Biology subjects

Dewhirst, F. E.

Publications and source records attributed to Dewhirst, F. E..

7 recordsLinked to original sources

bioRxiv2026

maniFasta and the AllOralsDB: simplifying construction of comprehensive reference databases for metaproteomics

Metaproteomics aims to capture a taxonomically comprehensive snapshot of proteins in a sample. Design of reference databases is a key aspect of metaproteomic workflows, as these define what is ultimately seen. Databases tailored to focal biomes offer optimal performance, yet their construction often requires drawing on heterogeneous data sources, posing a challenge to reproducibility and documentation. Here we present maniFasta, a tool enabling users to generate standardized, reproducible, and robustly documented protein reference sets from diverse input sources and datatypes. Users provide information on their desired input types and sources, and the output is an integrated database comprising a protein sequence file (FASTA), with harmonized identifiers and standardized headers, and an associated provenance metadata table (manifest). We highlight the value of maniFasta in the context of salivary metaproteomics, addressing the need for a taxonomically comprehensive reference database. The AllOralsDB resource includes human proteins, as well as proteins from bacteria and archaea, fungi and other microeukaryotes, viruses and viroid-like elements, dietary sources, and common contaminants. Together, this work provides a community resource for oral and salivary metaproteomics (https://www.homd.org/ftp/AllOralsDB/), and a versatile and accessible tool for constructing protein databases for metaproteomics generally (https://github.com/KauffmanLab/maniFasta).

microbiology↗

bioRxiv2025

Complete genome sequences of Fusobacterium watanabei sp. isolates

We report the complete genome sequences of eight Fusobacterium watanabei clinical isolates, ranging from 1.95 to 2.09 Mbp. Analysis against the Genome Taxonomy Database (GTDB) indicates that Fusobacterium watanabei genomes are part of the "Fusobacterium nucleatum_J" group, which also encompasses the previously published FNU strain and Fna C1 isolates.

microbiology↗

bioRxiv2023

Fusobacterium sphaericum sp. nov., isolated from a human colon tumor, is prevalent in various human body sites and induces IL-8 secretion from colorectal cancer cells

Cancerous tissue is a largely unexplored microbial niche that provides a unique environment for the colonization and growth of specific bacterial communities, and with it, the opportunity to identify novel bacterial species. Here, we report distinct features of a novel Fusobacterium species, F. sphaericum sp. nov. (Fs), isolated from primary colon adenocarcinoma tissue. We acquire the complete closed genome and associated methylome of this organism and phylogenetically confirm its classification into the Fusobacterium genus, with F. perfoetens as its closest neighbor. Fs is phenotypically and genetically distinct, with morphological analysis revealing its coccoid shape, that while similar to F. perfoetens is rare for most Fusobacterium members. Fs displays a metabolic profile and antibiotic resistance repertoire consistent with other Fusobacterium species. In vitro, Fs has adherent and immunomodulatory capabilities, as it intimately associates with human colon cancer epithelial cells and promotes IL-8 secretion. Analysis of the prevalence and abundance of Fs in >20,000 human metagenomic samples shows that it is a low-prevalence member within human stool with variable relative abundance, found in both healthy controls and patients with colorectal cancer (CRC). Our study sheds light on a novel bacterial species isolated directly from the human CRC tumor niche, and given its interaction with cancer epithelial cells suggests that its role in human health and disease warrants further investigation.

microbiology↗

bioRxiv2022

Phages are important unrecognized players in the ecology of the oral pathogen Porphyromonas gingivalis

