Metcalf %A Donna M Muzny %A Richard A Gibbs %A Vatanen, Tommi %A Huttenhower, Curtis %A Xavier, Ramnik J %A Rewers, Marian %A Hagopian, William %A Toppari, Jorma %A Ziegler, Anette-G %A She, Jin-Xiong %A Akolkar, Beena %A Lernmark, Ake %A Hyoty, Heikki %A Vehik, Kendra %A Krischer, Jeffrey P %A Petrosino, Joseph F %K Adolescent %K Animals %K Bifidobacterium %K Breast Feeding %K Case-Control Studies %K Child %K Child, Preschool %K Cluster Analysis %K Datasets as Topic %K Diabetes Mellitus, Type 1 %K Female %K Firmicutes %K Gastrointestinal Microbiome %K Humans %K Infant %K Male %K Milk, Human %K Pets %K RNA, Ribosomal, 16S %K Siblings %K Surveys and Questionnaires %K Time Factors %X

The development of the microbiome from infancy to childhood is dependent on a range of factors, with microbial-immune crosstalk during this time thought to be involved in the pathobiology of later life diseases such as persistent islet autoimmunity and type 1 diabetes. However, to our knowledge, no studies have performed extensive characterization of the microbiome in early life in a large, multi-centre population. Here we analyse longitudinal stool samples from 903 children between 3 and 46 months of age by 16S rRNA gene sequencing (n = 12,005) and metagenomic sequencing (n = 10,867), as part of the The Environmental Determinants of Diabetes in the Young (TEDDY) study. We show that the developing gut microbiome undergoes three distinct phases of microbiome progression: a developmental phase (months 3-14), a transitional phase (months 15-30), and a stable phase (months 31-46). Receipt of breast milk, either exclusive or partial, was the most significant factor associated with the microbiome structure. Breastfeeding was associated with higher levels of Bifidobacterium species (B. breve and B. bifidum), and the cessation of breast milk resulted in faster maturation of the gut microbiome, as marked by the phylum Firmicutes. Birth mode was also significantly associated with the microbiome during the developmental phase, driven by higher levels of Bacteroides species (particularly B. fragilis) in infants delivered vaginally. Bacteroides was also associated with increased gut diversity and faster maturation, regardless of the birth mode. Environmental factors including geographical location and household exposures (such as siblings and furry pets) also represented important covariates. A nested case-control analysis revealed subtle associations between microbial taxonomy and the development of islet autoimmunity or type 1 diabetes. These data determine the structural and functional assembly of the microbiome in early life and provide a foundation for targeted mechanistic investigation into the consequences of microbial-immune crosstalk for long-term health.

%B Nature %V 562 %P 583-588 %8 2018 Oct %G eng %N 7728 %1 https://www.ncbi.nlm.nih.gov/pubmed/30356187?dopt=Abstract %R 10.1038/s41586-018-0617-x %0 Journal Article %J Microbiome %D 2015 %T Structure and function of the healthy pre-adolescent pediatric gut microbiome. %A Hollister, Emily B %A Riehle, Kevin %A Luna, Ruth Ann %A Weidler, Erica M %A Rubio-Gonzales, Michelle %A Mistretta, Toni-Ann %A Raza, Sabeen %A Doddapaneni, Harsha V %A Metcalf, Ginger A %A Muzny, Donna M %A Gibbs, Richard A %A Petrosino, Joseph F %A Shulman, Robert J %A Versalovic, James %K Adult %K Age Factors %K Biodiversity %K Child %K Cluster Analysis %K DNA Barcoding, Taxonomic %K Female %K Gastrointestinal Microbiome %K Healthy Volunteers %K Humans %K Male %K Metagenome %K RNA, Ribosomal, 16S %X

BACKGROUND: The gut microbiome influences myriad host functions, including nutrient acquisition, immune modulation, brain development, and behavior. Although human gut microbiota are recognized to change as we age, information regarding the structure and function of the gut microbiome during childhood is limited. Using 16S rRNA gene and shotgun metagenomic sequencing, we characterized the structure, function, and variation of the healthy pediatric gut microbiome in a cohort of school-aged, pre-adolescent children (ages 7-12 years). We compared the healthy pediatric gut microbiome with that of healthy adults previously recruited from the same region (Houston, TX, USA).

