Biology subjects

Seedorf, H.

Publications and source records attributed to Seedorf, H..

13 recordsLinked to original sources

bioRxiv2026

Comparative analysis of adhesin-like proteins from Methanobacteriales species

Methanogenic archaea are key syntrophic partners in animal and human guts. However, the molecular basis of physical and functional interactions of methanogens with other cells remains poorly understood. Adhesin-like proteins (ALPs) are abundant, unusually large, and repeat-rich surface proteins and are potential prime candidates for mediating cell-cell interactions, however, due to poor characterization, ALPs often remain neglected in annotations of genomes and large-scale datasets. Here, we combined structure-guided analysis with comparative genomics to map ALP domain architectures across Methanobacteriales species, with emphasis on intestinal and rumen lineages. We curated predicted ALP structures and manually delineated domain boundaries to build a reference set encompassing ABD, RBH, membrane-anchoring domains (MAD), and miscellaneous accessory domains. Leveraging on a novel approach for ALP domain annotations, we generate ALP annotations and domain architectures for 17 Methanobacteriales species without reliance on primary-sequence homology. Applying this approach to strains of Methanobrevibacter smithii and Methanobrevibacter intestini, we assembled species-level "adhesiomes" and assessed conservation patterns of ALPs. Network analysis indicated that ALPs are more commonly shared among strains within a species than between species, suggesting species-specific adhesin repertoires. While total ALP counts differed significantly between M. smithii and M. intestini (Wilcoxon rank-sum p = 0.00295), median ALP lengths did not (p = 0.606). Our results provide a comprehensive overview of the ALP domain architectures in Methanobacteriales species and reveals species-specific adhesiomes that likely contribute to niche adaptation and syntrophic partnerships in gut ecosystems.

microbiology↗

bioRxiv2026

Sequence-independent protein domain detection and classification with PRISM

The explosion of predicted protein structures has revealed countless novel domain families. However, gold-standard segmentation tools like Chainsaw and Merizo are trained on rapidly obsoleting CATH databases, lack automatic domain classification, and cannot be easily fine-tuned without deep learning expertise. We introduce PRISM, a unified framework enabling sequence-independent, one-shot fine-tuning for simultaneous domain segmentation and classification, bypassing traditional constraints to accurately resolve complex, novel protein architectures.

bioinformatics↗

bioRxiv2026

GuFi phages represent the most prevalent viral family-level clusters in the human gut microbiome

Despite being important ecological modulators of the gut microbiome, bacteriophage diversity and function remain under-characterized. We show that short-read metagenomic surveys can miss even globally highly prevalent viral family-level clusters (VFCs), that can be readily assembled and characterized with long-read metagenomic data from a relatively small cohort (n=109). While gut Bacteroidota phages have been the prevailing focus in the literature, we show that highly prevalent gut phage families frequently have Firmicutes hosts (termed GuFi phages), with broad host ranges verified using proximity-ligation (Hi-C) sequencing data. High-throughput sequencing of virus-like particles from fecal samples detected frequent enrichment of GuFi phages across samples, revealing their under-appreciated impact on the gut microbiome. We report the first in vitro induction and imaging of members of prevalent GuFi clades including the candidate orders Heliusvirales, Astravirales (VFC 2) and Suryavirales (VFC 4). Our findings underscore the importance of GuFi phages with broad host ranges in the gut microbiome, and the utility of long-read sequencing for viral discovery, paving the way for deeper insights into the role of bacteriophages in human health and disease.

microbiology↗

bioRxiv2025

High-throughput single-cell isolation of Bifidobacterium strains from the gut microbiome

