Rachel Dutton

• PhD
• Fellow at Harvard University

Diverse populations of bacteriophages infect and coevolve with their bacterial hosts. Although host recognition and infection occur within microbiomes, the molecular mechanisms underlying host–phage interactions within a community context remain poorly studied. The biofilms (rinds) of aged cheeses contain taxonomically diverse microbial communities...

Diverse populations of bacteriophages infect and co-evolve with their bacterial hosts. Although host recognition and infection occurs within microbiomes, the molecular mechanisms underlying host-phage interactions within a community context remain poorly studied. The biofilms (rinds) of aged cheeses contain taxonomically diverse microbial communiti...

Bacterial-fungal interactions (BFIs) can shape the structure of microbial communities, but the small molecules mediating these BFIs are often understudied. We explored various optimization steps for our microbial culture and chemical extraction protocols for bacterial-fungal co-cultures, and liquid chromatography-tandem mass spectrometry (LC-MS/MS)...

Bacterial-fungal interactions (BFIs) can shape the structure of microbial communities, but the small molecules mediating these BFIs are often understudied. We explored various optimization steps for our microbial culture and chemical extraction protocols for bacterial-fungal co-cultures, and liquid chromatography-tandem mass spectrometry (LC-MS/MS)...

Human untargeted metabolomics studies annotate only ~10% of molecular features. We introduce reference-data-driven analysis to match metabolomics tandem mass spectrometry (MS/MS) data against metadata-annotated source data as a pseudo-MS/MS reference library. Applying this approach to food source data, we show that it increases MS/MS spectral usage...

Although metals are essential for the molecular machineries of life, systematic methods for discovering metal–small molecule complexes from biological samples are limited. Here, we describe a two-step native electrospray ionization–mass spectrometry method, in which post-column pH adjustment and metal infusion are combined with ion identity molecul...

Genomics and metabolomics are widely used to explore specialized metabolite diversity. The Paired Omics Data Platform is a community initiative to systematically document links between metabolome and (meta)genome data, aiding the identification of natural product biosynthetic origins and metabolite structures.

Microbial interactions are expected to be major determinants of microbiome structure and function. Although fungi are found in diverse microbiomes, their interactions with bacteria remain largely uncharacterized. In this work, we characterize interactions in 16 different bacterial–fungal pairs, examining the impacts of 8 different fungi isolated fr...

The human metabolome has remained largely unknown, with most studies annotating ~10% of features. In nucleic acid sequencing, annotating transcripts by source has proven essential for understanding gene function. Here we generalize this concept to stool, plasma, urine and other human metabolomes, discovering that food-based annotations increase the...

Microbial interactions are major determinants in shaping microbiome structure and function. Characterization of these interactions is not only essential to improve our understanding of microbiome ecology and microbiology in general, but also to identify novel molecules or processes with potential biotechnological applications. Interkingdom interact...

Gas chromatography-mass spectrometry (GC-MS) represents an analytical technique with significant practical societal impact. Spectral deconvolution is an essential step for interpreting GC-MS data. No public GC-MS repositories that also enable repository-scale analysis exist, in part because deconvolution requires significant user input. We therefor...

Microbial community structure and function rely on complex interactions whose underlying molecular mechanisms are poorly understood. To investigate these interactions in a simple microbiome, we introduced E. coli into an experimental community based on a cheese rind and identified the differences in E. coli’ s genetic requirements for growth in int...

Genome information. (a) Genome statistics for newly sequenced genomes, determined by IMG/ER. Gene IDs refer to IMG bioproject or RefSeq Accession. Genomes from Almeida et. al. do not yet have accession numbers. (b) Pairwise species comparison summary total. Protein coding sequences (column ‘Shared CDS’) and nucleotides (in base-pairs - column ‘Shar...

Acquisition of genes through horizontal gene transfer (HGT) allows microbes to rapidly gain new capabilities and adapt to new or changing environments. Identifying widespread HGT regions within multispecies microbiomes can pinpoint the molecular mechanisms that play key roles in microbiome assembly. We sought to identify horizontally transferred ge...

Mock communities are an important tool for validating, optimizing, and comparing bioinformatics methods for microbial community analysis. We present mockrobiota, a public resource for sharing, validating, and documenting mock community data resources, available at http://caporaso-lab.github.io/mockrobiota/ . The materials contained in mockrobiota i...

