Summary: A collective genome representative of the many organisms, primarily microorganisms, existing in a community.
- Xie C, Goi C, Huson D, Little P, Williams R. RiboTagger: fast and unbiased 16S/18S profiling using whole community shotgun metagenomic or metatranscriptome surveys. BMC Bioinformatics. 2016;17:508 pubmed publisher..The program targets all three domains of life, exhibits high sensitivity and specificity and is substantially faster than comparable programs. ..
- Wang Y, Leung H, Yiu S, Chin F. MetaCluster-TA: taxonomic annotation for metagenomic data based on assembly-assisted binning. BMC Genomics. 2014;15 Suppl 1:S12 pubmed publisher..MetaCluster-TA can outperform widely-used MEGAN4 and can annotate more reads with higher accuracy and higher efficiency. It also outperforms MetaCluster 5.0 as a binning tool. ..
- Galla S, Chakraborty S, Mell B, Vijay Kumar M, Joe B. Microbiotal-Host Interactions and Hypertension. Physiology (Bethesda). 2017;32:224-233 pubmed publisher..host genome, the genomes of all indigenous commensal micro-organisms, collectively referred to as the microbial metagenome or microbiome, are important, but largely understudied, determinants of BP...
- Bremges A, Maus I, Belmann P, Eikmeyer F, Winkler A, Albersmeier A, et al. Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural production-scale biogas plant. Gigascience. 2015;4:33 pubmed publisher..Most of the participating microbes are still unknown and non-cultivable. Accordingly, shotgun metagenome sequencing currently is the method of choice to obtain insights into community composition and the genetic ..
- Mitra S, Förster Fromme K, Damms Machado A, Scheurenbrand T, Biskup S, Huson D, et al. Analysis of the intestinal microbiota using SOLiD 16S rRNA gene sequencing and SOLiD shotgun sequencing. BMC Genomics. 2013;14 Suppl 5:S16 pubmed publisher..This study shows that SOLiD mate-pair sequencing is a viable and cost-efficient option for analyzing a complex microbiome. To the best of our knowledge, this is the first time that SOLiD sequencing has been used in a human sample. ..
- Festa S, Coppotelli B, Madueño L, Loviso C, Macchi M, Neme Tauil R, et al. Assigning ecological roles to the populations belonging to a phenanthrene-degrading bacterial consortium using omic approaches. PLoS ONE. 2017;12:e0184505 pubmed publisher..am). ..
- Wood D, Salzberg S. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 2014;15:R46 pubmed publisher..1 million reads per minute, 909 times faster than Megablast and 11 times faster than the abundance estimation program MetaPhlAn. Kraken is available at http://ccb.jhu.edu/software/kraken/. ..
- Clarke S, Brooks S, Inglis G, Yanke L, Green J, Petronella N, et al. Impact of ?2-1 fructan on faecal community change: results from a placebo-controlled, randomised, double-blinded, cross-over study in healthy adults. Br J Nutr. 2017;118:441-453 pubmed publisher..2-1 Fructan had no impact on the metagenome or glycoside hydrolase profiles in faeces from four subjects...
- Liu F, Yang X. Indole Derivatives Produced by the Metagenome Genes of the Escherichia coli-Harboring Marine Sponge Discodermia calyx. Molecules. 2017;22: pubmed publisher..allowing us to predict that the formation of 2 might be induced by exogenous genes derived from the sponge metagenome, whereas compound 1 could be formed through a non-enzymatic process during the isolation procedure.
- HUFFNAGLE G, Noverr M. GI microbiota and regulation of the immune system. Preface. Adv Exp Med Biol. 2008;635:v-vi pubmed
- Páez Espino D, Eloe Fadrosh E, Pavlopoulos G, Thomas A, Huntemann M, Mikhailova N, et al. Uncovering Earth's virome. Nature. 2016;536:425-30 pubmed..Our results highlight an extensive global viral diversity and provide detailed insight into viral habitat distribution and host–virus interactions. ..
- Kaliuzhnaia O, Krivich A, Itskovich V. [Diversity of 16S rRNA genes in metagenomic community of the freshwater sponge Lubomirskia baicalensis]. Genetika. 2012;48:1003-6 pubmed..The wide diversity of bacteria closely coexisting with the Baikal sponge indicate the complex ecological relationships in the community formed under the unique conditions of Lake Baikal. ..