While metagenomic studies can highlight strain-level diversity within microbial communities, the diversity obtained is often incomplete. Moreover, their utility for phenotypic characterizations remains hampered without the subjacent, systematic isolation procedures required with traditional culturomics. In this work, we examined the capabilities of a commercially available high-throughput single-cell dispensing solution to selectively target and isolate diverse strains of a genus of interest, Bifidobacterium, from fecal samples. The general performance of the single-cell dispenser was first assessed, revealing a low doublet frequency of 11.5% and an ability to preserve global genus diversity when a mixed culture of Bifidobacterium was dispensed. Culturing-related factors including the use of an effective selection medium, such as the Bifidus Selective Medium supplemented with mupirocin (BSM-MUP), and the length of incubation were found to be critical in determining isolation success. Leveraging these results, we obtained a total of 622 viable isolates from five Singaporean fecal samples, among which [~]98.7% were bifidobacteria. Whole-genome sequencing of 96 isolates revealed six different Bifidobacterium species with both inter- and intra-subject lineage diversity, and the majority of the assemblies were not previously captured using metagenomic sequencing. Our findings validate the ability of high-throughput culturomics to recover diverse, novel bacterial strains and open up the possibility to robustly interrogate their functional characteristics, advancing our understanding of important microbiomes. IMPORTANCEThe field of microbial culturomics is still in its early stages. Enhancing our ability to isolate and phenotypically test bacterial strains from their multicellular environment is crucial for advancing microbiome research and healthcare development. Given the time- and cost-inefficiencies of traditional culturing methods, a more efficient, high-throughput approach to obtain isolates is needed. In the present study, we assessed a single-cell dispensing platform and developed a workflow to isolate diverse Bifidobacterium strains from fecal samples. We demonstrated here the capability of this novel technology to efficiently obtain hundreds of isolates of a targeted organism, covering both species and strain diversities. This generalizable and scalable method allows for the high-throughput recovery of microbes with little optimization needed for novel targets, providing a fundamental step in improving the culturomic framework to complement metagenomic approaches and enable isolate-level functional studies of important microbiomes.

microbiology↗

bioRxiv2025

Comparative genomics of DH5α-inhibiting Escherichia coli isolates from human feces reveals common co-occurrence of bacteriocin genes with virulence factors and antibiotic resistance genes.

The presence of multi-drug-resistant (MDR) bacteria in healthy individuals poses a significant public health concern, as these strains may contribute to or even facilitate the dissemination of antibiotic resistance genes (ARGs) and virulence factors. In this study, we investigated the genomic features of antimicrobial-producing Escherichia coli strains from the gut microbiota of healthy individuals in Singapore. Using a large-scale screening approach, we analyzed 3,107 E. coli isolates from 109 fecal samples for inhibitory activity against E. coli DH5 and performed whole-genome sequencing on 37 representative isolates. Our findings reveal genetically diverse strains, with isolates belonging to five phylogroups (A, B1, B2, D, and F) and 23 unique sequence types (STs). Bacteriocin gene clusters were widespread, with colicins and microcins dominating the profiles. Notably, we identified a hcp-et3-4 gene cluster, encoding an effector linked to Type VI secretion system. Approximately 40% of the sequenced isolates were MDR, with resistance for up to eight antibiotic classes in one strain. Plasmids were the primary vehicles for ARG dissemination, but chromosomal resistance determinants were also detected. Additionally, over 55% of isolates were classified as potential extraintestinal pathogenic E. coli (ExPEC), raising concerns about their potential pathogenicity outside the intestinal tract. Our study highlights the co-occurrence of bacteriocins, ARGs, and virulence genes in gut-residing E. coli, underscoring their potential role in shaping microbial dynamics and antibiotic resistance. While bacteriocin-producing strains show potential as probiotic alternatives, careful assessment of their safety and genetic stability is necessary for therapeutic applications. ImportanceThis study provides genomic insights into the diverse repertoire of potential bacteriocin production in E. coli strains isolated from a cohort of healthy human subjects in Southeast Asia. Our findings suggest that the co-occurrence of bacteriocin genes with multiple antibiotic resistance and virulence genes is a common feature among non-clinical isolates. This genetic linkage could contribute to the increased abundance of multi-drug-resistant and virulent strains within individual hosts. Moreover, this co-occurrence may facilitate the host colonization with strains carrying antibiotic resistance and virulence determinants, potentially also contributing to the dissemination of resistant and pathogenic strains within the local population and beyond.

