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PubMed2005

Comparative modelling of protein structure and its impact on microbial cell factories.

Comparative modeling is becoming an increasingly helpful technique in microbial cell factories as the knowledge of the three-dimensional structure of a protein would be an invaluable aid to solve problems on protein production. For this reason, an introduction to comparative modeling is presented, with special emphasis on the basic concepts, opportunities and challenges of protein structure prediction. This review is intended to serve as a guide for the biologist who has no special expertise and who is not involved in the determination of protein structure. Selected applications of comparative modeling in microbial cell factories are outlined, and the role of microbial cell factories in the structural genomics initiative is discussed.

Journal Article↗
PubMed2026

Association between the gut microbiome and plasma metabolites linked to vocalization-based temperament in Merino sheep.

BACKGROUND: Temperament, as a determinant of behavioural and emotional responses, has a substantial adaptive value in different environments. This study aims to investigate the association between the gut microbiota and temperament plasticity, and clarify the potential metabolic mechanism that underpins that association by running a multi-omics study in sheep. METHODS: The TrackSheep research cohort was generated using 200 healthy juvenile Merino ewes, and the rumen microbiota, plasma metabolome, and temperament phenotype was measured. RESULTS: Rumen metagenomic analysis identified 25 microbial species and 16 MetaCyc pathways that explained 37.5% and 11.1%, respectively, of the variation in temperament as estimated using the vocal reactivity to stress. Among these, the γ-aminobutyric acid (GABA) shunt and allantoin degradation pathways showed the strongest associations with vocal behaviour. Multi-omic integration linked these microbial pathways to plasma metabolites that are involved in neurotransmission, antioxidant defense, and energy metabolism, including acetyl-L-carnitine (ALCAR) and urocortisone, which partially mediated the effects of microbial pathways on vocalisations. Notably, functional genomic and mediation analyses indicated that the abundance of Cryptobacteroides sp902761655 was associated with the activity of GABA shunt pathway, where GABA co-occurred with succinate production, in turn correlating with reduced inhibitory effects of ALCAR on stress-susceptible temperament. Although plasma metabolite shifts observed immediately after behavioural tests reflected stress exposure, their associations with rumen microbiota highlight microbiome-metabolite interplay that could underly behavioural variation. CONCLUSIONS: Our study provides the first large-scale multi-omics evidence linking the rumen microbiome to a dimension of emotional reactivity in livestock, while underscoring the need for longitudinal and experimental validation to establish causal mechanisms. Video Abstract.

Animals↗
PubMed2006

Introns regulate RNA and protein abundance in yeast.

The purpose of introns in the architecturally simple genome of Saccharomyces cerevisiae is not well understood. To assay the functional relevance of introns, a series of computational analyses and several detailed deletion studies were completed on the intronic genes of S. cerevisiae. Mining existing data from genomewide studies on yeast revealed that intron-containing genes produce more RNA and more protein and are more likely to be haplo-insufficient than nonintronic genes. These observations for all intronic genes held true for distinct subsets of genes including ribosomal, nonribosomal, duplicated, and nonduplicated. Corroborating the result of computational analyses, deletion of introns from three essential genes decreased cellular RNA levels and caused measurable growth defects. These data provide evidence that introns improve transcriptional and translational yield and are required for competitive growth of yeast.

Actins↗
PubMed2002

Viral binding proteins as antibody surrogates in immunoassays of cytokines.

Cytokines are pivotal to a balanced innate or cell-mediated immune response, can be indicative of disease progression and/or resolution, and are being evaluated as therapeutics. There is a need to purify and/or to measure key cytokines rapidly with accuracy, precision, and sensitivity. The current assay technologies, which are based on RT-PCR, immunoassays, or bioassays, are limited in their use in the clinic, in particular because of the long time (1-3 h) required to carry out the assays. An alternative approach explored here is the use of pathogen-encoded cytokine-binding proteins, which have Kd in the nanomolar range. It is anticipated that pathogens have evolved binding proteins, antagonists, and/or specific neutralizing phenotypes directed against key signaling and effector molecules involved in the multifaceted host defense system. Thus, by screening the genomes of a wide range of microbial agents, we would expect to find coding sequences for binding proteins for the most important cytokines. Consistent with this view is the identification of poxvirus genes encoding binding activities for TNF type I and type II interferons, interleukin (IL)-1beta, IL-18, and beta-chemokines. These high-affinity receptors have the potential to act as surrogate antibodies in a number of applications in cytokine quantification and purification and could be potentially useful reagents to complement the existing panel of anti-cytokine, monoclonal, polyclonal, or engineered antibodies that are currently available.