RESULTS: Although healthy children and adults harbored similar numbers of taxa and functional genes, their composition and functional potential differed significantly. Children were enriched in Bifidobacterium spp., Faecalibacterium spp., and members of the Lachnospiraceae, while adults harbored greater abundances of Bacteroides spp. From a functional perspective, significant differences were detected with respect to the relative abundances of genes involved in vitamin synthesis, amino acid degradation, oxidative phosphorylation, and triggering mucosal inflammation. Children's gut communities were enriched in functions which may support ongoing development, while adult communities were enriched in functions associated with inflammation, obesity, and increased risk of adiposity.

CONCLUSIONS: Previous studies suggest that the human gut microbiome is relatively stable and adult-like after the first 1 to 3 years of life. Our results suggest that the healthy pediatric gut microbiome harbors compositional and functional qualities that differ from those of healthy adults and that the gut microbiome may undergo a more prolonged development than previously suspected.

%B Microbiome %V 3 %P 36 %8 2015 Aug 26 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/26306392?dopt=Abstract %R 10.1186/s40168-015-0101-x %0 Journal Article %J BMC Med Genet %D 2013 %T Exome sequencing of a patient with suspected mitochondrial disease reveals a likely multigenic etiology. %A Craigen, William J %A Graham, Brett H %A Wong, Lee-Jun %A Scaglia, Fernando %A Lewis, Richard Alan %A Bonnen, Penelope E %K Adult %K Computational Biology %K DNA Helicases %K Exome %K Genetic Diseases, X-Linked %K Genetic Loci %K Homozygote %K Humans %K Male %K Mitochondrial Diseases %K Multifunctional Enzymes %K Mutation, Missense %K Nephrolithiasis %K Oculocerebrorenal Syndrome %K Pedigree %K Phenotype %K Phosphoric Monoester Hydrolases %K RNA Helicases %K RNA, Ribosomal, 16S %K Sequence Analysis, DNA %K Spinocerebellar Ataxias %K Spinocerebellar Degenerations %X

BACKGROUND: The clinical features of mitochondrial disease are complex and highly variable, leading to challenges in establishing a specific diagnosis. Despite being one of the most commonly occurring inherited genetic diseases with an incidence of 1/5000, ~90% of these complex patients remain without a DNA-based diagnosis. We report our efforts to identify the pathogenetic cause for a patient with typical features of mitochondrial disease including infantile cataracts, CPEO, ptosis, progressive distal muscle weakness, and ataxia who carried a diagnosis of mitochondrial disease for over a decade.

METHODS: Whole exome sequencing and bioinformatic analysis of these data were conducted on the proband.

RESULTS: Exome sequencing studies showed a homozygous splice site mutation in SETX, which is known to cause Spinocerebellar Ataxia, Autosomal Recessive 1 (SCAR1). Additionally a missense mutation was identified in a highly conserved position of the OCRL gene, which causes Lowe Syndrome and Dent Disease 2.

CONCLUSIONS: This patient's complex phenotype reflects a complex genetic etiology in which no single gene explained the complete clinical presentation. These genetic studies reveal that this patient does not have mitochondrial disease but rather a genocopy caused by more than one mutant locus. This study demonstrates the benefit of exome sequencing in providing molecular diagnosis to individuals with complex clinical presentations.

%B BMC Med Genet %V 14 %P 83 %8 2013 Aug 16 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/23947751?dopt=Abstract %R 10.1186/1471-2350-14-83 %0 Journal Article %J PLoS One %D 2013 %T Metagenomic analyses of alcohol induced pathogenic alterations in the intestinal microbiome and the effect of Lactobacillus rhamnosus GG treatment. %A Bull-Otterson, Lara %A Feng, Wenke %A Kirpich, Irina %A Wang, Yuhua %A Qin, Xiang %A Liu, Yanlong %A Gobejishvili, Leila %A Joshi-Barve, Swati %A Ayvaz, Tulin %A Petrosino, Joseph %A Kong, Maiying %A Barker, David %A McClain, Craig %A Barve, Shirish %K Animals %K Anti-Infective Agents, Local %K Bacteria %K Biodiversity %K Claudin-1 %K Ethanol %K Feces %K Gene Expression %K Genetic Variation %K Hydrogen-Ion Concentration %K Intestinal Mucosa %K Intestines %K Lacticaseibacillus rhamnosus %K Liver Diseases, Alcoholic %K Male %K Metagenome %K Metagenomics %K Mice %K Mice, Inbred C57BL %K Probiotics %K Reverse Transcriptase Polymerase Chain Reaction %K RNA, Ribosomal, 16S %K Sequence Analysis, DNA %K Species Specificity %K Zonula Occludens-1 Protein %X