Importance: Decades of culture-based studies and more recent metagenomic studies have demonstrated that bacterial species in agriculture, medicine, industry, and nature are unevenly distributed across time and space. The ecological processes and molecular mechanisms that shape these distributions are not well understood because it is challenging t...

Gene clusters identified by pan-genome analysis pipeline (PGAP) present in all strains from each species.

Abiotic niche assays for more strains of each Staphylococcus species. Heat maps represent the growth of each strain across a gradient of salt and pH values as measured by OD600 after 48 h. Data for BC9, BC4, and BC10 are presented in more detail in Fig. 2. Data represent means of results of 3 replicates. Figure S1 relates to Fig. 2. Download

(A) The thiamine biosynthesis pathway. The part of the pathway highlighted with thick lines was differentially expressed (green = increased expression, red = decreased expression) in S. equorum grown with fungi. Small yellow boxes indicate if differential expression was observed with just Penicillium (P), with just Scopulariopsis (S), or with both...

Metabolites detected in cheese curd agar (CCA) with and without Scopulariopsis by the use of capillary electrophoresis-time of flight mass spectrometry (CE-TOF MS) and liquid chromatography-time of flight mass spectrometry (LT-TOF MS).

Spearman’s rank correlation coefficients of relative abundances of Staphylococcus species (from shotgun metagenomic data) and relative abundances of other members of the cheese rind community (from amplicon sequencing data). Correlations highlighted in bold are statistically significant (P < 0.01). See Results for discussion of caveats with respect...

Shotgun metagenome metadata and features.

Genome metadata and statistics.

Significantly differentially expressed genes in plus-Penicillium and plus-Scopulariopsis treatments based on results of RNA-seq experiments.

Mock communities are an important tool for validating, optimizing, and comparing bioinformatics methods for microbial community analysis. We present mockrobiota, a public resource for sharing, validating, and documenting mock community data resources, available at https://github.com/caporaso-lab/mockrobiota. The materials contained in mockrobiota i...

Mock communities are an important tool for validating, optimizing, and comparing bioinformatics methods for microbial community analysis. We present mockrobiota, a public resource for sharing, validating, and documenting mock community data resources, available at https://github.com/caporaso-lab/mockrobiota. The materials contained in mockrobiota i...

The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization o...

Multi-omics methods have greatly advanced our understanding of the biological organism and its microbial associates. However, they are not routinely used in clinical or industrial applications, due to the length of time required to generate and analyze omics data. Here, we applied a novel integrated omics pipeline for the analysis of human and envi...

Background : Taxonomic classification of marker-gene (i.e., amplicon) sequences represents an important step for molecular identification of microorganisms. Results : We present three advances in our ability to assign and interpret taxonomic classifications of short marker gene sequences: two new methods for taxonomy assignment, which reduce runtim...

Background : Taxonomic classification of marker-gene (i.e., amplicon) sequences represents an important step for molecular identification of microorganisms. Results : We present three advances in our ability to assign and interpret taxonomic classifications of short marker gene sequences: two new methods for taxonomy assignment, which reduce runtim...

Meat scavenged by early Homo could have contributed importantly to a higher-quality diet. However, it has been suggested that because carrion would normally have been contaminated by bacteria it would have been dangerous and therefore eaten rarely prior to the advent of cooking. In this study, we quantified bacterial loads on two tissues apparently...

Background: Taxonomic classification of marker-gene (i.e., amplicon) sequences represents an important step for molecular identification of microorganisms. Results: We present three advances in our ability to assign and interpret taxonomic classifications of short marker gene sequences: two new methods for taxonomy assignment, which reduce runtime...

Microbial communities of fermented foods have provided humans with tools for preservation and flavor development for thousands of years. These simple, reproducible, accessible, culturable, and easy-to-manipulate systems also provide opportunities for dissecting the mechanisms of microbial community formation. Fermented foods can be valuable models...

In bacteria, disulfide bonds confer stability on many proteins exported to the cell envelope or beyond. These proteins include numerous bacterial virulence factors, and thus bacterial enzymes that promote disulfide bond formation represent targets for compounds inhibiting bacterial virulence. Here, we describe a new target- and cell-based screening...