Antibodies↗
PubMed2003

Computational inference of regulatory pathways in microbes: an application to phosphorus assimilation pathways in Synechococcus sp. WH8102.

We present a computational protocol for inference of regulatory and signaling pathways in a microbial cell, through literature search, mining "high-throughput'' biological data of various types, and computer-assisted human inference. This protocol consists of four key components: (a) construction of template pathways for microbial organisms related to the target genome, which either have been extensively studied and/or have a significant amount of (relevant) experimental data, (b) inference of initial pathway models for the target genome, through combining the template pathway models and target genome-specific information, (c) refinement and expansion of the initial pathway models through applications of various data mining tools, including phylogenetic profile analysis, inference of protein-protein interactions, and prediction of transcription factor binding sites, and (d) validation and refinement of the pathway models using pathway-specific experimental data or other information. To demonstrate the effectiveness of this procedure, we have applied it to the construction of the phosphorus assimilation pathways in cyanobacterium sp. WH8102. We present, in this paper, a model of the core components of this pathway.

Bacterial Proteins↗
PubMed2026

Complete genome sequence of Bacillus subtilis strain S-LA1, a potential plant probiotic endophyte from the medicinal plant Leucas aspera.

Bacillus subtilis strain S-LA1 is an endophytic bacterium isolated from Leucas aspera roots that harbors a 4.2 Mbp genome predicted to encode several traits for nutrient acquisition, plant growth promotion, and plant probiotic efficacy. Genomic characterization underscores its potential as a microbial resource supporting sustainable agriculture and crop disease management strategies.

Bacillus↗
PubMed2001

Pathogenicity and resistance islands of staphylococci.

Variable genetic elements including plasmids, transposons and prophages are involved in pathogenesis and antibiotic resistance, and are an important component of the staphylococcal genome. This review covers a set of newly described variable chromosomal elements, pathogenicity and resistance islands, carrying superantigen and resistance genes, especially toxic shock and methicillin resistance, respectively.

Anti-Bacterial Agents↗
PubMed2026

Multidimensional prophage profiling of carbapenem-resistant Enterobacteriaceae in Thailand: a nationwide, multicentre, genomic study.

BACKGROUND: Prophages influence bacterial fitness, resistance, and evolution, yet their epidemiology remains poorly understood in carbapenem-resistant Enterobacteriaceae (CRE). In this nationwide study in Thailand, we aimed to describe prophage repertoires in clinical CRE isolates and to explore their potential relevance for molecular epidemiology. METHODS: We performed a nationwide, retrospective, genomic analysis of all CRE clinical isolates collected through our previous national surveillance study involving 11 hospitals in 11 provinces in Thailand between March 25, 2012, and Jul 21, 2017. Whole-genome sequencing data from 747 CRE isolates were analysed. Intact prophages were identified using PHAge Search Tool Enhanced Release (PHASTER) and clustered by nucleotide sequence similarity. Prophage profiles were compared across multilocus sequence types, carbapenemase genotypes, specimens, geography, and patient demographics (age and sex). FINDINGS: Of the included 747 CRE isolates, 170 (23%) were Escherichia coli and 577 (77%) were Klebsiella pneumoniae. 220 (29%) of 747 strains had been isolated from female patients and 264 (35%) from male patients; metadata on patient sex were missing for 263 (35%) isolates. The median patient age was 63 years (IQR 50-72). 71 (10%) of isolates were from blood, 283 (38%) from sputum, 284 (38%) from urine, and 109 (15%) from other specimens. 374 distinct prophage clusters were identified, with significantly more prophages per genome in K pneumoniae (mean 3&#xb7;01 [SD 1&#xb7;55]) than in E coli (1&#xb7;64 [1&#xb7;46]; p<0&#xb7;0001). Prophage repertoires largely mirrored bacterial multilocus sequence types. However, even within the highly clonal K pneumoniae sequence type 16 lineage, discrete prophage variation was identified, with common profiles observed in geographically dispersed patients. Respiratory K pneumoniae frequently carried a mosaic prophage with environmental signatures and a type VI secretion system, whereas blood-derived E coli harboured a prophage with immune-modulating genes. Distinct prophage clusters were observed across clinical specimens, age groups, carbapenemase genotype, and geographical region. Strains coharbouring blaNDM-1 plus blaOXA-232 (114 [15%] of 747) had the highest prophage loads. INTERPRETATION: The prophage content was shaped by the bacterial lineage, ecological niche, and temporal dynamics, providing an additional layer of epidemiological resolution beyond conventional genome typing. Integrating prophage profiling into molecular surveillance frameworks could help to identify transmission events, improve infectious source attribution, and enhance infection control strategies. FUNDING: Japan Agency for Medical Research and Development.