Enteric dysbiosis plays an essential role in the pathogenesis of alcoholic liver disease (ALD). Detailed characterization of the alterations in the gut microbiome is needed for understanding their pathogenic role in ALD and developing effective therapeutic approaches using probiotic supplementation. Mice were fed liquid Lieber-DeCarli diet without or with alcohol (5% v/v) for 6 weeks. A subset of mice were administered the probiotic Lactobacillus rhamnosus GG (LGG) from 6 to 8 weeks. Indicators of intestinal permeability, hepatic steatosis, inflammation and injury were evaluated. Metagenomic analysis of the gut microbiome was performed by analyzing the fecal DNA by amplification of the V3-V5 regions of the 16S rRNA gene and large-scale parallel pyrosequencing on the 454 FLX Titanium platform. Chronic ethanol feeding caused a decline in the abundance of both Bacteriodetes and Firmicutes phyla, with a proportional increase in the gram negative Proteobacteria and gram positive Actinobacteria phyla; the bacterial genera that showed the biggest expansion were the gram negative alkaline tolerant Alcaligenes and gram positive Corynebacterium. Commensurate with the qualitative and quantitative alterations in the microbiome, ethanol caused an increase in plasma endotoxin, fecal pH, hepatic inflammation and injury. Notably, the ethanol-induced pathogenic changes in the microbiome and the liver were prevented by LGG supplementation. Overall, significant alterations in the gut microbiome over time occur in response to chronic alcohol exposure and correspond to increases in intestinal barrier dysfunction and development of ALD. Moreover, the altered bacterial communities of the gut may serve as significant therapeutic target for the prevention/treatment of chronic alcohol intake induced intestinal barrier dysfunction and liver disease.

%B PLoS One %V 8 %P e53028 %8 2013 %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/23326376?dopt=Abstract %R 10.1371/journal.pone.0053028 %0 Journal Article %J PLoS One %D 2012 %T Evaluation of 16S rDNA-based community profiling for human microbiome research. %K Bacteria %K Bayes Theorem %K Humans %K Metagenome %K RNA, Ribosomal, 16S %X

The Human Microbiome Project will establish a reference data set for analysis of the microbiome of healthy adults by surveying multiple body sites from 300 people and generating data from over 12,000 samples. To characterize these samples, the participating sequencing centers evaluated and adopted 16S rDNA community profiling protocols for ABI 3730 and 454 FLX Titanium sequencing. In the course of establishing protocols, we examined the performance and error characteristics of each technology, and the relationship of sequence error to the utility of 16S rDNA regions for classification- and OTU-based analysis of community structure. The data production protocols used for this work are those used by the participating centers to produce 16S rDNA sequence for the Human Microbiome Project. Thus, these results can be informative for interpreting the large body of clinical 16S rDNA data produced for this project.

%B PLoS One %V 7 %P e39315 %8 2012 %G eng %N 6 %1 https://www.ncbi.nlm.nih.gov/pubmed/22720093?dopt=Abstract %R 10.1371/journal.pone.0039315 %0 Journal Article %J Nature %D 2012 %T A framework for human microbiome research. %K Adolescent %K Adult %K Bacteria %K Female %K Humans %K Male %K Metagenome %K Metagenomics %K Reference Standards %K RNA, Ribosomal, 16S %K Statistics as Topic %K Young Adult %X

A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 or 18 body sites up to three times, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far. In parallel, approximately 800 reference strains isolated from the human body have been sequenced. Collectively, these data represent the largest resource describing the abundance and variety of the human microbiome, while providing a framework for current and future studies.