- Han K, Bose S, Wang J, Lim S, Chin Y, Kim Y, et al. In vivo therapeutic effect of combination treatment with metformin and Scutellaria baicalensis on maintaining bile acid homeostasis. PLoS ONE. 2017;12:e0182467 pubmed publisher..Further study is needed to find the specific strains of bacteria which contribute to FXR-related cholesterol and bile acid regulations. ..
- Mahana D, Trent C, Kurtz Z, Bokulich N, Battaglia T, Chung J, et al. Antibiotic perturbation of the murine gut microbiome enhances the adiposity, insulin resistance, and liver disease associated with high-fat diet. Genome Med. 2016;8:48 pubmed..These studies form the basis for new models of type 2 diabetes and NAFLD that involve microbiome perturbation. ..
- Fukuyama J, Rumker L, Sankaran K, Jeganathan P, Dethlefsen L, Relman D, et al. Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment. PLoS Comput Biol. 2017;13:e1005706 pubmed publisher..We provide complete code and illustrations of new sparse statistical methods for high-dimensional, longitudinal multidomain data that provide greater interpretability than existing methods. ..
- Chen H, Peng S, Dai L, Zou Q, Yi B, Yang X, et al. Oral microbial community assembly under the influence of periodontitis. PLoS ONE. 2017;12:e0182259 pubmed publisher..We argue that the 'phenotypic' changes explain the observed link (not necessarily causal) between periodontitis and community dysbiosis, which is certainly worthy of further investigation. ..
- Kusnezowa A, Leichert L. In silico approach to designing rational metagenomic libraries for functional studies. BMC Bioinformatics. 2017;18:267 pubmed publisher..About 6.1 million predicted proteins from the Global Ocean Sampling Expedition Metagenome project were distributed into classes based either on homology to existing hidden markov models (HMMs) of known ..
- Mezzasalma V, Sandionigi A, Bruni I, Bruno A, Lovicu G, Casiraghi M, et al. Grape microbiome as a reliable and persistent signature of field origin and environmental conditions in Cannonau wine production. PLoS ONE. 2017;12:e0184615 pubmed publisher..For these reasons, a reliable wine genotyping should include the entire holobiont (plant and all its symbionts), and bioprospecting activities on grape microbiota could lead to improved viticulture yields and wine quality. ..
- Lloyd Price J, Mahurkar A, Rahnavard G, Crabtree J, Orvis J, Hall A, et al. Strains, functions and dynamics in the expanded Human Microbiome Project. Nature. 2017;550:61-66 pubmed publisher..This study furthers our knowledge of baseline human microbial diversity and enables an understanding of personalized microbiome function and dynamics...
- Ackerman J. The ultimate social network. Sci Am. 2012;306:36-43 pubmed
- Ai D, Huang R, Wen J, Li C, Zhu J, Xia L. Integrated metagenomic data analysis demonstrates that a loss of diversity in oral microbiota is associated with periodontitis. BMC Genomics. 2017;18:1041 pubmed publisher..Apart from P. gingivalis, we identified three additional keystone species potentially mediating the progression of periodontitis progression based on pathogenic characteristics similar to those of known keystone pathogens. ..
- Yan J, Chuai G, Qi T, Shao F, Zhou C, Zhu C, et al. MetaTopics: an integration tool to analyze microbial community profile by topic model. BMC Genomics. 2017;18:962 pubmed publisher..MetaTopics is the first interactive R package to integrate the state-of-arts topic model derived from statistical learning community to analyze and visualize the metagenomics taxonomy data. ..
- Weng F, Yang Y, Wang D. Functional analysis for gut microbes of the brown tree frog (Polypedates megacephalus) in artificial hibernation. BMC Genomics. 2016;17:1024 pubmed publisher..We infer that artificial hibernation may impose potential effects on primary immunodeficiency and increase the risk of bacterial infections in the brown tree frog. ..
- Brenner S. Blue-green algae or cyanobacteria in the intestinal micro-flora may produce neurotoxins such as Beta-N-Methylamino-L-Alanine (BMAA) which may be related to development of amyotrophic lateral sclerosis, Alzheimer's disease and Parkinson-Dementia-Compl. Med Hypotheses. 2013;80:103 pubmed publisher
- Shahinas D, Silverman M, Sittler T, Chiu C, Kim P, Allen Vercoe E, et al. Toward an understanding of changes in diversity associated with fecal microbiome transplantation based on 16S rRNA gene deep sequencing. MBio. 2012;3: pubmed publisher..Genus- and species-level analysis revealed a cocktail of microorganisms in the Bacteroidetes and Firmicutes phyla that may ultimately be used as a probiotic to treat CDI. ..
