Metatranscriptome of human faecal microbial communities in a cohort of adult men

Nature Microbiology

Volumn 3, Issue 3, 2018, Pages 356-366

  Abu Ali, Galeb S ^a,b   Mehta, Raaj S ^c   Lloyd Price, Jason ^a,b   Mallick, Himel ^a,b   Branck, Tobyn ^a,d   Ivey, Kerry L ^a,e   Drew, David A ^c   Dulong, Casey ^a   Rimm, Eric ^a,f   Izard, Jacques ^g   Chan, Andrew T ^b,c,f   Huttenhower, Curtis ^a,b  

^a HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^b BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^c MASSACHUSETTS GENERAL HOSPITAL   (United States)

^d DEVELOPMENT AND ENGINEERING CENTER   (United States)

^e FLINDERS UNIVERSITY   (Australia)

^f BRIGHAM AND WOMEN S HOSPITAL   (United States)

^g UNIVERSITY OF NEBRASKA LINCOLN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; BACTERIAL RNA;

ADULT; AGED; ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; CLINICAL STUDY; COHORT ANALYSIS; CONTROLLED STUDY; FECES MICROFLORA; FOLLOW UP; GENETIC VARIABILITY; HUMAN; MALE; MEN'S HEALTH; METAGENOME; METATRANSCRIPTOME; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; ORGANISMAL INTERACTION; PHYLOGENY; POPULATION ABUNDANCE; PRIORITY JOURNAL; SPECIES DIVERSITY; TRANSCRIPTOMICS; VERY ELDERLY; FECES; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORK; INTESTINE FLORA; LONGITUDINAL STUDY; METAGENOMICS; MICROBIOLOGY; MICROFLORA; PROSPECTIVE STUDY;

AGED; AGED, 80 AND OVER; FECES; FOLLOW-UP STUDIES; GASTROINTESTINAL MICROBIOME; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORKS; HUMANS; LONGITUDINAL STUDIES; MALE; METAGENOME; METAGENOMICS; MICROBIOTA; PHYLOGENY; PROSPECTIVE STUDIES;

EID: 85040707169     PISSN: None     EISSN: 20585276     Source Type: Journal    
DOI: 10.1038/s41564-017-0084-4     Document Type: Article

References (45)