%B Nature %V 486 %P 215-21 %8 2012 Jun 13 %G eng %N 7402 %1 https://www.ncbi.nlm.nih.gov/pubmed/22699610?dopt=Abstract %R 10.1038/nature11209 %0 Journal Article %J Anim Health Res Rev %D 2012 %T High throughput sequencing methods for microbiome profiling: application to food animal systems. %A Highlander, Sarah K %K Animals %K Animals, Domestic %K Archaea %K Bacteria %K DNA, Ribosomal %K Genes, rRNA %K High-Throughput Nucleotide Sequencing %K Humans %K Meat %K Metagenome %K Metagenomics %K RNA, Ribosomal, 16S %K Sequence Analysis, RNA %K Viruses %X

Analysis of microbial communities using high throughput sequencing methods began in the mid 2000s permitting the production of 1000s to 10,000s of sequence reads per sample and megabases of data per sequence run. This then unprecedented depth of sequencing allowed, for the first time, the discovery of the 'rare biosphere' in environmental samples. The technology was quickly applied to studies in several human subjects. Perhaps these early studies served as a reminder that though the microbes that inhabit mammals are known to outnumber host cells by an order of magnitude or more, most of these are unknown members of our second genome, or microbiome (as coined by Joshua Lederberg), because of our inability to culture them. High throughput methods for microbial 16S ribosomal RNA gene and whole genome shotgun (WGS) sequencing have now begun to reveal the composition and identity of archaeal, bacterial and viral communities at many sites, in and on the human body. Surveys of the microbiota of food production animals have been published in the past few years and future studies should benefit from protocols and tools developed from large-scale human microbiome studies. Nevertheless, production animal-related resources, such as improved host genome assemblies and increased numbers and diversity of host-specific microbial reference genome sequences, will be needed to permit meaningful and robust analysis of 16S rDNA and WGS sequence data.

%B Anim Health Res Rev %V 13 %P 40-53 %8 2012 Jun %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/22853944?dopt=Abstract %R 10.1017/S1466252312000126 %0 Journal Article %J Nature %D 2012 %T Structure, function and diversity of the healthy human microbiome. %K Adolescent %K Adult %K Bacteria %K Biodiversity %K Ecosystem %K Female %K Health %K Humans %K Male %K Metabolic Networks and Pathways %K Metagenome %K Metagenomics %K Phenotype %K RNA, Ribosomal, 16S %K Young Adult %X

Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat's signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81-99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome.

%B Nature %V 486 %P 207-14 %8 2012 Jun 13 %G eng %N 7402 %1 https://www.ncbi.nlm.nih.gov/pubmed/22699609?dopt=Abstract %R 10.1038/nature11234 %0 Journal Article %J Gastroenterology %D 2011 %T Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome. %A Saulnier, Delphine M %A Riehle, Kevin %A Mistretta, Toni-Ann %A Diaz, Maria-Alejandra %A Mandal, Debasmita %A Raza, Sabeen %A Weidler, Erica M %A Qin, Xiang %A Coarfa, Cristian %A Milosavljevic, Aleksandar %A Petrosino, Joseph F %A Highlander, Sarah %A Gibbs, Richard %A Lynch, Susan V %A Shulman, Robert J %A Versalovic, James %K Abdominal Pain %K Case-Control Studies %K Child %K DNA Probes %K Female %K Gastrointestinal Tract %K Haemophilus parainfluenzae %K Humans %K Incidence %K Irritable Bowel Syndrome %K Male %K Metagenome %K Phenotype %K Phylogeny %K RNA, Ribosomal, 16S %K Ruminococcus %X

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). Data were analyzed using phylogenetic-based clustering (Unifrac), or an operational taxonomic unit (OTU) approach using a supervised machine learning tool (randomForest). Most samples were also hybridized to a microarray that can detect 8741 bacterial taxa (16S rRNA PhyloChip).

RESULTS: Microbiomes associated with pediatric IBS were characterized by a significantly greater percentage of the class γ-proteobacteria (0.07% vs 0.89% of total bacteria, respectively; P < .05); 1 prominent component of this group was Haemophilus parainfluenzae. Differences highlighted by 454 sequencing were confirmed by high-resolution PhyloChip analysis. Using supervised learning techniques, we were able to classify different subtypes of IBS with a success rate of 98.5%, using limited sets of discriminant bacterial species. A novel Ruminococcus-like microbe was associated with IBS, indicating the potential utility of microbe discovery for gastrointestinal disorders. A greater frequency of pain correlated with an increased abundance of several bacterial taxa from the genus Alistipes.