BackgroundPorphyromonas gingivalis (hereafter "Pg") is an oral pathogen that can act as a keystone driver of inflammation and periodontal disease. Although Pg is most readily recovered from individuals with actively progressing periodontal disease, healthy individuals and those with stable non-progressing disease are also colonized by Pg. Insights into the factors shaping the striking strain-level variation in Pg, and its variable associations with disease, are needed to achieve a more mechanistic understanding of periodontal disease and its progression. A key force shaping strain level diversity in all microbial communities is infection of bacteria by their viral (phage) predators and symbionts. Surprisingly, although Pg has been the subject of study for over 40 years, essentially nothing is known of its phages, and the prevailing paradigm is that phages are not important in the ecology of Pg. ResultsHere we systematically addressed the question of whether Pg are infected by phages - and we found that they are. We found that prophages are common in Pg, they are genomically diverse, and they encode genes that have the potential to alter Pg physiology and interactions. We found that phages represent unrecognized targets of the prevalent CRISPR-Cas defense systems in Pg, and that Pg strains encode numerous additional mechanistically diverse candidate anti-phage defense systems. We also found that phages and candidate anti-phage defense system elements together are major contributors to strain level diversity and the species pangenome of this oral pathogen. Finally, we demonstrate that prophages harbored by a model Pg strain are active in culture, producing extracellular viral particles in broth cultures. DiscussionThis work definitively establishes that phages are a major unrecognized force shaping the ecology and intraspecies strain-level diversity of the well-studied oral pathogen Pg. The foundational phage sequence datasets and model systems that we establish here add to the rich context of all that is already known about Pg, and point to numerous avenues of future inquiry that promise to shed new light on fundamental features of phage impacts on human health and disease broadly.

microbiology↗

bioRxiv2019

Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets

BackgroundThe low cost of 16S rRNA gene sequencing facilitates population-scale molecular epidemiological studies. Existing computational algorithms can parse 16S rRNA gene sequences to high-resolution Amplicon Sequence Variants (ASVs), which represent consistent labels comparable across studies. Assigning these ASVs to species-level taxonomy strengthens the ecological and/or clinical relevance of 16S rRNA gene-based microbiota studies and further facilitates data comparison across studies. ResultsTo achieve this, we developed a broadly applicable method for constructing high-resolution training sets based on the phylogenic relationships among microbes found in a habitat of interested. When used with the naive Bayesian Ribosomal Database Project (RDP) Classifier, this training set achieved species/supraspecies-level taxonomic assignment of 16S rRNA gene-derived ASVs. The key steps for generating such a training set are: 1) constructing an accurate and comprehensive phylogenetic-based, habitat-specific database; 2) compiling multiple 16S rRNA gene sequences to represent the natural sequence variability of each taxon in the database; 3) trimming the training set to match the sequenced regions, if necessary; and 4) placing species sharing closely related sequences into a supraspecies taxonomic level to preserve subgenus-level resolution. As proof of principle, we developed a V1-V3 region training set for the bacterial microbiota of the human aerodigestive tract using the full-length 16S rRNA gene reference sequences compiled in our expanded Human Oral Microbiome Database (eHOMD). We also overcame technical limitations to successfully use Illumina sequences for the 16S rRNA gene V1-V3 region, the most informative segment for classifying bacteria native to the human aerodigestive tract. Finally, we generated a full-length eHOMD 16S rRNA gene training set, which we used in conjunction with an independent PacBio Single Molecule, Real-Time (SMRT)-sequenced sinonasal dataset to validate the representation of species in our training set. This also established the effectiveness of a full-length training set for assigning taxonomy of long-read 16S rRNA gene datasets. ConclusionHere, we present a systematic approach for constructing a phylogeny-based, high-resolution, habitat-specific training set that permits species/supraspecies-level taxonomic assignment to short- and long-read 16S rRNA gene-derived ASVs. This advancement enhances the ecological and/or clinical relevance of 16S rRNA gene-based microbiota studies.

microbiology↗

bioRxiv2018

New insights into human nostril microbiome from the expanded Human Oral Microbiome Database (eHOMD): a resource for species-level identification of microbiome data from the aerodigestive tract

