This page shows publications that are most reflective of our interests. For a complete list, please see Meren’s Google Scholar page.
2021
Adaptive ecological processes and metabolic independence drive microbial colonization and resilience in the human gut
- A Fecal Microbiota Transplantation (FMT) study that reveals unexpected parallels between the adaptive ecological processes that shape the recipient gut microbial composition after FMT and those that influence microbial diversity in patients with Inflammatory Bowel Disease (IBD).
- Includes an observation that links the presence of superior metabolic competence in bacterial populations to their expansion in IBD.
- Here is a Twitter thread that explains key points of the study.
- Includes an observation that links the presence of superior metabolic competence in bacterial populations to their expansion in IBD.
- Here is a Twitter thread that explains key points of the study.
High molecular weight DNA extraction strategies for long-read sequencing of complex metagenomes
- A study that benchmarks six high molecular weight DNA extraction strategies (commercially available kits, phenol-chloroform extraction, and agarose encasement followed by agarase digestion) for long-read sequencing of metagenomes with MinION.
- It turns out the protocol that works best for sequencing DNA from microbial isolates may not be the most effetive method for long-read sequencing of metagenomes ¯\_(ツ)_/¯
- It turns out the protocol that works best for sequencing DNA from microbial isolates may not be the most effetive method for long-read sequencing of metagenomes ¯\_(ツ)_/¯
2020
Community-led, integrated, reproducible multi-omics with anvi'o
- A summary of the progress of anvi'o during the past five years.
Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome
- A multi-omics study that combines genome-resolved metagenomics, pangenomics, phylogenomics, and microbial population genetics to investigate the ecology and evolution of Saccharibacteria (TM7) in the human oral cavity, and offers a formal description of 'functional enrichment' statistic for phylogenomics and pangenomics.
- Demonstrates that TM7s split into tongue specialists and plaque specialists, and plaque TM7s group with environmental TM7s, leading to an hypothesis that the dental plaque may have served as a stepping stone for environmental microbes to adapt to host environments at least for some clades of microbes
- A news article by Alison Caldwell, PhD: Microbes in dental plaque look more like relatives in soil than those on the tongue.
- Public raw and intermediate data. Reviewer comments and responses.
- Demonstrates that TM7s split into tongue specialists and plaque specialists, and plaque TM7s group with environmental TM7s, leading to an hypothesis that the dental plaque may have served as a stepping stone for environmental microbes to adapt to host environments at least for some clades of microbes
- A news article by Alison Caldwell, PhD: Microbes in dental plaque look more like relatives in soil than those on the tongue.
- Public raw and intermediate data. Reviewer comments and responses.
Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity
- An application of metapangenomics that links the gene pool of two major oral microbial taxa, Haemophilus parainfluenzae and the genus Rothia, to their ecology using the Human Microbiome Project metageonomes generated from tongue, buccal mucosa, and dental plaque samples.
- Reveals that seemingly generalist organisms are composed of cryptic subpopulations with distinct ecology that is associated with only a small number of genes.
- Reviewer comments and responses. Reproducible bioinformatics workflow.
- Reveals that seemingly generalist organisms are composed of cryptic subpopulations with distinct ecology that is associated with only a small number of genes.
- Reviewer comments and responses. Reproducible bioinformatics workflow.
Droplet-based high-throughput cultivation for accurate screening of antibiotic resistant gut microbes
- An aneorobic microfluidics platform for high-throughput cultivation of microbes that grows single microbial cells in millions of picoliter droplets.
- Populations of gut microbes that compete poorly in plates grow well in droplets regardless of culture media. Furthermore, taxonomic profile of droplets resembles droplets much better than plate scrapings even at the level of oligotypes.
- Demonstrates that not detecting microbes in plate-based screening of antibiotic resistance may not mean that the original sample does not contain microbes resistant to antibiotics.
- Populations of gut microbes that compete poorly in plates grow well in droplets regardless of culture media. Furthermore, taxonomic profile of droplets resembles droplets much better than plate scrapings even at the level of oligotypes.
- Demonstrates that not detecting microbes in plate-based screening of antibiotic resistance may not mean that the original sample does not contain microbes resistant to antibiotics.
Accurate and complete genomes from metagenomes
- A review on genome-resolved metagenomics that discusses the importance of using assembly and careful binning strategies to study metagenomes.
- Case studies include a demonstration of how single-copy core genes can fail to predict the quality of metagenome-assembled genomes, and automated strategies that yield tens of thousands of metagenome-assembled genomes will include extensive contamination.