CONCLUSIONS: Using 16S metagenomics by PhyloChip DNA hybridization and deep 454 pyrosequencing, we associated specific microbiome signatures with pediatric IBS. These findings indicate the important association between gastrointestinal microbes and IBS in children; these approaches might be used in diagnosis of functional bowel disorders in pediatric patients.

%B Gastroenterology %V 141 %P 1782-91 %8 2011 Nov %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/21741921?dopt=Abstract %R 10.1053/j.gastro.2011.06.072 %0 Journal Article %J Methods Mol Biol %D 2009 %T Horizontal gene transfer in cyanobacterial signature genes. %A Yerrapragada, Shailaja %A Siefert, Janet L %A Fox, George E %K Cyanobacteria %K Gene Transfer, Horizontal %K Genes, Bacterial %K Models, Genetic %K Phenotype %K Phylogeny %K RNA, Bacterial %K RNA, Ribosomal, 16S %X

Comparison of 15 phylogenetically diverse cyanobacterial genomes identified an updated list of 183 signature genes that are widely found in cyanobacteria but absent in non-cyanobacterial species. These signature genes comprise the unique portion of the core cyanobacterial phenotype, and their absence from other lineages implies that if they arose by horizontal gene transfer (HGT), it likely occurred before the last shared cyanobacterial ancestor. A remaining issue is whether or not these signature genes would be relatively immune to HGT within the cyanobacterial lineage. Phylogenetic trees for each signature gene were constructed and compared to cyanobacterial groupings based on 16S rRNA sequences, with clear incongruence considered indicative of HGT. Approximately 18% of the signature genes exhibited such anomalies, indicating that the incidence of inter-lineage HGT has been significant. A preliminary analysis of intra-lineage transfer was conducted using four Synechococcus/Prochlorococcus species. In this case, it was found that 13% of the signature genes had likely been involved in within group HGT. In order to compare this level of likely HGT to other gene types, the analysis was extended to 1380 genes shared by the four Synechococcus/Prochlorococcus species. Successful HGT events appear to be most frequent among genes involved in photosynthesis/respiration and genes of unknown function, many of which are signature genes. This is consistent with the hypothesis that genes that most directly effect competition and adaptation of similar species in neighboring niches would be most usefully transferred. Such genes may be more easily integrated into a new genomic environment due to close similarities in regulatory circuits. In summary, signature genes are not immune from HGT and in fact may be favored candidates for HGT among closely related cyanobacterial strains.

%B Methods Mol Biol %V 532 %P 339-66 %8 2009 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/19271195?dopt=Abstract %R 10.1007/978-1-60327-853-9_20 %0 Journal Article %J Clin Chem %D 2009 %T Metagenomic pyrosequencing and microbial identification. %A Petrosino, Joseph F %A Highlander, Sarah %A Luna, Ruth Ann %A Gibbs, Richard A %A Versalovic, James %K Computational Biology %K DNA, Bacterial %K Genomics %K Humans %K Metagenome %K RNA, Ribosomal, 16S %K Sequence Analysis, DNA %X

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. Bioinformatics-related topics include taxonomic systems, sequence databases, sequence-alignment tools, and classifiers. DNA sequencing based on 16S rRNA genes or entire genomes is summarized with respect to potential pyrosequencing applications.

SUMMARY: Both the approach of 16S rDNA amplicon sequencing and the whole-genome sequencing approach may be useful for human metagenomics, and numerous bioinformatics tools are being deployed to tackle such vast amounts of microbiological sequence diversity. Metagenomics, or genetic studies of microbial communities, may ultimately contribute to a more comprehensive understanding of human health, disease susceptibilities, and the pathophysiology of infectious and immune-mediated diseases.

%B Clin Chem %V 55 %P 856-66 %8 2009 May %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/19264858?dopt=Abstract %R 10.1373/clinchem.2008.107565