Microbial 'omics



Early Transcriptomic Changes in the Ileal Pouch Provide Insight into the Molecular Pathogenesis of Pouchitis and Ulcerative Colitis.

Huang, Y., Dalal, S., Antonopoulos, D., Hubert, N., Raffals, L. H., Dolan, K., Weber, C., Messer, J. S., Jabri, B., Bendelac, A., Eren, A. M., Rubin, D. T., Sogin, M. L., and Chang, E. B. Inflammatory Bowel Disiseases. 23(3):366-378

A Few Pseudomonas Oligotypes Dominate in the Meat and Dairy Processing Environment.

Stellato, G., Utter, D. R., Voorhis, A., De Angelis, M., Eren, A. M., and Ercolini, D. Front Microbiol. 8:264



High-resolution tracking of microbial colonization in Fecal Microbiota Transplantation experiments via metagenome-assembled genomes.

Lee, S. T. M., Kahn, S. A., Delmont, T. O., Hubert, N. A., Morrison, H. G., Antonopoulos, D. A., Rubin, D. T., and Eren, A. M.
- An FMT study with metagenome-assembled genomes (MAGs). Bacteroidales: high-colonization rate, Clostridiales: low colonization rate.
- Colonization success is negatively correlated with the number of genes related to sporulation.
- MAGs with the same taxonomy showed different colonization properties, highlighting the limitation of low-resolution approaches.
BioRxiv. pre-print

Patient-specific Bacteroides genome variants in pouchitis.

Vineis, J. H., Ringus, D. L., Morrison, H. G., Delmont, T. O., Dalal, S., Raffals, L. H., Antonopoulos, D. A., Rubin, D. T., Eren, A. M., Chang, E. B., and Sogin, M. L mBio. 7(6):e01713-16

De novo extraction of microbial strains from metagenomes reveals intra-species niche partitioning.

Quince, C., Connely, S., Raguideau, S., Alneberg, J., Shin, S. G., Collins, G., and Eren, A. M. BioRxiv. pre-print

New insights into microbial ecology through subtle nucleotide variation.

Eren, A. M., Sogin, M. L., and Maignien, L. Front Microbiol. 7:1318

Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes.

Bálint, M., Bahram, M., Eren, A. M., Faust, K., Fuhrman, J. A., Lindahl, B., O'Hara, R. B., Öpik, M., Sogin, M. L., Unterseher, M., and Tedersoo, L. FEMS Microbiology Reviews. na:na

Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies.

Delmont, T. O., and Eren, A. M.
- A holistic approach to visualize and curate genomic and metagenomic assemblies.
- A re-analysis of the first released Tardigrade genome reveals a likely symbiont among other contaminants.
- A practical approach to estimate the number bacterial genomes in an assembly.
PeerJ. 4:e1839

Bacterial communities in penile skin, male urethra, and vaginas of heterosexual couples with and without bacterial vaginosis.

Zozaya, M., Ferris, M. J., Siren, J. D., Lillis, R., Myers, L., Nsuami, M. J., Eren, A. M., Brown, J., Taylor, C. M., and Martin, D. H. Microbiome. 4:16



Anvi’o: An advanced analysis and visualization platform for ‘omics data.

Eren, A. M., Esen, Ö. C., Quince, C., Vineis, J. H., Morrison, H. G., Sogin, M. L., and Delmont, T. O.
- The methods paper for anvi'o.
- Binning, and single-nucleotide variant analysis of a human gut time series metagenome.
- Re-analysis of cultivar genomes, metagenomes, and metatranscriptomes associated with the Deepwater Horizon oil spill.
PeerJ. 6:358

Comparison of sewage and animal fecal microbiomes using oligotyping reveals potential human fecal indicators in multiple taxonomic groups.

Fisher, J. C., Eren, A. M., Green, H. C., Shanks, O. C., Morrison, H. G., Vineis, J. H., Sogin, M. L., and McLellan, S. L. Appl Environ Microbiol. 81, 7023–7033

Reconstructing Rare Soil Microbial Genomes using in situ Enrichments and Metagenomics.

Delmont, T. O., Eren, A. M., Maccario, L., Prestat, E., Esen, Ö. C., Pelletier, E., LePaslier, D., Simonet, P., and Vogel, T.
- Application of in situ enrichments to shape the diversity of complex metagenomes prior to sequencing.
- The first successful attempt to assemble multiple near-complete bacterial genomes directly from a soil sample.
- The abundance of reconstructed genomes ranged from rare (<0.0001%) to relatively abundant (>0.01%) in pristine soil metagenomes.
Front Microbiol. 6:358

A single genus in the gut microbiome reflects host preference and specificity.

Eren, A. M., Sogin, M. L., Morrison, H. G., Vineis, J. H., Fisher, J. C., Newton, R. J., and McLellan, S. L. ISME J. 9(1), 90-100

Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences.

Eren, A. M., Morrison, H. G., Lescault, P. J., Reveillaud, J., Vineis, J. H., and Sogin, M. L. ISME J. 9, 968-79

Sewage reflects the microbiomes of human populations.