Female↗
PubMed2005

How genomics has affected the concept of microbiology.

Genomics influences multiple areas of microbiology, and thus affects key microbiological concepts. Recent reports that describe the large genome and unusual coding capacity of mimivirus, the minimized fungal genomes that contain elements of bacterial metabolism, and the 'signature' eukaryotic proteins in bacteria are introducing grey shades into the black-and-white distinctions between microbial domains. The concept of the 'universal' minimal genome is being challenged, and the ability of minimal genomes to support cellular complexity is under investigation. There have been intriguing insights into microbe-microbe relationships, for example conflict mediation in competing bacteriophages that rapidly evolve survival mechanisms when cooperation is experimentally enforced. Genomics has given birth to metagenomics, but has also stimulated the development of improved cultivation techniques. Lastly, the taxonomic potential of genomics is emerging, as studies of multiple strains allow us to revise and refine the bacterial species concept as well as the idea of a static genome.

Eukaryotic Cells↗
PubMed2026

Comparative genomic characterization and antimicrobial resistance of bacteremia-causing Enterococcus faecium and Enterococcus faecalis in a Chinese hospital.

Enterococci are common commensals of the human gut and important opportunistic pathogens, with Enterococcus faecium and Enterococcus faecalis being the most clinically prevalent species. A significant epidemiological shift has emerged with an increasing clinical burden of E. faecium. To compare genomic evolution of E. faecium and E. faecalis, we performed whole-genome sequencing on 93 E. faecium and 32 E. faecalis isolates causing bloodstream infections at a single hospital (2022-2024). Analysis of patient demographics revealed that E. faecium infections originated from fewer sources than E. faecalis, with a higher proportion deriving from intra-abdominal infections. Multilocus sequence typing identified ST78 and ST789 as the predominant sequence types for E. faecium, whereas ST16 and ST179 were most common for E. faecalis. E. faecium carried more antimicrobial resistance genes and putative virulence marker (PVM)-type virulence genes than E. faecalis, with vancomycin resistance predominantly mediated by vanHAX (33/93, 35.5%) and a single E. faecalis isolate also carrying vanHAX (1/32, 3.1%); the structurally incomplete vanHMX gene cluster was detected in 11 E. faecium isolates. Pan-genome analysis indicated a larger core genome in E. faecalis compared to E. faecium, consistent with greater plasmid replicon diversity in the latter. Intra-host comparisons showed that two E. faecalis pairs from the same patient were clonally related, with one isolate acquiring a vanHAX plasmid conferring vancomycin resistance. In contrast, E. faecium isolates exhibited marked genomic diversity even among clonally related pairs. These findings suggest that E. faecium possesses greater genomic plasticity and adaptive potential to the clinical environment.IMPORTANCEThis study provides a detailed comparison of clinical and genomic features between Enterococcus faecium and Enterococcus faecalis from the same hospital setting. We show that E. faecium isolates, mainly ST78/ST789, carry more antimicrobial resistance genes and a higher number of putative virulence marker (PVM) genes than E. faecalis, reflecting their hospital-adapted nature. E. faecium also exhibits a smaller core genome and greater diversity of plasmid replicon types, indicating higher genomic plasticity and capacity for horizontal gene transfer. By contrast, E. faecalis retains a larger core genome and a set of classical virulence factors, and its within-host isolates are clonally related. These distinct genomic profiles help to understand how the two species adapt to clinical environments and may inform more targeted infection control strategies and resistance surveillance.