The expanded Human Oral Microbiome Database (eHOMD) is a comprehensive microbiome database for sites along the human aerodigestive tract that revealed new insights into the nostril microbiome. The eHOMD provides well-curated 16S rRNA gene reference sequences linked to available genomes and enables assignment of species-level taxonomy to most NextGeneration sequences derived from diverse aerodigestive tract sites, including the nasal passages, sinuses, throat, esophagus and mouth. Using Minimum Entropy Decomposition coupled with the RDP Classifier and our eHOMD V1-V3 training set, we reanalyzed 16S rRNA V1-V3 sequences from the nostrils of 210 Human Microbiome Project participants at the species level revealing four key insights. First, we discovered that Lawsonella clevelandensis, a recently named bacterium, and Neisseriaceae [G-1] HMT-174, a previously unrecognized bacterium, are common in adult nostrils. Second, just 19 species accounted for 90% of the total sequences from all participants. Third, one of these 19 belonged to a currently uncultivated genus. Fourth, for 94% of the participants, two to ten species constituted 90% of their sequences, indicating nostril microbiome may be represented by limited consortia. These insights highlight the strengths of the nostril microbiome as a model system for studying interspecies interactions and microbiome function. Also, in this cohort, three common nasal species (Dolosigranulum pigrum and two Corynebacterium species) showed positive differential abundance when the pathobiont Staphylococcus aureus was absent, generating hypotheses regarding colonization resistance. By facilitating species-level taxonomic assignment to microbes from the human aerodigestive tract, the eHOMD is a vital resource enhancing clinical relevance of microbiome studies.\n\nIMPORTANCEThe eHOMD (ehomd.org) is a valuable resource for researchers, from basic to clinical, who study the microbiomes, and the individual microbes, in health and disease of body sites in the human aerodigestive tract, which includes the nasal passages, sinuses, throat, esophagus and mouth, and the lower respiratory tract. The eHOMD is an actively curated, web-based, open-access resource. eHOMD provides the following: (1) species-level taxonomy based on grouping 16S rRNA gene sequences at 98.5% identity, (2) a systematic naming scheme for unnamed and/or uncultivated microbial taxa, (3) reference genomes to facilitate metagenomic, metatranscriptomic and proteomic studies and (4) convenient cross-links to other databases (e.g., PubMed and Entrez). By facilitating the assignment of species names to sequences, the eHOMD is a vital resource for enhancing the clinical relevance of 16S rRNA gene-based microbiome studies, as well as metagenomic studies.

microbiology↗

bioRxiv2018

Cargo Transport Shapes the Spatial Organization of a Microbial Community

The human microbiome is an assemblage of diverse bacteria that interact with one another to form communities. Bacteria in a given community are arranged in a three-dimensional matrix with many degrees of freedom. Snapshots of the community display well-defined structures, but the steps required for their assembly are not understood. Here, we show that this construction is carried out with the help of gliding bacteria. Gliding is defined as the motion of cells over a solid or semi-solid surface without the necessity of growth or the aid of pili or flagella. Genomic analysis suggests that gliding bacteria are present in human microbial communities. We focus on Capnocytophaga gingivalis which is present in abundance in the human oral microbiome. Tracking of fluorescently-labeled single cells and of gas bubbles carried by fluid flow shows that swarms of C. gingivalis are layered, with cells in the upper layers moving more rapidly than those in the lower layers. Thus, cells also glide on top of one another. Cells of non-motile bacterial species attach to the surface of C. gingivalis and are propelled as cargo. The cargo cell moves along the length of a C. gingivalis cell, looping from one pole to the other. Multi-color fluorescent spectral imaging of cells of different live but non-motile bacterial species reveals their long-range transport in a polymicrobial community. A swarm of C. gingivalis transports some non-motile bacterial species more efficiently than others and helps shape the spatial organization of a polymicrobial community.\n\nSignificanceWe describe a situation in which bacteria typical of the human oral microbiome are organized spatially by gliding cells, species of Capnocytophaga, that move backwards and forwards over the substratum. The mobile adhesins that pull the cells over the substratum also attach to cells of non-motile bacterial species, which are carried up and down the motile cells as cargo. The synchronized transport of non-motile cargo bacteria helps shape a polymicrobial community.

microbiology↗