Microbial 'omics



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

Delmont, T. O., Quince, C., Shaiber, A., Esen, Ö. C., Lee, S. T. M., Rappé, M. S., McLellan, S. L., Lücker, S., and Eren, A. M.
- First genomic evidence for abundant and widespread non-cyanobacterial nitrogen-fixing populations in the surface ocean.
- Nearly 1,000 non-redundant, high-quality bacterial, archaeal, and eukaryotic population genomes from TARA Oceans metagenomes.
- A "behind the paper" blog post by Meren, a press release by the MBL, and an extensive description of the bioinformatics workflow.
Nature Microbiology. 3:804–813

Linking pangenomes and metagenomes: the Prochlorococcus metapangenome.

Delmont, T. O., and Eren, A. M.
- A big-data study in which a pangenome of 31 Prochlorococcus isolates meets 31 billion Tara Oceans metagenomic sequences.
- Metapangenomes reveal to what extent genes that may be linked to the ecology and fitness of microbes are conserved within a phylogenetic clade.
- Reproducible bioinformatics workflow: http://merenlab.org/data/2018_Delmont_and_Eren_Metapangenomics/
PeerJ. 6:e4320

Gut microbes contribute to variation in solid organ transplant outcomes in mice.

McIntosh, C. M., Chen, L., Shaiber, A., Eren, A. M., and Alegre, M. L.
- Two groups of genetically identical mice with different microbial community structures differ in their response to skin transplants from genetically identical sources: one group rejects the skin faster than the other.
- Transferring poop from slow-rejecting mice into fast-rejecting mice turns fast-rejecting mice into slow-rejecting mice.
- These suggest that differences in 'resident microbiome' in healthy individuals may contribute to interpersonal variability in graft outcomes, and fecal microbiota transplantation may play a therapeutic role to reverse that phenotype.
- Basically, "we do not have a mechanistic understanding, but this is definitely very interesting".
Microbiome. 6:96

Microbial signals drive pre-leukaemic myeloproliferation in a Tet2-deficient host.

Meisel, M., Hinterleitner, R., Pacis, A., Chen, L., Earley, Z. M., Mayassi, T., Pierre, J. F., Ernest, J. D., Galipeau, H. J., Thuille, N., Bouziat, R., Buscarlet, M., Ringus, D. L., Wang, Y., Li, Y., Dinh, V., Kim, S. M., McDonald, B. D., Zurenski, M. A., Musch, M. W., Furtado, G. C., Lira, S. A., Baier, G., Chang, E. B., Eren, A. M., Weber, C. R., Busque, L., Godley, L. A., Verdú, E. F., Barreiro, L. B., and Jabri, B.
- TET2 deficiency ➡️ deteriorating small intestinal barrier ➡️ bacterial translocation ➡️ incrased IL-6 signalling ➡️ pre-leukemic myeloproliferation (a leukemia precursor).
- ScienceDaily: Under certain conditions, bacterial signals set the stage for leukemia.
Nature. 557:580–584



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

Simulations predict microbial responses in the environment? This environment disagrees retrospectively.

Delmont, T. O., and Eren, A. M.
- A letter that re-analyzes some of the findings published in Hu et al.
- Here is a rebuttal from Probst et al. challenging our findings in this letter.
- Here is our response to Probst et al., and the recovery of DWH O. Desum v2.
Proc Natl Acad Sci U S A. published online before print

Genomic variation in microbial populations inhabiting the marine subseafloor at deep-sea hydrothermal vents.

Anderson, R. E., Reveillaud, J., Reddington, E., Delmont, T. O., Eren, A. M., McDermott, J. M., Seewald, J. S., and Huber, J. A. Nature Communications. 8:1114

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

Recurrent patterns of microdiversity in a temperate coastal marine environment.

Chafee, M., Fernàndez-Guerra, A., Buttigieg, P. L., Gerdts, G., Eren, A. M., Teeling, H., and Amann, R. I. ISME J. 12, 237–252

DESMAN: a new tool for de novo extraction of strains from metagenomes.

Quince, C., Delmont, T. O., Raguideau, S., Alneberg, J., Darling, A. E., Collins, G., and Eren, A. M. Genome Biology. 18:181

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

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



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

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

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

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