Enterococcus faecium↗
PubMed2003

Molecular diagnostics in medical microbiology: yesterday, today and tomorrow.

Clinical microbiology is clearly on the move, and various new diagnostic technologies have been introduced into laboratory practice over the past few decades. However, Henri D Isenberg recently stated that molecular biology techniques promised to revolutionise the diagnosis of infectious disease, but that, to date, this promise is still in its infancy. Molecular diagnostics have now surpassed these early stages and have definitely reached puberty. Currently, a second generation of automated molecular approaches is already within the microbiologists' reach. Quantitative amplification tests in combination with genomics, transcriptomics, proteomics and related methodologies will pave the way to further enhancement of innovative microbial detection and identification.

Genomics↗
PubMed2026

Rumen DNA virome plasticity and viral metabolic potential are associated with seasonal adaptation in grazing yak and cattle on the Qinghai-Tibet Plateau.

BACKGROUND: As a diverse and abundant component of the rumen ecosystem, viruses interact with other microorganisms and are thought to influence microbial metabolism and host productivity. However, how the rumen virome responds to seasonal fluctuations in extreme environments remains poorly understood. Here, metagenomic analyses were used to investigate temporal dynamics of viral diversity, functional potential, and virus-host associations in the rumen virome of yak and cattle on the Qinghai-Tibet Plateau across warm and cold seasons. RESULTS: Rumen viral communities exhibited pronounced seasonal variation in both yaks and cattle, with higher alpha diversity observed during the cold season than in the warm season. Across seasons, the yak rumen virome showed greater alpha diversity and community stability than that of cattle. In total, 27,353 temperate and 31,976 virulent viral operational taxonomic units (vOTUs) were identified, predominantly belonging to the class Caudoviricetes. These viruses were linked to microbial hosts spanning 24 bacterial and 8 archaeal phyla, with Bacteroidota and Bacillota representing the dominant lineages. Virus-host associations were more numerous in the cold season and showed distinct host-specific patterns between yaks and cattle. Cold-season virome exhibited reduced diversity of anti-defense genes and enrichment of auxiliary metabolic genes (AMGs) associated with fatty acid metabolism and hemicellulose degradation. Notably, greater divergence between yaks and cattle was observed during the cold season: the yak rumen virome was enriched in pathways related to amino acid, lipid, and energy metabolism, as well as cellulose-degrading CAZyme families, whereas the cattle rumen virome showed enrichment in general carbohydrate metabolism and replication and repair processes. CONCLUSION: Seasonal plasticity of rumen DNA virome and pronounced interspecific divergence between yaks and cattle provide insight into their distinct microbial processes in the harsh environment of the Qinghai-Tibet Plateau. These findings suggest that the rumen DNA virome exhibits complex ecological and functional responses to seasonal variation and may be associated with host-microbiome interactions and nutrient utilization under environmental stress. This study highlights the ecological relevance of rumen viral genomes in understanding virus-microbiome interactions, microbial adaptation, and nutrient utilization in high-altitude ruminants.

Auxiliary metabolic genes↗
PubMed2004

Metagenomics: application of genomics to uncultured microorganisms.