microbiology↗

bioRxiv2024

Dissecting the heat stress altering immune responses and skin microbiota in fish in a recirculating aquaculture system in Singapore

Environmental factors, probiotics and feed additives affect microbiota diversity in fish. Water temperature disrupts the composition and diversity of microbiota, with temperature changes triggering stress and immune responses in fish. In Singapore, water heat treatment is used to control and prevent disease outbreaks in farmed fish. Although gut microbiota responses to heat stress have been reported, little is known about the effects of heat treatment on fish immune responses and fish skin microbiota dynamics. Over a 3-mo interval, we investigated microbiota dynamics and fish immune responses associated with a heat treatment practice in a commercial fish farm with a recirculating aquaculture system (RAS). Tank water temperature was raised to 37-39 {degrees}C for 1 hour, every 2 weeks. Tank water and fish microbial communities were analysed by 16S amplicon sequencing, and host molecular expressions were determined by qPCR. We inferred that heat treatment increased stress and immune responses that protected fish from opportunistic infections. However, overreaction to temperature stress can cause dysbiosis of the skin microbiota and death. We also suggested the value of the skin microbiota Pseudomonadota: Bacteroidota (P:B) ratio as a biomarker for aquaculture fish health. IMPORTANCEAquaculture is an emerging economic activity to supply high-quality animal protein and reduce reliance on wild-caught fish products. Recently, there has been emphasis on intensive aquaculture, using a Recirculating Aquaculture System (RAS). In RAS, management of pathogens/parasites prevalence is a major challenge. Developing practical solutions for producing healthy juveniles in nursery systems will make profound contributions to sustainable aquaculture. In this study, we used an unconventional strategy, exposing juveniles to the pathobiome in the environment, followed by non-lethal heat shock treatments to enhance immunity. Short-term stress induced heat shock proteins that protected fish from opportunistic infections. We concluded that manipulating environmental-microbial-host interactions, together with enhanced functional capacity of fish immune response, has potential for disease control in aquaculture.

systems biology↗

bioRxiv2023

Comparison of tet(X4)-containing contigs from metagenomic sequencing data with plasmid sequences of isolates from a cohort of healthy subjects.

The recently discovered tigecycline-inactivating enzyme Tet(X4) can confer high-level tigecycline resistance on its hosts, which makes it a public health concern. This study focused on detection, analysis, and characterization of Tet(X4)-positive Enterobacteriaceae from the gut microbiota of a healthy cohort of individuals in Singapore using cultivation-dependent and cultivation-independent approaches. Twelve Tet(X4)-positive Enterobacteriaceae strains that were previously obtained from the cohort were fully genome-sequenced and comparatively analysed. A metagenomic sequencing (MS) dataset of the same samples was mined for contigs that harboured the tet(X4) resistance gene. The sequences of tet(X4)-containing contigs and plasmids sequences were compared. The presence of the resistance genes floR and catD (also annotated as estT) was detected in the same cassette in 10 and 12 out of the 12 tet(X4)-carrying plasmids, respectively. MS detected tet(X4)-containing contigs in two out of 109 subjects, while cultivation-dependent analysis previously reported a prevalence of 10.1%. Contig sequences are relatively short ([~]14-33 kb) but show high similarity to the respective plasmid sequences of the isolates. The frequent co-occurrence of florR and catD with tet(X4) corroborates the hypothesis that the transmission of tet(X4) may have originated from the veterinary sector. Our findings show that MS can complement efforts in the surveillance of antibiotic resistance genes for clinical samples, while it has a lower sensitivity than a cultivation-based method when the target organism have a low abundance. Further optimisation is required if MS is to be utilised in antibiotic resistance surveillance.