- Burke D, Fouhy F, Harrison M, Rea M, Cotter P, O Sullivan O, et al. The altered gut microbiota in adults with cystic fibrosis. BMC Microbiol. 2017;17:58 pubmed publisher..The data show the impact that CF and it's management have on gut microbiota, presenting the opportunity to develop CF specific probiotics to minimise microbiota alterations. ..
- ..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. ..
- Blasco G, Moreno Navarrete J, Rivero M, Perez Brocal V, Garre Olmo J, Puig J, et al. The Gut Metagenome Changes in Parallel to Waist Circumference, Brain Iron Deposition, and Cognitive Function. J Clin Endocrinol Metab. 2017;102:2962-2973 pubmed publisher..To study potential relationships among the gut metagenome, brain microstructure, and cognitive performance in middle-aged, apparently healthy, obese and nonobese subjects ..
- Abecia L, Jiménez E, Martínez Fernández G, Martín García A, Ramos Morales E, Pinloche E, et al. Natural and artificial feeding management before weaning promote different rumen microbial colonization but not differences in gene expression levels at the rumen epithelium of newborn goats. PLoS ONE. 2017;12:e0182235 pubmed publisher..However, the rumen epithelial immune development does not differentially respond to distinct microbial colonization patterns. ..
- Nascimento M, Zaura E, Mira A, Takahashi N, Ten Cate J. Second Era of OMICS in Caries Research: Moving Past the Phase of Disillusionment. J Dent Res. 2017;96:733-740 pubmed publisher..These observations apply equally to the study of other oral diseases. ..
- Nabizadeh E, Jazani N, Bagheri M, Shahabi S. Association of altered gut microbiota composition with chronic urticaria. Ann Allergy Asthma Immunol. 2017;119:48-53 pubmed publisher..This is the first study, to our knowledge, to show the change of microbiota composition in patients with CU. ..
- Syranidou E, Karkanorachaki K, Amorotti F, Repouskou E, Kroll K, Kolvenbach B, et al. Development of tailored indigenous marine consortia for the degradation of naturally weathered polyethylene films. PLoS ONE. 2017;12:e0183984 pubmed publisher..Taking into account the results, we can suggest that the tailored indigenous marine community represents an efficient consortium for degrading weathered PE plastics. ..
- Schubert A, Rogers M, Ring C, Mogle J, Petrosino J, Young V, et al. Microbiome data distinguish patients with Clostridium difficile infection and non-C. difficile-associated diarrhea from healthy controls. MBio. 2014;5:e01021-14 pubmed publisher..Our results emphasize the importance of considering the microbiome in mediating colonization resistance and may also direct the design of future multispecies probiotic therapies. ..
- Karlsson O, Belak S, Granberg F. The effect of preprocessing by sequence-independent, single-primer amplification (SISPA) on metagenomic detection of viruses. Biosecur Bioterror. 2013;11 Suppl 1:S227-34 pubmed publisher..More specifically, a synthetic metagenome was divided into 2 samples, 1 unamplified and 1 diluted, and amplified by SISPA...
- Liang C, Tseng H, Chen H, Wang W, Chiu C, Chang J, et al. Diversity and enterotype in gut bacterial community of adults in Taiwan. BMC Genomics. 2017;18:932 pubmed publisher..We used NGS technology to characterize the microbiota and constructed a predictive model. The most significant finding was that Enterobacteriaceae, the predominant subtype, could be a new subtype of enterotypes in the Asian population. ..
- Broeksema B, Calusinska M, McGee F, Winter K, Bongiovanni F, Goux X, et al. ICoVeR - an interactive visualization tool for verification and refinement of metagenomic bins. BMC Bioinformatics. 2017;18:233 pubmed publisher..to benchmark ICoVeR against a previously validated dataset, we used Sharon's dataset representing an infant gut metagenome. ICoVeR is an open source software package that allows curation of disparate genome bins generated with ..