Metagenomics (also referred to as environmental and community genomics) is the genomic analysis of microorganisms by direct extraction and cloning of DNA from an assemblage of microorganisms. The development of metagenomics stemmed from the ineluctable evidence that as-yet-uncultured microorganisms represent the vast majority of organisms in most environments on earth. This evidence was derived from analyses of 16S rRNA gene sequences amplified directly from the environment, an approach that avoided the bias imposed by culturing and led to the discovery of vast new lineages of microbial life. Although the portrait of the microbial world was revolutionized by analysis of 16S rRNA genes, such studies yielded only a phylogenetic description of community membership, providing little insight into the genetics, physiology, and biochemistry of the members. Metagenomics provides a second tier of technical innovation that facilitates study of the physiology and ecology of environmental microorganisms. Novel genes and gene products discovered through metagenomics include the first bacteriorhodopsin of bacterial origin; novel small molecules with antimicrobial activity; and new members of families of known proteins, such as an Na(+)(Li(+))/H(+) antiporter, RecA, DNA polymerase, and antibiotic resistance determinants. Reassembly of multiple genomes has provided insight into energy and nutrient cycling within the community, genome structure, gene function, population genetics and microheterogeneity, and lateral gene transfer among members of an uncultured community. The application of metagenomic sequence information will facilitate the design of better culturing strategies to link genomic analysis with pure culture studies.

Biotechnology↗
PubMed2025

GRUMB: a genome-resolved metagenomic framework for monitoring urban microbiomes and diagnosing pathogen risk.

SUMMARY: Urban infrastructure hosts dynamic microbial communities that complicate biosurveillance and AMR monitoring. Existing tools rarely combine genome-resolved reconstruction with ecological modeling and batch-aware analytics tailored to infrastructure-scale studies. We present GRUMB (Genome-Resolved Urban Microbiome Biosurveillance), an open-source, SLURM-compatible pipeline that reconstructs high-quality metagenome-assembled genomes (MAGs) from shotgun sequencing reads and integrates taxonomic/functional annotation (CARD, VFDB), batch-aware normalization, ecological diagnostics and machine learning classification of environment types with uncertainty and risk scoring. GRUMB accepts either SRA project accessions or paired-end FASTQ files with metadata, and produces assemblies, MAGs, taxonomic and functional profiles, ecological outputs and risk-informed classification. Its modular design enables reproducible, infrastructure-scale biosurveillance across diverse environments. AVAILABILITY AND IMPLEMENTATION: GRUMB is freely available under the MIT License at: https://github.com/SuleimanAminu/genome-resolved-urban-microbiome-biosurveillance; Zenodo DOI: https://doi.org/10.5281/zenodo.15505402. Requirements: Linux (Ubuntu 20.04+), Python 3.11, R 4.2+, SLURM. Issues and feature requests are tracked on GitHub.

Microbiota↗
PubMed2001

Metabolic modeling of microbial strains in silico.

The large volume of genome-scale data that is being produced and made available in databases on the World Wide Web is demanding the development of integrated mathematical models of cellular processes. The analysis of reconstructed metabolic networks as systems leads to the development of an in silico or computer representation of collections of cellular metabolic constituents, their interactions and their integrated function as a whole. The use of quantitative analysis methods to generate testable hypotheses and drive experimentation at a whole-genome level signals the advent of a systemic modeling approach to cellular and molecular biology.

Genome↗
PubMed2001

Advances in the bacteriology of the coliform group: their suitability as markers of microbial water safety.

Advances in the elaboration of novel genomic types of beta-galactosidase-positive Enterobacteriaceae and comprehensive studies of their habitats have resulted in an innovative approach to the assessment of the merits and shortcomings of the thermotrophic and fecal species Escherichia coli and all other coliforms as markers of the microbiological safety of water. As one of the consequences, it is recommended to abolish the "technical" designation fecal coliforms because their current method of detection will result in the isolation of thermotrophic organisms that have been demonstrated, beyond a doubt, to be of environmental, rather than uniquely enteric origin. Additional population studies have demonstrated that none of the coliforms can function as reliable markers for all enteric pathogens (index organisms sensu Ingram), nor be of use in validating adequate processing for safety of raw water, which represents the indicator function of markers, as defined by Ingram. Future studies along these lines will have to provide the data required to assess the suitability of additional markers for the reliable monitoring of drinking water for microbiological safety.

Enterobacteriaceae↗