microbiology↗

bioRxiv2022

Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians

Despite extensive efforts to address it, the vastness of uncharacterized dark matter microbial genetic diversity can impact short-read sequencing based metagenomic studies. Population-specific biases in genomic reference databases can further compound this problem. Leveraging advances in long-read and Hi-C technologies, we deeply characterized 109 gut microbiomes from three ethnicities in Singapore to comprehensively reconstruct 4,497 medium and high-quality metagenome assembled genomes, 1,708 of which were missing in short-read only analysis and with >28x N50 improvement. Species-level clustering identified 70 (>10% of total) novel gut species out of 685, improved reference genomes for 363 species (53% of total), and discovered 3,413 strains that are unique to these populations. Among the top 10 most abundant gut bacteria in our study, one of the species and >80% of all strains were not represented in existing databases. Annotation of biosynthetic gene clusters (BGCs) uncovered more than 27,000 BGCs with a large fraction (36-88%) not represented in current databases, and with several unique clusters predicted to produce bacteriocins that could significantly alter microbiome community structure. These results reveal the significant uncharacterized gut microbial diversity in Southeast Asian populations and highlight the utility of hybrid metagenomic references for bioprospecting and disease-focused studies.

genomics↗

bioRxiv2021

Longitudinal changes in diet cause repeatable and largely reversible shifts in gut microbial communities of laboratory mice and are observed across segments of the entire intestinal tract

Dietary changes are known to alter the composition of the gut microbiome. However, it is less understood how repeatable and reversible these changes are and how diet-switches affect the microbiota in the various segments of the gastrointestinal tract. Here, a treatment group of conventionally raised laboratory mice is subjected to two periods of western diet (WD) interrupted by a period of standard diet (SD) of the same duration. Beta-diversity analyses show that diet-induced microbiota changes are largely reversible (q = 0.1501; PERMANOVA, weighted-UniFrac comparison of the treatment-SD group to the control-SD group) and repeatable (q = 0.032; PERMANOVA, weighted-UniFrac comparison of both WD treatments). Furthermore, we report that diet switches alter the gut microbiota composition along the length of the intestinal tract in a segment-specific manner, leading to gut segment-specific Firmicutes/Bacteroidota ratios. We identified prevalent and distinct Amplicon Sequencing Variants (ASVs), particularly in genera of the recently described Muribaculaceae, along the gut as well as ASVs that are differentially abundant between segments of treatment and control groups. Overall, this study provides insights into the reversibility of diet-induced microbiota changes and highlights the importance to expand sampling efforts beyond the collections of fecal samples to characterize diet-dependent and segment-specific microbiome differences.

microbiology↗

bioRxiv2021

Whole-genome analysis of antimicrobial-resistant Escherichia coli in human gut microbiota reveals its origin and flexibility in transmitting mcr-1

Multidrug resistant (MDR) Escherichia coli strains that carry extended-spectrum {beta}-lactamases (ESBLs) or colistin resistance gene mcr-1 have been identified in the human gut at an increasing incidence worldwide. In this study, we sampled and characterized MDR Enterobacteriaceae from the gut microbiota of healthy Singaporeans and show that the prevalence of ESBL-producing and mcr-positive Enterobacteriaceae is 26.6% and 7.3%, respectively. Whole-genome sequencing of 37 E. coli isolates identified 25 sequence types and assigned them into six different phylogroups, suggesting that the human intestinal MDR E. coli strains are highly diverse. In addition, we found that E. coli isolates belonging to phylogroup D, B2 and F carry a higher number of virulence genes, whereas isolates of phylogroup A, B1 and E carry fewer virulence factor genes but are frequent carriers of florfenicol resistance gene floR and colistin resistance gene mcr-1. Comparison of the seven mcr-1-positive E. coli isolates revealed that mcr-1 is carried by conjugative plasmids or embedded in composite transposons, which could potentially mobilize mcr-1 to other pathogenic Enterobacteriaceae strains or MDR plasmids. Finally, we found that 12 out of the 37 MDR E. coli isolates in this study show high similarity to ESBL-producing E. coli isolates from raw meats from local markets, suggesting a potential transmission of MDR E. coli from meat products to the human gut microbiota. Our findings show diverse antibiotic resistance and virulence profiles of intestinal E. coli and call for better countermeasures to block the transmission of MDR E. coli via the food chain. ImportanceThe human gut can harbor both antibiotic resistant and virulent E. coli which may subsequently cause infections. In this study, the antibiotic resistance and virulence traits of antibiotic-resistant E. coli isolates from human gut microbiota of healthy subjects were investigated. The isolated E. coli strains carry a diverse range of antibiotic resistance mechanisms and virulence factor genes, are highly diverse to each other, and are likely to originate from raw meat products from the local markets. Of particular concern are seven E. coli isolates which carry colistin resistance gene mcr-1. This gene can be mobilized into other pathogens and MDR plasmids, thereby spreading resistance to the last-resort antibiotic colistin. Our findings also suggest that raw meat could serve as important source to transmit MDR bacteria into the human gut microbiota.