Tractable microbial communities are needed to bridge the gap between observations of patterns of microbial diversity and mechanisms that can explain these patterns. We developed cheese rinds as model microbial communities by characterizing in situ patterns of diversity and by developing an in vitro system for community reconstruction. Sequencing of...

Long-term dietary intake influences the structure and activity of the trillions of microorganisms residing in the human gut, but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change. Here we show that the short-term consumption of diets composed entirely of animal or plant products alt...

Towards an Ecosystem Approach to Cheese Microbiology, Page 1 of 2 Abstract While microbes have traditionally been studied as individuals in the laboratory, they exist not as individuals in nature but as parts of complex, multispecies communities. Microbial communities have long been acknowledged as crucial for the proper functioning of our global...

Microorganisms such as bacteria and fungi produce a variety of specialized metabolites that are invaluable for agriculture, biological research, and drug discovery. However, the screening of microbial metabolic output is usually a time intensive task. Here we utilize a liquid micro-junction surface sampling probe for electrospray ionization mass sp...

Humans harbor microbial communities throughout the gastrointestinal tract that both respond to and modify orally ingested macronutrients, bioactive compounds, and xenobiotics; for example, the metabolism of polyphenols, heterocyclic amines, and phosphatidylcholine. However, the composition and physiological impact of our diet is also linked to the...

Escherichia coli uses the DsbA/DsbB system for introducing disulphide bonds into proteins in the cell envelope. Deleting either dsbA or dsbB or both reduces disulphide bond formation but does not entirely eliminate it. Whether such background disulphide bond forming activity is enzyme-catalysed is not known. To identify possible cellular factors th...

Unlabelled: The Escherichia coli membrane protein DsbD functions as an electron hub that dispatches electrons received from the cytoplasmic thioredoxin system to periplasmic oxidoreductases involved in protein disulfide isomerization, cytochrome c biogenesis, and sulfenic acid reduction. Here, we describe a new class of DsbD proteins, named ScsB,...

CcscsC can complement the mucoid phenotype in dsbC mdoG E. coli. (A) Sequence alignment of CcScsC and EcDsbC using BLAST. The letters in yellow boxes in the alignment indicate Cys–Xaa–Xaa–Cys and cis-Pro regions in the active sites of the Trx family. The box lined in red shows the big mismatches of the two proteins in their N termini. EcDsbC and Cc...

Distribution of DsbD, CcdA, ScsB, ScsC, PprX, and PrxL from 529 bacteria.

Supplemental materials and methods. Download Text S1, DOC file, 0.1 MB.

Prediction of the electron donor of PprX. (A) Thioredoxin-like proteins predicted to be exported in C. crescentus. CC0374, CC0375, CC1879, and CC0220 are already described in the main text. For the others, we used the sequences of known thioredoxin-like proteins as queries for BLAST analysis. Their potential export to the envelope was predicted by...

In vivo redox states of CcScsC and EcDsbC (A) and PprX (B) expressed in the dsbD E. coli strain. As indicated, additional wild-type or cysteine-mutant EcDsbD or CcScsB was expressed. Cells were induced by 0.2% l-arabinose for pdsbD (pEJS92) and pscsB (pSC27) and by 10 µM IPTG for expression of CcScsC (pSC129) and pSC127 (PprX). (A) Strains transfor...

Strains and plasmids (A) and primers (B) used in this study.

Amino acid sequence analyses of ScsB and DsbD. Sequence alignments of ScsB (A), DsbD (B), and ScsBα (C). The alignments were performed using ClustalW (http://www.ebi.ac.uk/Tools/msa/clustalw2/). In panels A and B, two putative reactive cysteines in each domain are indicated in red and bold on top of the alignments. Putative linker regions separate...

Prediction of substrate proteins of CcScsB. Sequence alignment of Salmonella Typhimurium ScsC (StScsC) and EcDsbG (A), and that of EcDsbC and StScsC (B) using BLAST analyses. (C) STRING analysis of CcScsB (http://string-db.org/). CC0220, CC1879, and CC1673 are indicated as PrxL, ScsC, and PprX in red, respectively. Download Figure S2, PDF file, 0.5...