- Lewandowska D, Schreiber P, Schuurmans M, Ruehe B, Zagordi O, Bayard C, et al. Metagenomic sequencing complements routine diagnostics in identifying viral pathogens in lung transplant recipients with unknown etiology of respiratory infection. PLoS ONE. 2017;12:e0177340 pubmed publisher..This study highlights the potential of metagenomic sequencing for virus diagnostics in cases with previously unknown etiology of infection and in complex diagnostic situations such as in immunocompromised hosts. ..
- Gontang E, Aylward F, Carlos C, Glavina del Rio T, Chovatia M, Fern A, et al. Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach. PLoS ONE. 2017;12:e0177189 pubmed publisher..Our work underscores the prominence of community changes throughout gut microbiomes and highlights ecological factors that underpin the structure and function of the symbiotic microbial communities of metazoans. ..
- Elderman M, Sovran B, Hugenholtz F, Graversen K, Huijskes M, Houtsma E, et al. The effect of age on the intestinal mucus thickness, microbiota composition and immunity in relation to sex in mice. PLoS ONE. 2017;12:e0184274 pubmed publisher..Our data contribute to a better understanding of the interplay between mucus-microbiota-and immune responses and ultimately may lead to more tailored design of strategies to modulate mucus production in targeted groups. ..
- Stepanov V, Xiao Y, Tran Q, Rojas M, Willson R, Fofanov Y, et al. The presence of nitrate dramatically changed the predominant microbial community in perchlorate degrading cultures under saline conditions. BMC Microbiol. 2014;14:225 pubmed publisher..These Rhodobacteraceae especially, as well as other organisms present in these communities may be a promising source of unique salt-tolerant enzymes for perchlorate reduction. ..
- MartÃnez del Campo A, Bodea S, Hamer H, Marks J, Haiser H, Turnbaugh P, et al. Characterization and detection of a widely distributed gene cluster that predicts anaerobic choline utilization by human gut bacteria. MBio. 2015;6: pubmed publisher..Both our analyses of the cut gene cluster and this molecular tool will aid efforts to further understand the role of choline metabolism in the human gut microbiota and its link to disease. ..
- Liu R, Hong J, Xu X, Feng Q, Zhang D, Gu Y, et al. Gut microbiome and serum metabolome alterations in obesity and after weight-loss intervention. Nat Med. 2017;23:859-868 pubmed publisherEmerging evidence has linked the gut microbiome to human obesity. We performed a metagenome-wide association study and serum metabolomics profiling in a cohort of lean and obese, young, Chinese individuals...
- Lindsay B, Oundo J, Hossain M, Antonio M, Tamboura B, Walker A, et al. Microbiota that affect risk for shigellosis in children in low-income countries. Emerg Infect Dis. 2015;21:242-50 pubmed publisher..are protective against Shigella spp.-induced diarrhea. Bacterial diversity of gut microbiota was associated with diarrhea status, not high levels of the Shigella spp. ipaH gene. ..
- ..High-throughput technologies are revealing interactions between these complex communities and their hosts in unprecedented detail. ..
- Levin B, Huang Y, Peck S, Wei Y, Martínez Del Campo A, Marks J, et al. A prominent glycyl radical enzyme in human gut microbiomes metabolizes trans-4-hydroxy-l-proline. Science. 2017;355: pubmed publisher..This "chemically guided functional profiling" workflow can therefore use ecological context to facilitate the discovery of enzymes in microbial communities. ..
- . Evaluation of 16S rDNA-based community profiling for human microbiome research. PLoS ONE. 2012;7:e39315 pubmed publisher..Thus, these results can be informative for interpreting the large body of clinical 16S rDNA data produced for this project. ..
- Landry Z, Swan B, Herndl G, Stepanauskas R, Giovannoni S. SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter. MBio. 2017;8: pubmed publisher..These pathways are tied to a proliferation of oxidative enzymes. This research illuminates dark-ocean biochemistry that is broadly consequential for reconstructing the global carbon cycle. ..
- Liljeqvist M, Ossandon F, GonzÃ¡lez C, Rajan S, Stell A, Valdes J, et al. Metagenomic analysis reveals adaptations to a cold-adapted lifestyle in a low-temperature acid mine drainage stream. FEMS Microbiol Ecol. 2015;91: pubmed publisher..In addition, metagenome contigs were most similar to other Acidithiobacillus species, an Acidobacteria-like species, and a ..