Strategies to Improve Reference Databases for Soil Microbiomes

Overview

Journal ISME J

Publisher Oxford University Press

Specialties Environmental Health
Microbiology

Date 2016 Dec 10

PMID 27935589

Citations 56

Authors

Jinlyung Choi

Fan Yang

Ramunas Stepanauskas

Erick Cardenas

Aaron Garoutte

Ryan Williams

Jared Flater

James M Tiedje

Kirsten S Hofmockel

Brian Gelder

Adina Howe

Affiliations

Soon will be listed here.

Citing Articles

From Soil to Surface: Exploring the Impact of Green Infrastructure on Microbial Communities in the Built Environment.

Mcgonigal M, Ito K J Genomics. 2025; 13:10-23.

PMID: 39925382 PMC: 11803137. DOI: 10.7150/jgen.106245.

How do various strategies for returning residues change microbiota modulation: potential implications for soil health.

Jiang N, Chen Z, Ren Y, Xie S, Yao Z, Jiang D Front Microbiol. 2025; 15:1495682.

PMID: 39906540 PMC: 11790580. DOI: 10.3389/fmicb.2024.1495682.

Impact of supernatant on screening bacterial strains with potential for biotechnological applications.

Cunha-Ferreira I, Vizzotto C, Frederico T, Peixoto J, Carvalho L, Totola M Eng Microbiol. 2024; 4(3):100163.

PMID: 39629112 PMC: 11610968. DOI: 10.1016/j.engmic.2024.100163.

Genomic profiling of Antarctic geothermal microbiomes using long-read, Hi-C, and single-cell techniques.

Myeong N, Choe Y, Shin S, Kim J, Sul W, Kim M Sci Data. 2024; 11(1):1023.

PMID: 39300163 PMC: 11413225. DOI: 10.1038/s41597-024-03875-z.

From soil to sequence: filling the critical gap in genome-resolved metagenomics is essential to the future of soil microbial ecology.

Anthony W, Allison S, Broderick C, Rodriguez L, Clum A, Cross H Environ Microbiome. 2024; 19(1):56.

PMID: 39095861 PMC: 11295382. DOI: 10.1186/s40793-024-00599-w.

References

Segata N, Waldron L, Ballarini A, Narasimhan V, Jousson O, Huttenhower C . Metagenomic microbial community profiling using unique clade-specific marker genes. Nat Methods. 2012; 9(8):811-4. PMC: 3443552. DOI: 10.1038/nmeth.2066. View

Kashtan N, Roggensack S, Rodrigue S, Thompson J, Biller S, Coe A . Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus. Science. 2014; 344(6182):416-20. DOI: 10.1126/science.1248575. View

Buffie C, Pamer E . Microbiota-mediated colonization resistance against intestinal pathogens. Nat Rev Immunol. 2013; 13(11):790-801. PMC: 4194195. DOI: 10.1038/nri3535. View

Janssen P, Yates P, Grinton B, Taylor P, Sait M . Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia. Appl Environ Microbiol. 2002; 68(5):2391-6. PMC: 127570. DOI: 10.1128/AEM.68.5.2391-2396.2002. View

. Structure, function and diversity of the healthy human microbiome. Nature. 2012; 486(7402):207-14. PMC: 3564958. DOI: 10.1038/nature11234. View

Swan B, Martinez-Garcia M, Preston C, Sczyrba A, Woyke T, Lamy D . Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean. Science. 2011; 333(6047):1296-300. DOI: 10.1126/science.1203690. View

Rupnik M, Wilcox M, Gerding D . Clostridium difficile infection: new developments in epidemiology and pathogenesis. Nat Rev Microbiol. 2009; 7(7):526-36. DOI: 10.1038/nrmicro2164. View

Rideout J, He Y, Navas-Molina J, Walters W, Ursell L, Gibbons S . Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences. PeerJ. 2014; 2:e545. PMC: 4145071. DOI: 10.7717/peerj.545. View

Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova N . A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature. 2009; 462(7276):1056-60. PMC: 3073058. DOI: 10.1038/nature08656. View

10.

Delmont T, Prestat E, Keegan K, Faubladier M, Robe P, Clark I . Structure, fluctuation and magnitude of a natural grassland soil metagenome. ISME J. 2012; 6(9):1677-87. PMC: 3498926. DOI: 10.1038/ismej.2011.197. View

11.

Fierer N, Leff J, Adams B, Nielsen U, Bates S, Lauber C . Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc Natl Acad Sci U S A. 2012; 109(52):21390-5. PMC: 3535587. DOI: 10.1073/pnas.1215210110. View

12.

Pham V, Kim J . Cultivation of unculturable soil bacteria. Trends Biotechnol. 2012; 30(9):475-84. DOI: 10.1016/j.tibtech.2012.05.007. View

13.

Wang Q, Garrity G, Tiedje J, Cole J . Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007; 73(16):5261-7. PMC: 1950982. DOI: 10.1128/AEM.00062-07. View

14.

da Rocha U, van Overbeek L, van Elsas J . Exploration of hitherto-uncultured bacteria from the rhizosphere. FEMS Microbiol Ecol. 2009; 69(3):313-28. DOI: 10.1111/j.1574-6941.2009.00702.x. View

15.

Stepanauskas R . Single cell genomics: an individual look at microbes. Curr Opin Microbiol. 2012; 15(5):613-20. DOI: 10.1016/j.mib.2012.09.001. View

16.

Fierer N, Ladau J, Clemente J, Leff J, Owens S, Pollard K . Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States. Science. 2013; 342(6158):621-4. DOI: 10.1126/science.1243768. View

17.

Gawad C, Koh W, Quake S . Single-cell genome sequencing: current state of the science. Nat Rev Genet. 2016; 17(3):175-88. DOI: 10.1038/nrg.2015.16. View

18.

Gilbert J, Jansson J, Knight R . The Earth Microbiome project: successes and aspirations. BMC Biol. 2014; 12:69. PMC: 4141107. DOI: 10.1186/s12915-014-0069-1. View

19.

Rinke C, Schwientek P, Sczyrba A, Ivanova N, Anderson I, Cheng J . Insights into the phylogeny and coding potential of microbial dark matter. Nature. 2013; 499(7459):431-7. DOI: 10.1038/nature12352. View

20.

Hultman J, Waldrop M, Mackelprang R, David M, McFarland J, Blazewicz S . Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes. Nature. 2015; 521(7551):208-12. DOI: 10.1038/nature14238. View