- Promotes approaches to reconstruct 'complete' genomes from metagenomes and the use of GC skew as a metric for checking genome correctness.
- Tutorial on scaffold extension and gap closing, reproducible workflow for binning and phylogenomics of a Parcubacterium genome from human blood metagenomes.
- Case studies include a demonstration of how single-copy core genes can fail to predict the quality of metagenome-assembled genomes, and automated strategies that yield tens of thousands of metagenome-assembled genomes will include extensive contamination.
- Promotes approaches to reconstruct 'complete' genomes from metagenomes and the use of GC skew as a metric for checking genome correctness.
- Tutorial on scaffold extension and gap closing, reproducible workflow for binning and phylogenomics of a Parcubacterium genome from human blood metagenomes.
2019
Single-amino acid variants reveal evolutionary processes that shape the biogeography of a global SAR11 subclade
- A study that introduces 'single-amino acid variants' (SAAVs) and demonstrates the use of SAAVs to tease apart evolutionary processes that shape the biogeography and genomic heterogeneity within a SAR11 population through metagenomics.
- A first attempt to link population genetics and the predicted protein structures to explore in silico the intersection beetween protein biochemistry and evolutionary processes acting on an environmental microbe.
- An application of metapangenomics to define subclades of SAR11 based on gene content and ecology.
- Reproducible bioinformatics workflow is here. Reviewer criticism and our responses are also available.
- A first attempt to link population genetics and the predicted protein structures to explore in silico the intersection beetween protein biochemistry and evolutionary processes acting on an environmental microbe.
- An application of metapangenomics to define subclades of SAR11 based on gene content and ecology.
- Reproducible bioinformatics workflow is here. Reviewer criticism and our responses are also available.
Composite Metagenome-Assembled Genomes Reduce the Quality of Public Genome Repositories
- A letter that stresses that the composite metagenome-assembled genomes influence phylogenomic, pangenomic, and ecological insights (peer reviews and responses).
- A reproducible workflow to detail the steps of genome refinement and make available the refined versions of some key genomes.
- A reproducible workflow to detail the steps of genome refinement and make available the refined versions of some key genomes.
The Wolbachia mobilome in Culex pipiens includes a putative plasmid
- The first report of a Wolbachia plasmid through genome-resolved metagenomics on microsurgically removed individual mosquito ovary samples (peer reviews and responses).
- Yet another application of metapangenomics and an applicatoin of minION long-read sequencing on extremely low-biomass samples.
- Reproducible bioinformatics workflow with all data items, a 'behind the paper' blog post by Julie Reveillaud, and a press release from the Marine Biological Laboratory.
- Yet another application of metapangenomics and an applicatoin of minION long-read sequencing on extremely low-biomass samples.
- Reproducible bioinformatics workflow with all data items, a 'behind the paper' blog post by Julie Reveillaud, and a press release from the Marine Biological Laboratory.
Genome-resolved insights into a novel Spiroplasma symbiont of the Wheat Stem Sawfly (Cephus cinctus)
- A study that uses (1) genome-resolved metagenomics to reconstruct a population genome from fly metagenomes that resolves to the genus Spiroplasma, (2) pangenomics to put this genome in the context of other Spiroplasma genomes, (3) phylogenomics to infer ancestral relationships between Spiroplasma genomes, and (4) includes an ANI-based distance estimation between all genomes for comprehensive reporting.
- It is a particularly good example that demonstrates how pangenomics can reveal appropriate targets for high-resolution phylogenomics.
- A fully reproducible bioinformatics workflow for this multi'omics analysis is here. Anvi'o databases to interactively reproduce and explore the Spiroplasma pangenome is also available.
- It is a particularly good example that demonstrates how pangenomics can reveal appropriate targets for high-resolution phylogenomics.
- A fully reproducible bioinformatics workflow for this multi'omics analysis is here. Anvi'o databases to interactively reproduce and explore the Spiroplasma pangenome is also available.
Global phylogeography and ancient evolution of the widespread human gut virus crAssphage
- A monumental effort lead by Rob Edwards and Bas Dutilh to explore with the help of 114 scientists from around the world the global phylogeorgraphy and evolution of crAssphage, one of the most numerous viruses in the human gut that infect bacteria.
- A curated list of press coverage of this study is available on Rob Edwards' web site.
- A curated list of press coverage of this study is available on Rob Edwards' web site.
Co-occurring genomic capacity for anaerobic methane and dissimilatory sulfur metabolisms discovered in the Korarchaeota
- Yesllowstone National Park, archaeal evolution, genome-resolved metagenomics, phylogenomics, and pangenomics (cool stuff all over).