microbiology↗

bioRxiv2020

Host-age prediction from fecal microbiome composition in laboratory mice

The life-long relationship between microorganisms and hosts has a profound impact on the overall health and physiology of the holobiont. Changes in microbiome composition throughout the lifespan of a host remain, however, largely understudied. In this study, the fecal microbiome of conventionally raised C57BL/6J mice was analyzed throughout almost the entire expected lifespan, from maturing (9 weeks) until very old age (112 weeks). Analysis of alpha and beta diversity suggests that gradual microbiome changes occur throughout the entire murine life but appear to be more pronounced in maturing to middle-aged phases. Phylum-level analysis indicates a shift in the Firmicutes/Bacteroidetes ratio in favor of the Firmicutes in the second year of adulthood. Varying successional patterns throughout life were observed for many Firmicutes OTUs, while relative abundances of Bacteroidetes OTUs varied primarily in the early life phases. Microbiome configurations at given time points were used as training sets in a Bayesian model, which in turn effectively enabled the prediction of host age. The fecal microbiome composition may therefore serve as an accurate biomarker for aging. This study further suggests that age-associated compositional differences may have considerable implications for the interpretation and comparability of animal model-based microbiome studies. ImportanceThe life-long relationship between microorganisms and hosts has a profound impact on the overall physiology of the holobiont. Understanding the extent of gut microbiome compositional changes over the expected mouse lifespan may allow to better understand the interplay of microbiome and the host at the different life stages. In this study, we performed a two-year longitudinal study of murine fecal microbiome. Using fine-scale microbiome profiling we were able to predict the host age from the fecal microbiome composition. Moreover, we observed that the rate of compositional change appears to slow with age. The description of the compositional changes in commonly used C57BL/6J mice can be used to optimize selection of age-associated mouse models and highlights the use of microbiome-profiling as biomarker for aging.

microbiology↗

bioRxiv2018

Description of Schaedlerella arabinophila gen. nov., sp. nov., a D-arabinose utilizing bacterium isolated from feces of C57BL/6J mice and a close relative of Clostridium sp. ASF 502