1. O'Doherty, K. C., Virani, A. &Wilcox, E. S. The human microbiome and public health: social and ethical considerations. Am. J. Public Health 106, 414-420 (2016).
2. Shreiner, A. B., Kao, J. Y. &Young, V. B. The gut microbiome in health and in disease. Curr. Opin. Gastroen. 31, 69-75 (2015).
3. Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 486, 207-214 (2012).
4. Vatanen, T. et al. Variation in microbiome LPS immunogenicity contributes to autoimmunity in humans. Cell 165, 842-853 (2016).
5. Le Chatelier, E. et al. Richness of human gut microbiome correlates with metabolic markers. Nature 500, 541-546 (2013).
6. Korpela, K. et al. Intestinal microbiome is related to lifetime antibiotic use in Finnish pre-school children. Nat. Commun. 7, 10410 (2016).
7. Satinsky, B. M. et al. Microspatial gene expression patterns in the Amazon River plume. Proc. Natl Acad. Sci. USA 111, 11085-11090 (2014).
8. Turnbaugh, P. J. et al. Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins. Proc. Natl Acad. Sci. USA 107, 7503-7508 (2010).
9. Franzosa, E. A. et al. Relating the metatranscriptome and metagenome of the human gut. Proc. Natl Acad. Sci. USA 111, E2329-E2338 (2014).
10. Segata, N. et al. Computational meta'omics for microbial community studies. Mol. Syst. Biol. 9, 666 (2013).
11. Haiser, H. J. et al. Predicting and manipulating cardiac drug inactivation by the human gut bacterium Eggerthella lenta. Science 341, 295-298 (2013).
12. Byron, S. A., Van Keuren-Jensen, K. R., Engelthaler, D. M., Carpten, J. D. &Craig, D. W. Translating RNA sequencing into clinical diagnostics: opportunities and challenges. Nat. Rev. Genet. 17, 257-271 (2016).
13. Chan, A. T. et al. Aspirin dose and duration of use and risk of colorectal cancer in men. Gastroenterology 134, 21-28 (2008).
14. Mehta, R. et al. Stability of the human faecal microbiome in a cohort of adult men. Nat. Microbiol. (in press).
15. Truong, D. T. et al. MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Nat. Methods 12, 902-903 (2015).
16. Abubucker, S. et al. Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput. Biol. 8, e1002358 (2012).
17. Caspi, R. et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 44, D471-D480 (2016).
18. Qin, J. et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59-65 (2010).
19. Claesson, M. J. et al. Gut microbiota composition correlates with diet and health in the elderly. Nature 488, 178-184 (2012).
20. Claesson, M. J. et al. Composition, variability, and temporal stability of the intestinal microbiota of the elderly. Proc. Natl Acad. Sci. USA 108, 4586-4591 (2011).
21. Virgin, H. W. The virome in mammalian physiology and disease. Cell 157, 142-150 (2014).
22. McCarty, R. M. &Bandarian, V. Biosynthesis of pyrrolopyrimidines. Bioorg. Chem. 43, 15-25 (2012).
23. Vinayak, M. &Pathak, C. Queuosine modification of tRNA: its divergent role in cellular machinery. Biosci. Rep. 30, 135-148 (2009).
24. Hauryliuk, V., Atkinson, G. C., Murakami, K. S., Tenson, T. &Gerdes, K. Recent functional insights into the role of (p)ppGpp in bacterial physiology. Nat. Rev. Microbiol. 13, 298-309 (2015).
25. Chistoserdova, L., Kalyuzhnaya, M. G. &Lidstrom, M. E. The expanding world of methylotrophic metabolism. Annu. Rev. Microbiol. 63, 477-499 (2009).
26. Faust, K. et al. Microbial co-occurrence relationships in the human microbiome. PLoS Comput. Biol. 8, e1002606 (2012).
27. Levy, R. &Borenstein, E. Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules. Proc. Natl Acad. Sci. USA 110, 12804-12809 (2013).
28. Lloyd-Price, J. et al. Strains, functions and dynamics in the expanded Human Microbiome Project. Nature 550, 61-66 (2017).
29. Truong, D. T., Tett, A., Pasolli, E., Huttenhower, C. &Segata, N. Microbial strain-level population structure and genetic diversity from metagenomes. Genome Res. 27, 626-638 (2017).
30. Gosalbes, M. J. et al. Metatranscriptomic approach to analyze the functional human gut microbiota. PLoS ONE 6, e17447 (2011).
31. Sanchez, A. &Golding, I. Genetic determinants and cellular constraints in noisy gene expression. Science 342, 1188-1193 (2013).
32. Pande, S. et al. Fitness and stability of obligate cross-feeding interactions that emerge upon gene loss in bacteria. ISME J. 8, 953-962 (2014).
33. D'Souza, G. &Kost, C. Experimental evolution of metabolic dependency in bacteria. PLoS Genet. 12, e1006364 (2016).
34. Morgan, X. C. et al. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol. 13, R79 (2012).
35. Li, J. et al. An integrated catalog of reference genes in the human gut microbiome. Nat. Biotechnol. 32, 834-841 (2014).
36. Pimentel, D. Population regulation and genetic feedback. Science 159, 1432-1437 (1968).
37. O'Toole, P. W. &Jeffery, I. B. Gut microbiota and aging. Science 350, 1214-1215 (2015).
38. Bolger, A. M., Lohse, M. &Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114-2120 (2014).
39. Human Microbiome Project Consortium. A framework for human microbiome research. Nature 486, 215-221 (2012).
40. Langmead, B. &Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-359 (2012).
41. Suzek, B. E., Huang, H., McGarvey, P., Mazumder, R. &Wu, C. H. UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics 23, 1282-1288 (2007).
42. Buchfink, B., Xie, C. &Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59-60 (2015).
43. Ye, Y. &Doak, T. G. A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes. PLoS Comput. Biol. 5, e1000465 (2009).
44. Kimura, M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16, 111-120 (1980)
45. Schwager, E., Mallick, H., Ventz, S. &Huttenhower, C. A Bayesian method for detecting pairwise associations in compositional data. PLoS Comput. Biol. 13, e1005852 (2017).