Newton, R. J., McLellan, S. L., Dila, D. K., Vineis, J. H., Morrison, H. G., Eren, A. M., and Sogin, M. L. mBio. 6:2

Extensive Modulation of the Fecal Metagenome in Children With Crohn's Disease During Exclusive Enteral Nutrition.

Quince, C., Ijaz, U. Z., Loman, N., Eren, A. M., Saulnier, D., Russell, J., Haig, S. J., Calus, S. T., Quick, J., Barclay, A., Bertz, M., Hansen, R., McGrogan, P., Russel, K. R., Edwards, C. A., and Gerasimidis, K. Am J Gastroenterol. 110:1718–1729



Oligotyping analysis of the human oral microbiome.

Eren, A. M., Borisy, G. G., Huse, S. M., and Mark Welch, J. L. Proc Natl Acad Sci U S A. 111(28), E2875-84

DRISEE overestimates errors in metagenomic sequencing data.

Eren, A. M., Morrison, H. G., Huse, S. M., and Sogin, M. L. Brief Bioinform. 15(5), 783-7

Humpback whale populations share a core skin bacterial community: towards a health index for marine mammals?

Apprill, A., Robbins, J., Eren, A. M., Pack, A. A., Reveillaud, J., Mattila, D., Moore, M., Niemeyer, M., Moore, K. M., and Mincer, T. J. PLoS One. 9(3), e90785

Ecological succession and stochastic variation in the assembly of Arabidopsis thaliana phyllosphere communities.

Maignien, L., DeForce, E. A., Chafee, M. E., Eren, A. M., and Simmons, S. L. MBio. 5(1), e00682-13

SeaBase: a multispecies transcriptomic resource and platform for gene network inference.

Fischer, A. H., Mozzherin, D., Eren, A. M., Lans, K. D., Wilson, N., Cosentino, C., and Smith, J. Integr Comp Biol. 54(2), 250-63

VAMPS: a website for visualization and analysis of microbial population structures.

Huse, S. M., Mark Welch, D. B., Voorhis, A., Shipunova, A., Morrison, H. G., Eren, A. M., and Sogin, M. L. BMC Bioinformatics. 15(1), 41

Blautia and Prevotella sequences distinguish human and animal fecal pollution in Brazil surface waters.

Koskey, A. M., Fisher, J. C., Eren, A. M., Ponce-Terashima, R., Reis, M. G., Blanton, R. E., and McLellan, S. L. Environ Microbiol Rep. 6(6), 696-704

Discovering new indicators of fecal pollution.

McLellan, S. L., and Eren, A. M. Trends Microbiol. 22(12), 697-706

Host-specificity among abundant and rare taxa in the sponge microbiome.

Reveillaud, J., Maignien, L., Eren, A. M., Huber, J. A., Apprill, A., Sogin, M. L., and Vanreusel, A. ISME J. 8(6), 1198-209

Dynamics of tongue microbial communities with single-nucleotide resolution using oligotyping.

Mark Welch, J. L., Utter, D. R., Rossetti, B. J., Mark Welch, D. B., Eren, A. M., and Borisy, G. G. Front Microbiol. 5:568



Oligotyping: Differentiating between closely related microbial taxa using 16S rRNA gene data.

Eren, A. M., Maignien, L., Sul, W. J., Murphy, L. G., Grim, S. L., Morrison, H. G., and Sogin, M. L. Methods Ecol Evol. 4(12)

A filtering method to generate high quality short reads using illumina paired-end technology.

Eren, A. M., Vineis, J. H., Morrison, H. G., and Sogin, M. L. PLoS One. 8(6), e66643

Histamine-2 receptor blockers alter the fecal microbiota in premature infants.

Gupta, R. W., Tran, L., Norori, J., Ferris, M. J., Eren, A. M., Taylor, C. M., Dowd, S. E., and Penn, D. J Pediatr Gastroenterol Nutr. 56(4), 397-400

Sewage reflects the distribution of human faecal Lachnospiraceae.

McLellan, S. L., Newton, R. J., Vandewalle, J. L., Shanks, O. C., Huse, S. M., Eren, A. M., and Sogin, M. L. Environ Microbiol. 15(8), 2213-27

Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis.

Young, V. B., Raffals, L. H., Huse, S. M., Vital, M., Dai, D., Schloss, P. D., Brulc, J. M., Antonopoulos, D. A., Arrieta, R. L., Kwon, J. H., Reddy, K. G., Hubert, N. A., Grim, S. L., Vineis, J. H., Dalal, S., Morrison, H. G., Eren, A. M., Meyer, F., Schmidt, T. M., Tiedje, J. M., Chang, E. B., and Sogin, M. L. Microbiome. 1(1), 9



Exploring the diversity of Gardnerella vaginalis in the genitourinary tract microbiota of monogamous couples through subtle nucleotide variation.

Eren, A. M., Zozaya, M., Taylor, C. M., Dowd, S. E., Martin, D. H., and Ferris, M. J. PLoS One. 6(10), e26732