- First description of a microbial population with both anaerobic methane and dissimilatory sulfur metabolisms.
- A news article by Montana State University with the photographs of cools scientists: An organism in Yellowstone hot spring potentially linked to earliest life on Earth"
- First description of a microbial population with both anaerobic methane and dissimilatory sulfur metabolisms.
- A news article by Montana State University with the photographs of cools scientists: An organism in Yellowstone hot spring potentially linked to earliest life on Earth"
Transcriptome-wide reprogramming of N 6-methyladenosine modification by the mouse microbiome
- N6-methyladenosine (m6A) is the most abundant mesenger RNA modification in mammalian cells, occurring at ~3 modified adenosine residues per transcript.
- Using liquid chromatography/mass spectrometry, this study shows differential occurrence of m6A modifications in brain, liver, and intestinal cells between germ-free and conventional mice, demonstrating that the microbiome has a strong effect on host m6A mRNA modification.
- Using liquid chromatography/mass spectrometry, this study shows differential occurrence of m6A modifications in brain, liver, and intestinal cells between germ-free and conventional mice, demonstrating that the microbiome has a strong effect on host m6A mRNA modification.
B cell superantigens in the human intestinal microbiota
Science Translational Medicine, 11(507):eaau9356 🔗2018
Microbiome characterization by high-throughput transfer RNA sequencing and modification analysis
- First application of tRNA sequencing to microbiomes (peer reviews and responses).
- tRNA-seq distinguishes high-fat- and low-fat-fed mice in a comparable fashion to 16S rRNA gene amplicons, reveals taxon- and diet-dependent variations in tRNA modifications, and provides in situ insights into tRNA gene expression dynamics and post-transcriptional modifications.
- "New RNA sequencing strategy provides insight into microbiomes", by Matt Wood.
- "RNA sequencing offers novel insights into the microbiome", by Liji Thomas, MD, and Kate Anderton, B.Sc.
- tRNA-seq distinguishes high-fat- and low-fat-fed mice in a comparable fashion to 16S rRNA gene amplicons, reveals taxon- and diet-dependent variations in tRNA modifications, and provides in situ insights into tRNA gene expression dynamics and post-transcriptional modifications.
- "New RNA sequencing strategy provides insight into microbiomes", by Matt Wood.
- "RNA sequencing offers novel insights into the microbiome", by Liji Thomas, MD, and Kate Anderton, B.Sc.
Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes
- 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.
- 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.
Linking pangenomes and metagenomes: the Prochlorococcus metapangenome
- A big-data study in which a pangenome of 31 Prochlorococcus isolates meets 31 billion Tara Oceans metagenomic sequences (Peer-review history).
- 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.
- 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.
Gut microbes contribute to variation in solid organ transplant outcomes in mice
- 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".
- 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".
Microbial signals drive pre-leukaemic myeloproliferation in a Tet2-deficient host
- 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.
- ScienceDaily: Under certain conditions, bacterial signals set the stage for leukemia.
2017
Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics
- 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).
- 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).
Simulations predict microbial responses in the environment? This environment disagrees retrospectively
- 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.
- 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.
Genomic variation in microbial populations inhabiting the marine subseafloor at deep-sea hydrothermal vents
Nature Communications, 8(1):1114 🔗DESMAN: a new tool for de novo extraction of strains from metagenomes
Genome Biology, 18(1):181 🔗Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
Nature biotechnology, 35(8):725 🔗Peripartum antibiotics promote gut dysbiosis, loss of immune tolerance, and inflammatory bowel disease in genetically prone offspring
- 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.
- Antibiotics given after the developmental period do not increase IBD.
- Antibiotic-perturbed maternal microbiota likely contribute to neonatal gut dysbiosis.
- Press release.
2016
Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies
- 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.
- 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.
Patient-specific bacteroides genome variants in pouchitis
mBio, 7(6):e01713-16 🔗New insights into microbial ecology through subtle nucleotide variation
Frontiers in microbiology, 7:1318 🔗Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes
FEMS Microbiology Reviews, 40(5):686-700 🔗2015
Anvi’o: an advanced analysis and visualization platform for ‘omics data
- 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.
- 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.
Minimum entropy decomposition: unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences
The ISME Journal, 9(4):968 🔗A single genus in the gut microbiome reflects host preference and specificity
The ISME Journal, 9(1):90 🔗Reconstructing rare soil microbial genomes using in situ enrichments and metagenomics
- 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.
- 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.