Open Access Highly Accessed Methodology article

Using phage display selected antibodies to dissect microbiomes for complete de novo genome sequencing of low abundance microbes

Devin W Close1, Fortunato Ferrara2, Armand EK Dichosa1, Sandeep Kumar1, Ashlynn R Daughton1, Hajnalka E Daligault1, Krista G Reitenga1, Nileena Velappan1, Timothy C Sanchez1, Srinivas Iyer1, Csaba Kiss1, Cliff S Han1 and Andrew RM Bradbury1*

  • * Corresponding author: Andrew RM Bradbury amb@lanl.gov

  • † Equal contributors

Author Affiliations

1 Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA

2 New Mexico Consortium, Los Alamos, NM, USA

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BMC Microbiology 2013, 13:270  doi:10.1186/1471-2180-13-270

Published: 27 November 2013

Abstract

Background

Single cell genomics has revolutionized microbial sequencing, but complete coverage of genomes in complex microbiomes is imperfect due to enormous variation in organismal abundance and amplification bias. Empirical methods that complement rapidly improving bioinformatic tools will improve characterization of microbiomes and facilitate better genome coverage for low abundance microbes.

Methods

We describe a new approach to sequencing individual species from microbiomes that combines antibody phage display against intact bacteria with fluorescence activated cell sorting (FACS). Single chain (scFv) antibodies are selected using phage display against a bacteria or microbial community, resulting in species-specific antibodies that can be used in FACS for relative quantification of an organism in a community, as well as enrichment or depletion prior to genome sequencing.

Results

We selected antibodies against Lactobacillus acidophilus and demonstrate a FACS-based approach for identification and enrichment of the organism from both laboratory-cultured and commercially derived bacterial mixtures. The ability to selectively enrich for L. acidophilus when it is present at a very low abundance (<0.2%) leads to complete (>99.8%) de novo genome coverage whereas the standard single-cell sequencing approach is incomplete (<68%). We show that specific antibodies can be selected against L. acidophilus when the monoculture is used as antigen as well as when a community of 10 closely related species is used demonstrating that in principal antibodies can be generated against individual organisms within microbial communities.

Conclusions

The approach presented here demonstrates that phage-selected antibodies against bacteria enable identification, enrichment of rare species, and depletion of abundant organisms making it tractable to virtually any microbe or microbial community. Combining antibody specificity with FACS provides a new approach for characterizing and manipulating microbial communities prior to genome sequencing.

Keywords:
Phage antibodies; Genome completion; Single cell genomics; MDA; Flow cytometry