Microbial 'omics

 

2017

The global biogeography of amino acid variants within a single SAR11 population is governed by natural selection.

Delmont, T. O., Kiefl, E., Kilinc, O., Esen, Ö. C., Uysal, I., Rappé, M. S., Giovannoni, S., and Eren, A. M.
- Using single-amino acid variants to investigate genome variation within a single SAR11 population across large geographies.
- Application of a novel Deep Learning algorithm to resolve relationships between metagenomes through complex SAAV data.
- Partitioning of SAAVs suggests natural selection, rather than neutral evolution, is the main driver of the evolution of SAR11.
BioRxiv. pre-print

Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in the surface ocean.

Delmont, T. O., Quince, C., Shaiber, A., Esen, Ö. C., Lee, S. T. M., Lücker, S., and Eren, A. M.
- Novel nitrogen-fixing populations (see public data).
- Nearly 1,000 non-redundant and high-quality bacterial, archaeal, and eukaryotic population genomes from TARA Oceans metagenomes.
- Extensive description of bioinformatics approaches.
BioRxiv. pre-print

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Bowers, R. M., Kyrpides, N. C., Stepanauskas, R., Harmon-Smith, M., Doud, D., Reddy, TBK., Schulz, F., Jarett, J., Rivers, A. R., Eloe-Fadrosh, E. A., Tringe, S. G., Ivanova, N. N., Copeland, A., Clum, A., Becraft, E. D., Malmstrom, R. R., Birren, B., Podar, M., Bork, P., Weinstock, G. M., Garrity, G. M., Dodsworth, J. A., Yooseph, S., Sutton, G., Glöckner, F. O., Gilbert, J. A., Nelson, W. C., Hallam, S. J., Jungbluth, S. P., Ettema, G., Tighe, S., Konstantinidis, K. T., Liu, W., Baker, B. J., Rattei, T., Eisen, J. A., Hedlund, B., McMahon, K. D., Fierer, N., Knight, R., Finn, R., Cochrane, G., Karsch-Mizrachi, I., Tyson, G. W., Rinke, C., Lapidus, A., Meyer, F., Yilmaz, P., Parks, D. H., Eren, A. M., Schriml, L., Banfield, J. F., Hugenholtz, P., Woyke, T. Nature Biotechnology. 35:725–731

Peripartum Antibiotics Promote Gut Dysbiosis, Loss of Immune Tolerance, and Inflammatory Bowel Disease in Genetically Prone Offspring.

Miyoshi, J., Bobe, A. M., Miyoshi, S., Huang, Y., Hubert, N., Delmont, T. O., Eren, A. M., Leone, V., and Chang, E. B.
- Antibiotics during pregnancy promote offspring gut dysbiosis, immune dysfunction, and IBD.
- Antibiotics given after the developmental period do not increase IBD.
- Antibiotic-perturbed maternal microbiota likely contribute to neonatal gut dysbiosis.
- Press release.
Cell Reports. 20:2

Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics.

Lee, S. T. M., Kahn, S. A., Delmont, T. O., Shaiber, A., Esen, Ö. C., Hubert, N. A., Morrison, H. G., Antonopoulos, D. A., Rubin, D. T., and Eren, A. M.
- An FMT study with metagenome-assembled genomes (see public data).
- 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 importance of high-resolution analyses.
- Populations colonized both recipients were also prevalent in the HMP cohort (and the ones that did not, distribute sporadically across the HMP cohort).
Microbiome. 5:50

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

 

2016

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

 

2015

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

 

2014

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

 

2013

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