Essentiality of ScsB in C. crescentus and complementation by Rhodobacter capsulatus CcdA (RcCcdA). The C. crescentus scsB deletion strain could be obtained only in the presence of a complementing plasmid, suggesting that scsB is essential in that bacterium. Note that the plasmid used to generate the mutant strain has a chloramphenicol (Cm) resistan...

CcScsC forms a homodimer. (A) Secondary structure prediction of EcDsbC, CcScsC, and StScsC using PSIPRED (http://bioinf.cs.ucl.ac.uk/psipred/). The boxes lined in red indicate the dimerization domain of DsbC and the putative one of CcScsC. The boxes lined in light green shows Cys–Xaa–Xaa–Cys and cis-Pro regions in the active sites of thioredoxin do...

The temporal and spatial expression of late flagellar genes in Caulobacter crescentus is activated by the transcription factor FlbD and its partner trans-acting factor FliX. The physical interaction of these two proteins represents an alternative mechanism for regulating the activity of σ54 transcription factors. This study is to characterize the i...

The hydrothermal vent clam Calyptogena magnifica (Bivalvia: Mollusca) is a member of the Vesicomyidae. Species within this family form symbioses with chemosynthetic Gammaproteobacteria. They exist in environments such as hydrothermal vents and cold seeps and have a rudimentary gut and feeding groove, indicating a large dependence on their endosymbi...

We have presented evidence that a homologue of vertebrate membrane protein vitamin K epoxide reductase (VKOR) is an important component of the protein disulfide bond-forming pathway in many bacteria. Bacterial VKOR appears to take the place of the nonhomologous DsbB found in Escherichia coli. We also determined the structure of a VKOR from a Cyanob...

Vitamin K epoxide reductase (VKOR) generates vitamin K hydroquinone to sustain gamma-carboxylation of many blood coagulation factors. Here, we report the 3.6 A crystal structure of a bacterial homologue of VKOR from Synechococcus sp. The structure shows VKOR in complex with its naturally fused redox partner, a thioredoxin-like domain, and correspon...

Blood coagulation in humans requires the activity of vitamin K epoxide reductase (VKOR), the target of the anticoagulant warfarin (Coumadin). Bacterial homologs of VKOR were recently found to participate in a pathway leading to disulfide bond formation in secreted proteins of many bacteria. Here we show that the VKOR homolog from the bacterium Myco...

Protein disulfide bond formation contributes to the folding and activity of many exported proteins in bacteria. However, information about disulfide bond formation is limited to only a few bacterial species. We used a multifaceted bioinformatic approach to assess the capacity for disulfide bond formation across this biologically diverse group of or...

The Chlamydia family of human pathogens uses outer envelope proteins that are highly cross-linked by disulfide bonds but nevertheless keeps an unusually high number of unpaired cysteines in its secreted proteins. To gain insight into chlamydial disulfide bond catalysis, the structure, function, and substrate interaction of a novel periplasmic oxido...

Chemoautotrophic endosymbionts are the metabolic cornerstone of hydrothermal vent communities, providing invertebrate hosts with nearly all of their nutrition. The Calyptogena magnifica (Bivalvia: Vesicomyidae) symbiont, Candidatus Ruthia magnifica, is the first intracellular sulfur-oxidizing endosymbiont to have its genome sequenced, revealing a s...

During Bacillus subtilis sporulation, SpoIIIE is required for translocation of the trapped forespore chromosome across the sporulation septum, for compartmentalization of cell-specific gene expression, and for membrane fusion after engulfment. We isolated mutations within the SpoIIIE membrane domain that block localization and function. One mutant...

In Caulobacter crescentus, the temporal and spatial expression of late flagellar genes is regulated by the sigma54 transcriptional activator, FlbD. Genetic experiments have indicated that the trans-acting factor FliX regulates FlbD in response to the progression of flagellar assembly, repressing FlbD activity until an early flagellar basal body str...

The expression of the flagellin proteins in Caulobacter crescentus is regulated by the progression of flagellar assembly both at the transcriptional and post-transcriptional levels. An early basal body structure is required for the transcription of flagellin genes, whereas the ensuing assembly of a hook structure is required for flagellin protein s...