The use of gnotobiotics has gained large interest in recent years due to technological advances that have revealed the importance of host-associated microbiomes for host physiology and health. One of the oldest and most important gnotobiotics mouse model, the Altered Schaedler Flora (ASF) has been used for several decades. ASF comprises eight different bacterial species, which have been characterized to different extent, but only few are available through public strain collections. Here, the isolation of a close relative to one of the less studied ASF strains, Clostridium sp. ASF 502, is reported. Isolate TLL-A1, which shares 99.6% 16S rRNA gene sequence identity with Clostridium sp. ASF 502, was obtained from feces of C57BL/6J mice where is was detectable at a relative abundance of less than one percent. D-arabinose was used as sole carbon source in the anaerobic cultivation medium. Growth experiments with TLL-A1 on different carbon sources and analysis of its ~6.5 gigabase genome indicate that TLL-A1 harbors a large gene repertoire to utilize different carbohydrates for growth. Comparative genome analyses of TLL-A1 and Clostridium sp. ASF 502 reveal differences in genome content between the two strains, in particular with regards to carbohydrate activating enzymes. Based on physiology and genomic analysis it is proposed to name TLL-A1 to gen. nov. sp. nov Schaedlerella arabinophila TLL-A1 (DSMZ 106076T; KCTC 15657T). The closely related Clostridium sp. ASF 502 is proposed to be renamed to Schaedlerella arabinophila to reflect its taxonomic standing and to keep ASF 502 as strain designation.\n\nImportanceThe Altered Schaedler Flora (ASF) remains an important tool to mechanistically investigate host-microbe interactions in the mammalian alimentary tract. Extensively characterizing the eight different bacterial strains, which are constituting ASF, has the potential to further increase the definition of this widely used model microbial community and to enhance our understanding of how individual microorganism interact with a host and/or how they may affect its physiology. However, some of the ASF strains have unfortunately been lost or are not easily accessible to the scientific community. The isolation and characterization of the here described species, proposed to be named Schaedlerella arabinophila, which is closely related to Clostridium species ASF502, may therefore be an important corner stone in further improving the value of studies using ASF or other defined synthetic microbial communities that require usage of autochthonous microorganisms in gnotobiotic mice.

microbiology↗

bioRxiv2018

Insights into the microbiota of Asian seabass (Lates calcarifer) with tenacibaculosis symptoms and description of sp. nov. Tenacibaculum singaporense

Outbreaks of diseases in farmed fish remain a recurring problem despite the development of vaccines and improved hygiene standards on aquaculture farms. One commonly observed bacterial disease in tropical aquaculture of the South-East Asian region is tenacibaculosis, which is attributed to members of the Bacteroidetes genus Tenacibaculum, most notably T. maritimum. The impact of tenacibaculosis on fish microbiota remains poorly understood. In this study, we analysed the microbiota of different tissue types of commercially reared Asian seabass (Lates calcarifer) that showed symptoms of tenacibaculosis and compared the microbial communities to those of healthy and experimentally infected fish that were exposed to diseased farm fish. The microbiota of diseased farm fish was dominated by Proteobacteria (relative abundance{+/-}standard deviation, 74.5%{+/-}22.8%) and Bacteroidetes (18.07%{+/-}21.7%), the latter mainly comprised by a high abundance of Tenacibaculum species (17.6%{+/-}20.7%). In healthy seabass Proteobacteria had also highest relative abundance (48.04%{+/-}0.02%), but Firmicutes (34.2%{+/-}0.02%) and Fusobacteria (12.0%{+/-}0.03%) were the next two major constituents. Experimentally infected fish developed lesions characteristic for tenacibaculosis, but the microbiota was primarily dominated by Proteobacteria (90.4%{+/-}0.2%) and Firmicutes (6.2%{+/-}0.1%). The relative abundance of Tenacibaculum species in experimentally infected fish was significantly lower than in the commercially reared diseased fish and revealed a higher prevalence of different Tenacibaculum species. One strain was isolated and is described here as sp. nov. Tenacibaculum singaporense TLL-A1T (=DSM 106434T, KCTC 62393T). The genome of T. singaporense was sequenced and compared to those of T. maritimum DSM 17995T and the newly sequenced T. mesophilum DSM 13764T.\n\nImportanceFish production from aquaculture facility has become a major source of protein for human consumption and is expected to further grow to meet the growing demands. Devastating fish diseases, such as tenacibaculosis, can eradicate entire stocks of aquaculture fish in a short time and pose a serious threat to individual fish farmers and overall fish production. Understanding the disease processes and the individual microbial players involved has the potential to develop methods to prevent or mitigate infections on aquaculture farms. This study provides important insights into the microbial ecology of tenacibaculosis from an aquaculture facility in Singapore and highlights the complexity of this fish disease at two different disease stages. Furthermore, the isolation of a novel Tenacibaculum species and comparative genome analysis of three different Tenacibaculum species enhance our view of this economically and environmentally important bacterial genus.

microbiology↗